Starting phenix.real_space_refine on Tue Jul 29 17:31:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6agf_9617/07_2025/6agf_9617_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6agf_9617/07_2025/6agf_9617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6agf_9617/07_2025/6agf_9617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6agf_9617/07_2025/6agf_9617.map" model { file = "/net/cci-nas-00/data/ceres_data/6agf_9617/07_2025/6agf_9617_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6agf_9617/07_2025/6agf_9617_neut.cif" } resolution = 3.2 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 88 5.16 5 C 7256 2.51 5 N 1689 2.21 5 O 1941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10980 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1138, 9163 Classifications: {'peptide': 1138} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 1105} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 278 Unusual residues: {'6OU': 6, '9Z9': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'6OU:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.64, per 1000 atoms: 0.60 Number of scatterers: 10980 At special positions: 0 Unit cell: (136.375, 129.829, 113.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 P 6 15.00 O 1941 8.00 N 1689 7.00 C 7256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 360 " distance=2.02 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 375 " distance=2.78 Simple disulfide: pdb=" SG CYS A 731 " - pdb=" SG CYS A 737 " distance=2.03 Simple disulfide: pdb=" SG CYS A 769 " - pdb=" SG CYS A 778 " distance=1.72 Simple disulfide: pdb=" SG CYS A1189 " - pdb=" SG CYS A1209 " distance=2.04 Simple disulfide: pdb=" SG CYS A1553 " - pdb=" SG CYS A1568 " distance=1.94 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.02 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.02 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 C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B 301 " - " ASN B 110 " " NAG B 302 " - " ASN B 114 " " NAG C 1 " - " ASN A 362 " " NAG D 1 " - " ASN A1205 " Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.4 seconds 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2474 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 5 sheets defined 67.6% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 120 through 129 removed outlier: 4.186A pdb=" N LYS A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 148 removed outlier: 3.661A pdb=" N MET A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 180 removed outlier: 3.556A pdb=" N TYR A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 189 removed outlier: 4.037A pdb=" N THR A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 210 removed outlier: 3.814A pdb=" N ASP A 197 " --> pdb=" O TRP A 193 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 226 removed outlier: 3.520A pdb=" N VAL A 223 " --> pdb=" O THR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 removed outlier: 4.004A pdb=" N THR A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 removed outlier: 3.750A pdb=" N ILE A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.716A pdb=" N LYS A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 244 through 249' Processing helix chain 'A' and resid 250 through 273 removed outlier: 3.664A pdb=" N LEU A 261 " --> pdb=" O THR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 removed outlier: 3.647A pdb=" N ARG A 277 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 278 " --> pdb=" O ASN A 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 274 through 278' Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 391 through 398 removed outlier: 3.541A pdb=" N ALA A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.600A pdb=" N MET A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 420 removed outlier: 3.979A pdb=" N LEU A 411 " --> pdb=" O TYR A 407 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 413 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 434 removed outlier: 4.148A pdb=" N PHE A 427 " --> pdb=" O TYR A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 454 removed outlier: 3.938A pdb=" N ALA A 444 " --> pdb=" O ASN A 440 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 463 removed outlier: 3.612A pdb=" N LEU A 458 " --> pdb=" O ASN A 454 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 577 removed outlier: 3.534A pdb=" N LYS A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE A 570 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 596 removed outlier: 3.670A pdb=" N CYS A 587 " --> pdb=" O GLY A 583 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A 589 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN A 591 " --> pdb=" O CYS A 587 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 596 " --> pdb=" O THR A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 632 removed outlier: 3.526A pdb=" N VAL A 609 " --> pdb=" O HIS A 605 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 610 " --> pdb=" O PHE A 606 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 621 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 660 removed outlier: 4.051A pdb=" N ILE A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 645 " --> pdb=" O GLY A 641 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 649 " --> pdb=" O PHE A 645 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 681 removed outlier: 4.544A pdb=" N ARG A 672 " --> pdb=" O ARG A 669 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 673 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 675 " --> pdb=" O ARG A 672 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS A 681 " --> pdb=" O LYS A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 698 removed outlier: 3.735A pdb=" N SER A 696 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 727 removed outlier: 3.619A pdb=" N LEU A 707 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LYS A 724 " --> pdb=" O GLN A 720 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N SER A 725 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS A 727 " --> pdb=" O GLY A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 733 removed outlier: 3.670A pdb=" N LYS A 732 " --> pdb=" O CYS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 760 removed outlier: 3.687A pdb=" N SER A 750 " --> pdb=" O ASP A 746 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 758 " --> pdb=" O VAL A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 773 removed outlier: 3.991A pdb=" N ASP A 768 " --> pdb=" O GLU A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 803 removed outlier: 3.605A pdb=" N LEU A 779 " --> pdb=" O GLN A 775 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 780 " --> pdb=" O ALA A 776 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A 784 " --> pdb=" O THR A 780 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET A 786 " --> pdb=" O PHE A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1029 removed outlier: 3.721A pdb=" N THR A1019 " --> pdb=" O LYS A1015 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A1026 " --> pdb=" O ARG A1022 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A1027 " --> pdb=" O ALA A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1047 removed outlier: 3.586A pdb=" N LEU A1042 " --> pdb=" O VAL A1038 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A1043 " --> pdb=" O PHE A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1056 removed outlier: 3.513A pdb=" N ILE A1055 " --> pdb=" O ASP A1052 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU A1056 " --> pdb=" O ILE A1053 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1052 through 1056' Processing helix chain 'A' and resid 1059 through 1079 removed outlier: 3.510A pdb=" N TYR A1067 " --> pdb=" O THR A1063 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS A1070 " --> pdb=" O GLU A1066 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A1073 " --> pdb=" O ASP A1069 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A1074 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A1077 " --> pdb=" O THR A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1088 removed outlier: 3.520A pdb=" N VAL A1085 " --> pdb=" O LEU A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1094 removed outlier: 3.952A pdb=" N PHE A1093 " --> pdb=" O PHE A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1117 removed outlier: 3.709A pdb=" N ILE A1104 " --> pdb=" O LEU A1100 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A1112 " --> pdb=" O SER A1108 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN A1115 " --> pdb=" O SER A1111 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP A1116 " --> pdb=" O LEU A1112 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A1117 " --> pdb=" O VAL A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1142 removed outlier: 3.637A pdb=" N ALA A1133 " --> pdb=" O THR A1130 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A1134 " --> pdb=" O LEU A1131 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A1135 " --> pdb=" O ARG A1132 " (cutoff:3.500A) Proline residue: A1136 - end of helix removed outlier: 3.647A pdb=" N SER A1141 " --> pdb=" O ARG A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1154 removed outlier: 3.554A pdb=" N VAL A1149 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1183 removed outlier: 4.101A pdb=" N ASN A1162 " --> pdb=" O PRO A1158 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A1163 " --> pdb=" O SER A1159 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A1166 " --> pdb=" O ASN A1162 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A1173 " --> pdb=" O ILE A1169 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE A1174 " --> pdb=" O PHE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1210 Processing helix chain 'A' and resid 1211 through 1213 No H-bonds generated for 'chain 'A' and resid 1211 through 1213' Processing helix chain 'A' and resid 1229 through 1242 removed outlier: 3.593A pdb=" N GLN A1239 " --> pdb=" O LEU A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1245 through 1256 removed outlier: 4.052A pdb=" N ILE A1249 " --> pdb=" O GLY A1245 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A1252 " --> pdb=" O ASP A1248 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP A1255 " --> pdb=" O TYR A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1270 No H-bonds generated for 'chain 'A' and resid 1268 through 1270' Processing helix chain 'A' and resid 1271 through 1282 removed outlier: 3.829A pdb=" N PHE A1275 " --> pdb=" O MET A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1305 removed outlier: 3.522A pdb=" N VAL A1293 " --> pdb=" O LEU A1289 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A1294 " --> pdb=" O PHE A1290 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP A1296 " --> pdb=" O GLY A1292 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN A1300 " --> pdb=" O ASP A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1325 removed outlier: 3.837A pdb=" N TYR A1319 " --> pdb=" O GLU A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1346 through 1351 removed outlier: 3.764A pdb=" N VAL A1350 " --> pdb=" O VAL A1346 " (cutoff:3.500A) Processing helix chain 'A' and resid 1353 through 1363 removed outlier: 3.678A pdb=" N ILE A1357 " --> pdb=" O GLN A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1372 removed outlier: 3.858A pdb=" N MET A1370 " --> pdb=" O ASN A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1405 removed outlier: 3.712A pdb=" N ASP A1383 " --> pdb=" O GLN A1379 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A1391 " --> pdb=" O ASN A1387 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A1394 " --> pdb=" O MET A1390 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS A1400 " --> pdb=" O PHE A1396 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A1402 " --> pdb=" O GLY A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1440 removed outlier: 3.501A pdb=" N VAL A1422 " --> pdb=" O ILE A1418 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A1423 " --> pdb=" O PHE A1419 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A1428 " --> pdb=" O VAL A1424 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N SER A1434 " --> pdb=" O GLY A1430 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP A1435 " --> pdb=" O LEU A1431 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A1436 " --> pdb=" O ALA A1432 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN A1438 " --> pdb=" O SER A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1451 removed outlier: 3.977A pdb=" N ILE A1450 " --> pdb=" O LEU A1446 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG A1451 " --> pdb=" O PHE A1447 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1446 through 1451' Processing helix chain 'A' and resid 1452 through 1464 removed outlier: 3.840A pdb=" N GLY A1456 " --> pdb=" O ALA A1453 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A1459 " --> pdb=" O GLY A1456 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY A1464 " --> pdb=" O LEU A1461 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1504 removed outlier: 3.617A pdb=" N LEU A1471 " --> pdb=" O GLY A1467 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE A1473 " --> pdb=" O ARG A1469 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A1475 " --> pdb=" O LEU A1471 " (cutoff:3.500A) Proline residue: A1480 - end of helix removed outlier: 3.687A pdb=" N ASN A1484 " --> pdb=" O PRO A1480 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A1485 " --> pdb=" O ALA A1481 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A1488 " --> pdb=" O ASN A1484 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A1503 " --> pdb=" O PHE A1499 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1532 removed outlier: 3.607A pdb=" N ILE A1527 " --> pdb=" O GLY A1523 " (cutoff:3.500A) Processing helix chain 'A' and resid 1533 through 1535 No H-bonds generated for 'chain 'A' and resid 1533 through 1535' Processing helix chain 'A' and resid 1537 through 1543 removed outlier: 3.603A pdb=" N LEU A1541 " --> pdb=" O GLY A1537 " (cutoff:3.500A) Processing helix chain 'A' and resid 1570 through 1606 removed outlier: 3.571A pdb=" N ILE A1575 " --> pdb=" O PRO A1571 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS A1576 " --> pdb=" O SER A1572 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A1583 " --> pdb=" O CYS A1579 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A1591 " --> pdb=" O LEU A1587 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A1596 " --> pdb=" O MET A1592 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A1599 " --> pdb=" O ALA A1595 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN A1602 " --> pdb=" O LEU A1598 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.557A pdb=" N HIS B 115 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER B 116 " --> pdb=" O TYR B 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 112 through 116' Processing helix chain 'B' and resid 154 through 191 removed outlier: 3.502A pdb=" N SER B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR B 164 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU B 177 " --> pdb=" O TRP B 173 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 186 " --> pdb=" O TYR B 182 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 279 through 282 Processing sheet with id=AA2, first strand: chain 'A' and resid 1188 through 1191 Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.797A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA5, first strand: chain 'B' and resid 50 through 51 removed outlier: 4.342A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) 533 hydrogen bonds defined for protein. 1500 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: 3.28 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1674 1.30 - 1.44: 3115 1.44 - 1.57: 6282 1.57 - 1.70: 14 1.70 - 1.84: 143 Bond restraints: 11228 Sorted by residual: bond pdb=" C16 6OU A1912 " pdb=" O18 6OU A1912 " ideal model delta sigma weight residual 1.327 1.431 -0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" C ASN A 381 " pdb=" N PRO A 382 " ideal model delta sigma weight residual 1.330 1.391 -0.061 1.22e-02 6.72e+03 2.51e+01 bond pdb=" C16 6OU A1913 " pdb=" O18 6OU A1913 " ideal model delta sigma weight residual 1.327 1.426 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C16 6OU A1910 " pdb=" O18 6OU A1910 " ideal model delta sigma weight residual 1.327 1.425 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C16 6OU A1909 " pdb=" O18 6OU A1909 " ideal model delta sigma weight residual 1.327 1.423 -0.096 2.00e-02 2.50e+03 2.32e+01 ... (remaining 11223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 14765 3.97 - 7.94: 349 7.94 - 11.91: 45 11.91 - 15.88: 5 15.88 - 19.85: 11 Bond angle restraints: 15175 Sorted by residual: angle pdb=" N VAL A 772 " pdb=" CA VAL A 772 " pdb=" C VAL A 772 " ideal model delta sigma weight residual 110.72 120.36 -9.64 1.01e+00 9.80e-01 9.11e+01 angle pdb=" N GLY A1464 " pdb=" CA GLY A1464 " pdb=" C GLY A1464 " ideal model delta sigma weight residual 112.73 123.36 -10.63 1.20e+00 6.94e-01 7.84e+01 angle pdb=" O24 6OU A1911 " pdb=" P23 6OU A1911 " pdb=" O25 6OU A1911 " ideal model delta sigma weight residual 118.72 98.87 19.85 3.00e+00 1.11e-01 4.38e+01 angle pdb=" N THR A 378 " pdb=" CA THR A 378 " pdb=" C THR A 378 " ideal model delta sigma weight residual 110.10 119.86 -9.76 1.49e+00 4.50e-01 4.29e+01 angle pdb=" C VAL A1442 " pdb=" N SER A1443 " pdb=" CA SER A1443 " ideal model delta sigma weight residual 122.85 115.77 7.08 1.10e+00 8.26e-01 4.15e+01 ... (remaining 15170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 6608 35.90 - 71.80: 201 71.80 - 107.70: 37 107.70 - 143.61: 14 143.61 - 179.51: 4 Dihedral angle restraints: 6864 sinusoidal: 3032 harmonic: 3832 Sorted by residual: dihedral pdb=" CB CYS A1553 " pdb=" SG CYS A1553 " pdb=" SG CYS A1568 " pdb=" CB CYS A1568 " ideal model delta sinusoidal sigma weight residual -86.00 -148.09 62.09 1 1.00e+01 1.00e-02 5.11e+01 dihedral pdb=" CA GLY B 63 " pdb=" C GLY B 63 " pdb=" N THR B 64 " pdb=" CA THR B 64 " ideal model delta harmonic sigma weight residual 180.00 -151.70 -28.30 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA PRO A1334 " pdb=" C PRO A1334 " pdb=" N ILE A1335 " pdb=" CA ILE A1335 " ideal model delta harmonic sigma weight residual 180.00 151.98 28.02 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 6861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1514 0.096 - 0.191: 204 0.191 - 0.287: 31 0.287 - 0.382: 1 0.382 - 0.478: 2 Chirality restraints: 1752 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 362 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.70e+00 chirality pdb=" CA TYR A1270 " pdb=" N TYR A1270 " pdb=" C TYR A1270 " pdb=" CB TYR A1270 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CB ILE A1335 " pdb=" CA ILE A1335 " pdb=" CG1 ILE A1335 " pdb=" CG2 ILE A1335 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1749 not shown) Planarity restraints: 1829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1246 " -0.029 2.00e-02 2.50e+03 2.82e-02 1.99e+01 pdb=" CG TRP A1246 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP A1246 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A1246 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A1246 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A1246 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A1246 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1246 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1246 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A1246 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 285 " 0.065 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO A 286 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO A 286 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 286 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 633 " 0.058 5.00e-02 4.00e+02 8.71e-02 1.22e+01 pdb=" N PRO A 634 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 634 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 634 " 0.048 5.00e-02 4.00e+02 ... (remaining 1826 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 130 2.63 - 3.20: 9479 3.20 - 3.76: 15848 3.76 - 4.33: 22640 4.33 - 4.90: 37108 Nonbonded interactions: 85205 Sorted by model distance: nonbonded pdb=" O PRO A1555 " pdb=" CG ASN A1556 " model vdw 2.059 3.270 nonbonded pdb=" OD2 ASP A1515 " pdb=" NH1 ARG B 46 " model vdw 2.198 3.120 nonbonded pdb=" O MET A1516 " pdb=" ND2 ASN A1524 " model vdw 2.213 3.120 nonbonded pdb=" NH2 ARG A 277 " pdb=" OD2 ASP A1375 " model vdw 2.230 3.120 nonbonded pdb=" O PHE A1174 " pdb=" OH TYR A1274 " model vdw 2.280 3.040 ... (remaining 85200 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 'D' selection = chain 'E' } 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 27.140 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 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 : 0.016 0.750 11244 Z= 0.736 Angle : 1.659 45.459 15215 Z= 0.853 Chirality : 0.070 0.478 1752 Planarity : 0.008 0.097 1825 Dihedral : 19.059 179.508 4366 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.00 % Favored : 93.47 % Rotamer: Outliers : 5.06 % Allowed : 7.46 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -4.93 (0.18), residues: 1301 helix: -3.59 (0.12), residues: 807 sheet: -2.11 (0.55), residues: 66 loop : -2.26 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.005 TRP A1246 HIS 0.015 0.003 HIS A 749 PHE 0.054 0.005 PHE A1243 TYR 0.052 0.005 TYR A 407 ARG 0.033 0.002 ARG A1257 Details of bonding type rmsd link_NAG-ASN : bond 0.01848 ( 4) link_NAG-ASN : angle 6.50652 ( 12) link_BETA1-4 : bond 0.01339 ( 4) link_BETA1-4 : angle 7.72855 ( 12) hydrogen bonds : bond 0.31323 ( 533) hydrogen bonds : angle 10.17391 ( 1500) SS BOND : bond 0.28832 ( 8) SS BOND : angle 17.24942 ( 16) covalent geometry : bond 0.01404 (11228) covalent geometry : angle 1.53796 (15175) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 245 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.7693 (mmp) cc_final: 0.7162 (mmm) REVERT: A 424 MET cc_start: 0.7200 (ttp) cc_final: 0.7000 (ttt) REVERT: A 433 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8734 (tp) REVERT: A 593 LEU cc_start: 0.9037 (mm) cc_final: 0.8808 (mt) REVERT: A 624 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7634 (tm-30) REVERT: A 1090 LYS cc_start: 0.8001 (mmpt) cc_final: 0.7641 (mptt) REVERT: A 1187 TYR cc_start: 0.8555 (m-10) cc_final: 0.8322 (m-80) REVERT: A 1235 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8576 (tp) REVERT: A 1370 MET cc_start: 0.8941 (mtt) cc_final: 0.8690 (mtt) REVERT: A 1460 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7517 (ttm170) REVERT: A 1466 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7581 (mppt) REVERT: A 1598 LEU cc_start: 0.8740 (mm) cc_final: 0.8490 (mt) REVERT: B 156 SER cc_start: 0.8601 (t) cc_final: 0.8330 (t) outliers start: 59 outliers final: 24 residues processed: 289 average time/residue: 0.2482 time to fit residues: 100.4204 Evaluate side-chains 194 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 769 CYS Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1304 LYS Chi-restraints excluded: chain A residue 1460 ARG Chi-restraints excluded: chain A residue 1466 LYS Chi-restraints excluded: chain A residue 1477 MET Chi-restraints excluded: chain A residue 1479 LEU Chi-restraints excluded: chain A residue 1488 LEU Chi-restraints excluded: chain A residue 1489 LEU Chi-restraints excluded: chain A residue 1556 ASN Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain B residue 101 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.0070 chunk 98 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 275 ASN A 278 GLN A 381 ASN A 687 ASN A 743 HIS A1214 HIS A1288 ASN A1297 ASN A1524 ASN A1570 ASN B 93 ASN B 135 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.153598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.118145 restraints weight = 13985.237| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.01 r_work: 0.3135 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 11244 Z= 0.156 Angle : 0.765 12.021 15215 Z= 0.383 Chirality : 0.043 0.214 1752 Planarity : 0.006 0.073 1825 Dihedral : 19.535 169.973 1968 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.15 % Favored : 95.54 % Rotamer: Outliers : 3.69 % Allowed : 11.92 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.21), residues: 1301 helix: -1.69 (0.16), residues: 814 sheet: -1.57 (0.56), residues: 66 loop : -1.67 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1246 HIS 0.007 0.001 HIS A1214 PHE 0.019 0.002 PHE A1278 TYR 0.020 0.002 TYR A1593 ARG 0.004 0.001 ARG A1257 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 4) link_NAG-ASN : angle 3.99216 ( 12) link_BETA1-4 : bond 0.01331 ( 4) link_BETA1-4 : angle 4.78514 ( 12) hydrogen bonds : bond 0.06102 ( 533) hydrogen bonds : angle 4.79862 ( 1500) SS BOND : bond 0.01049 ( 8) SS BOND : angle 2.67034 ( 16) covalent geometry : bond 0.00325 (11228) covalent geometry : angle 0.74072 (15175) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 PHE cc_start: 0.8134 (t80) cc_final: 0.7929 (t80) REVERT: A 174 ILE cc_start: 0.8270 (tt) cc_final: 0.8045 (tt) REVERT: A 202 MET cc_start: 0.7571 (mmp) cc_final: 0.7288 (mmm) REVERT: A 218 LEU cc_start: 0.7208 (mm) cc_final: 0.6680 (mm) REVERT: A 359 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8182 (mt) REVERT: A 424 MET cc_start: 0.8665 (ttp) cc_final: 0.8420 (ttt) REVERT: A 433 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8538 (tp) REVERT: A 604 GLU cc_start: 0.8062 (pm20) cc_final: 0.7546 (pt0) REVERT: A 746 ASP cc_start: 0.8524 (t0) cc_final: 0.8302 (m-30) REVERT: A 1040 MET cc_start: 0.9066 (mmp) cc_final: 0.8834 (mmp) REVERT: A 1090 LYS cc_start: 0.8266 (mmpt) cc_final: 0.7978 (pttp) REVERT: A 1187 TYR cc_start: 0.8900 (m-10) cc_final: 0.8605 (m-80) REVERT: A 1235 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8777 (tp) REVERT: A 1358 THR cc_start: 0.8573 (m) cc_final: 0.8359 (p) REVERT: A 1370 MET cc_start: 0.9240 (mtt) cc_final: 0.8916 (mtt) REVERT: A 1405 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.6944 (pp) REVERT: A 1592 MET cc_start: 0.9196 (mtm) cc_final: 0.8995 (mtp) REVERT: A 1593 TYR cc_start: 0.8799 (m-80) cc_final: 0.8566 (m-80) REVERT: B 93 ASN cc_start: 0.7979 (OUTLIER) cc_final: 0.7112 (m110) REVERT: B 96 ARG cc_start: 0.8518 (mtp180) cc_final: 0.8314 (mtp180) outliers start: 43 outliers final: 17 residues processed: 227 average time/residue: 0.2181 time to fit residues: 71.6070 Evaluate side-chains 182 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 368 HIS Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1489 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 116 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 6 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 58 optimal weight: 0.1980 chunk 30 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN B 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.152260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116438 restraints weight = 14084.097| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.01 r_work: 0.3063 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11244 Z= 0.149 Angle : 0.687 11.497 15215 Z= 0.345 Chirality : 0.042 0.324 1752 Planarity : 0.005 0.064 1825 Dihedral : 18.238 167.819 1927 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.00 % Favored : 94.85 % Rotamer: Outliers : 4.37 % Allowed : 12.95 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.49 (0.23), residues: 1301 helix: -0.58 (0.17), residues: 809 sheet: -1.32 (0.55), residues: 71 loop : -1.45 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1246 HIS 0.004 0.001 HIS A 749 PHE 0.019 0.002 PHE B 86 TYR 0.014 0.002 TYR A1593 ARG 0.009 0.001 ARG A 222 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 4) link_NAG-ASN : angle 3.50062 ( 12) link_BETA1-4 : bond 0.01187 ( 4) link_BETA1-4 : angle 4.75229 ( 12) hydrogen bonds : bond 0.04953 ( 533) hydrogen bonds : angle 4.24591 ( 1500) SS BOND : bond 0.00327 ( 8) SS BOND : angle 2.81796 ( 16) covalent geometry : bond 0.00336 (11228) covalent geometry : angle 0.66120 (15175) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 177 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 ILE cc_start: 0.8338 (tt) cc_final: 0.8052 (tt) REVERT: A 198 PHE cc_start: 0.7525 (t80) cc_final: 0.6881 (t80) REVERT: A 232 VAL cc_start: 0.8812 (t) cc_final: 0.8583 (t) REVERT: A 359 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8499 (mt) REVERT: A 424 MET cc_start: 0.8650 (ttp) cc_final: 0.8404 (ttt) REVERT: A 604 GLU cc_start: 0.8146 (pm20) cc_final: 0.7685 (pt0) REVERT: A 632 MET cc_start: 0.6789 (mtp) cc_final: 0.6441 (ttm) REVERT: A 746 ASP cc_start: 0.8639 (t0) cc_final: 0.8429 (m-30) REVERT: A 1040 MET cc_start: 0.9070 (mmp) cc_final: 0.8814 (mmp) REVERT: A 1090 LYS cc_start: 0.8240 (mmpt) cc_final: 0.7926 (pttt) REVERT: A 1187 TYR cc_start: 0.8902 (m-10) cc_final: 0.8594 (m-80) REVERT: A 1268 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8499 (t0) REVERT: A 1304 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7928 (tttt) REVERT: A 1358 THR cc_start: 0.8455 (m) cc_final: 0.8248 (p) REVERT: A 1370 MET cc_start: 0.9225 (mtt) cc_final: 0.8924 (mtt) REVERT: A 1389 ASN cc_start: 0.7649 (m-40) cc_final: 0.7339 (m110) REVERT: A 1405 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.6836 (pp) REVERT: A 1436 LEU cc_start: 0.5324 (OUTLIER) cc_final: 0.4826 (mt) REVERT: B 96 ARG cc_start: 0.8525 (mtp180) cc_final: 0.8259 (mtp180) REVERT: B 183 LYS cc_start: 0.8494 (mmtt) cc_final: 0.7751 (mtmt) outliers start: 51 outliers final: 26 residues processed: 218 average time/residue: 0.2134 time to fit residues: 68.3178 Evaluate side-chains 194 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1268 ASN Chi-restraints excluded: chain A residue 1304 LYS Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1489 LEU Chi-restraints excluded: chain A residue 1553 CYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 2 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 125 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 65 optimal weight: 0.0670 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1591 ASN A1600 ASN B 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.153917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.118104 restraints weight = 13859.503| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.99 r_work: 0.3090 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11244 Z= 0.137 Angle : 0.656 11.048 15215 Z= 0.326 Chirality : 0.041 0.235 1752 Planarity : 0.004 0.064 1825 Dihedral : 17.037 168.236 1923 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.15 % Favored : 94.70 % Rotamer: Outliers : 4.29 % Allowed : 13.89 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.80 (0.23), residues: 1301 helix: 0.03 (0.18), residues: 808 sheet: -1.03 (0.57), residues: 71 loop : -1.37 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1246 HIS 0.003 0.001 HIS B 122 PHE 0.018 0.002 PHE B 86 TYR 0.010 0.001 TYR A 407 ARG 0.004 0.000 ARG A 222 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 4) link_NAG-ASN : angle 3.40981 ( 12) link_BETA1-4 : bond 0.01188 ( 4) link_BETA1-4 : angle 4.66658 ( 12) hydrogen bonds : bond 0.04280 ( 533) hydrogen bonds : angle 3.98624 ( 1500) SS BOND : bond 0.00687 ( 8) SS BOND : angle 2.76564 ( 16) covalent geometry : bond 0.00309 (11228) covalent geometry : angle 0.63023 (15175) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 181 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7505 (tm-30) REVERT: A 198 PHE cc_start: 0.7585 (t80) cc_final: 0.6972 (t80) REVERT: A 232 VAL cc_start: 0.8798 (t) cc_final: 0.8590 (t) REVERT: A 359 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8256 (tt) REVERT: A 424 MET cc_start: 0.8644 (ttp) cc_final: 0.8409 (ttt) REVERT: A 604 GLU cc_start: 0.8179 (pm20) cc_final: 0.7679 (pt0) REVERT: A 632 MET cc_start: 0.6818 (mtp) cc_final: 0.6583 (ttm) REVERT: A 779 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8907 (mm) REVERT: A 1040 MET cc_start: 0.9046 (mmp) cc_final: 0.8778 (mmp) REVERT: A 1090 LYS cc_start: 0.8177 (mmpt) cc_final: 0.7896 (pttt) REVERT: A 1187 TYR cc_start: 0.8870 (m-10) cc_final: 0.8606 (m-80) REVERT: A 1268 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.8454 (t0) REVERT: A 1304 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7877 (tttt) REVERT: A 1370 MET cc_start: 0.9235 (mtt) cc_final: 0.8891 (mtt) REVERT: A 1402 LEU cc_start: 0.8469 (mm) cc_final: 0.8182 (tp) REVERT: A 1405 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.6767 (pp) REVERT: A 1436 LEU cc_start: 0.5291 (OUTLIER) cc_final: 0.4798 (mt) REVERT: B 96 ARG cc_start: 0.8577 (mtp180) cc_final: 0.8251 (mtp180) REVERT: B 183 LYS cc_start: 0.8510 (mmtt) cc_final: 0.7731 (mtmt) outliers start: 50 outliers final: 27 residues processed: 219 average time/residue: 0.2046 time to fit residues: 65.5450 Evaluate side-chains 201 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1268 ASN Chi-restraints excluded: chain A residue 1304 LYS Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1404 MET Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1489 LEU Chi-restraints excluded: chain A residue 1553 CYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 116 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 chunk 69 optimal weight: 0.6980 chunk 8 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN A1264 GLN A1600 ASN A1602 ASN B 102 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.150170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113934 restraints weight = 14054.282| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.92 r_work: 0.3089 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 11244 Z= 0.122 Angle : 0.628 11.008 15215 Z= 0.309 Chirality : 0.041 0.257 1752 Planarity : 0.004 0.065 1825 Dihedral : 15.840 171.509 1913 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.84 % Favored : 95.00 % Rotamer: Outliers : 4.46 % Allowed : 14.58 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.08 (0.24), residues: 1301 helix: 0.66 (0.19), residues: 794 sheet: -0.75 (0.56), residues: 69 loop : -1.17 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 156 HIS 0.003 0.001 HIS B 115 PHE 0.018 0.001 PHE A 805 TYR 0.016 0.001 TYR A 637 ARG 0.005 0.000 ARG A1454 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 4) link_NAG-ASN : angle 3.07587 ( 12) link_BETA1-4 : bond 0.01144 ( 4) link_BETA1-4 : angle 4.51961 ( 12) hydrogen bonds : bond 0.03726 ( 533) hydrogen bonds : angle 3.79475 ( 1500) SS BOND : bond 0.00506 ( 8) SS BOND : angle 2.31488 ( 16) covalent geometry : bond 0.00275 (11228) covalent geometry : angle 0.60559 (15175) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 178 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 PHE cc_start: 0.7632 (t80) cc_final: 0.7040 (t80) REVERT: A 232 VAL cc_start: 0.8736 (t) cc_final: 0.8519 (t) REVERT: A 359 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8307 (tt) REVERT: A 424 MET cc_start: 0.8611 (ttp) cc_final: 0.8377 (ttt) REVERT: A 779 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8880 (mm) REVERT: A 1040 MET cc_start: 0.9033 (mmp) cc_final: 0.8748 (mmp) REVERT: A 1090 LYS cc_start: 0.8045 (mmpt) cc_final: 0.7800 (pttt) REVERT: A 1109 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8477 (mt) REVERT: A 1187 TYR cc_start: 0.8883 (m-10) cc_final: 0.8603 (m-80) REVERT: A 1268 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8405 (t0) REVERT: A 1304 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7795 (tttt) REVERT: A 1366 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8465 (t0) REVERT: A 1370 MET cc_start: 0.9244 (mtt) cc_final: 0.8882 (mtt) REVERT: A 1402 LEU cc_start: 0.8366 (mm) cc_final: 0.8060 (tp) REVERT: A 1405 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.6674 (pp) REVERT: A 1436 LEU cc_start: 0.5299 (OUTLIER) cc_final: 0.4816 (mt) REVERT: A 1477 MET cc_start: 0.8914 (tpp) cc_final: 0.8616 (mmp) REVERT: A 1554 ASP cc_start: 0.8448 (t0) cc_final: 0.7912 (t0) REVERT: A 1602 ASN cc_start: 0.8527 (m-40) cc_final: 0.8279 (m110) REVERT: B 96 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8291 (mtp180) REVERT: B 183 LYS cc_start: 0.8471 (mmtt) cc_final: 0.7661 (mtmt) outliers start: 52 outliers final: 26 residues processed: 219 average time/residue: 0.2066 time to fit residues: 66.3499 Evaluate side-chains 202 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1268 ASN Chi-restraints excluded: chain A residue 1286 THR Chi-restraints excluded: chain A residue 1304 LYS Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1489 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 10 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 11 optimal weight: 0.0020 chunk 128 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1264 GLN A1556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.155575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.120954 restraints weight = 13909.925| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.70 r_work: 0.3151 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 11244 Z= 0.114 Angle : 0.610 10.937 15215 Z= 0.299 Chirality : 0.041 0.222 1752 Planarity : 0.004 0.068 1825 Dihedral : 15.054 169.984 1913 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.69 % Favored : 95.16 % Rotamer: Outliers : 3.60 % Allowed : 15.52 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.24), residues: 1301 helix: 1.11 (0.19), residues: 782 sheet: -1.32 (0.53), residues: 81 loop : -0.89 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1220 HIS 0.002 0.001 HIS A 368 PHE 0.020 0.001 PHE A1447 TYR 0.014 0.001 TYR A1593 ARG 0.004 0.000 ARG A1454 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 4) link_NAG-ASN : angle 3.03084 ( 12) link_BETA1-4 : bond 0.01123 ( 4) link_BETA1-4 : angle 4.46971 ( 12) hydrogen bonds : bond 0.03424 ( 533) hydrogen bonds : angle 3.63971 ( 1500) SS BOND : bond 0.00598 ( 8) SS BOND : angle 2.37620 ( 16) covalent geometry : bond 0.00254 (11228) covalent geometry : angle 0.58675 (15175) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 PHE cc_start: 0.7677 (t80) cc_final: 0.7101 (t80) REVERT: A 232 VAL cc_start: 0.8738 (t) cc_final: 0.8523 (t) REVERT: A 359 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8312 (tt) REVERT: A 424 MET cc_start: 0.8533 (ttp) cc_final: 0.8293 (ttt) REVERT: A 779 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8848 (mm) REVERT: A 1040 MET cc_start: 0.8995 (mmp) cc_final: 0.8711 (mmp) REVERT: A 1090 LYS cc_start: 0.8047 (mmpt) cc_final: 0.7831 (pttt) REVERT: A 1187 TYR cc_start: 0.8772 (m-10) cc_final: 0.8541 (m-80) REVERT: A 1213 MET cc_start: 0.7943 (mmm) cc_final: 0.7742 (mmm) REVERT: A 1268 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8399 (t0) REVERT: A 1304 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7847 (tttt) REVERT: A 1366 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8389 (t0) REVERT: A 1370 MET cc_start: 0.9258 (mtt) cc_final: 0.8903 (mtt) REVERT: A 1402 LEU cc_start: 0.8371 (mm) cc_final: 0.8052 (tp) REVERT: A 1405 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6703 (pp) REVERT: A 1436 LEU cc_start: 0.5528 (OUTLIER) cc_final: 0.5009 (mt) REVERT: A 1447 PHE cc_start: 0.7814 (t80) cc_final: 0.7597 (t80) REVERT: A 1477 MET cc_start: 0.8915 (tpp) cc_final: 0.8684 (mmp) REVERT: B 96 ARG cc_start: 0.8585 (mtp180) cc_final: 0.8242 (mtp180) outliers start: 42 outliers final: 23 residues processed: 216 average time/residue: 0.4148 time to fit residues: 133.8992 Evaluate side-chains 205 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1268 ASN Chi-restraints excluded: chain A residue 1286 THR Chi-restraints excluded: chain A residue 1304 LYS Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1489 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 126 optimal weight: 9.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 ASN ** A1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1602 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.153497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.118664 restraints weight = 14157.418| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.67 r_work: 0.3102 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11244 Z= 0.138 Angle : 0.639 10.588 15215 Z= 0.313 Chirality : 0.041 0.205 1752 Planarity : 0.004 0.071 1825 Dihedral : 14.544 168.540 1913 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.84 % Favored : 95.00 % Rotamer: Outliers : 3.60 % Allowed : 15.61 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.45 (0.24), residues: 1301 helix: 1.18 (0.19), residues: 789 sheet: -1.33 (0.53), residues: 81 loop : -0.93 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 156 HIS 0.004 0.001 HIS A 749 PHE 0.019 0.001 PHE A 805 TYR 0.013 0.001 TYR A 637 ARG 0.003 0.000 ARG A1454 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 4) link_NAG-ASN : angle 3.43042 ( 12) link_BETA1-4 : bond 0.00997 ( 4) link_BETA1-4 : angle 4.52412 ( 12) hydrogen bonds : bond 0.03681 ( 533) hydrogen bonds : angle 3.71372 ( 1500) SS BOND : bond 0.00631 ( 8) SS BOND : angle 2.12671 ( 16) covalent geometry : bond 0.00322 (11228) covalent geometry : angle 0.61625 (15175) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 2.115 Fit side-chains revert: symmetry clash REVERT: A 198 PHE cc_start: 0.7670 (t80) cc_final: 0.6991 (t80) REVERT: A 232 VAL cc_start: 0.8758 (t) cc_final: 0.8535 (t) REVERT: A 359 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8409 (tt) REVERT: A 424 MET cc_start: 0.8586 (ttp) cc_final: 0.8363 (ttt) REVERT: A 628 LYS cc_start: 0.8318 (mttm) cc_final: 0.8109 (mtpt) REVERT: A 779 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8765 (mm) REVERT: A 1040 MET cc_start: 0.9023 (mmp) cc_final: 0.8755 (mmp) REVERT: A 1090 LYS cc_start: 0.8169 (mmpt) cc_final: 0.7904 (pttt) REVERT: A 1213 MET cc_start: 0.7949 (mmm) cc_final: 0.7728 (mmm) REVERT: A 1268 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8461 (t0) REVERT: A 1304 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7942 (tttt) REVERT: A 1370 MET cc_start: 0.9280 (mtt) cc_final: 0.8943 (mtt) REVERT: A 1402 LEU cc_start: 0.8347 (mm) cc_final: 0.8009 (tp) REVERT: A 1405 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6487 (pp) REVERT: A 1447 PHE cc_start: 0.7826 (t80) cc_final: 0.7601 (t80) REVERT: A 1477 MET cc_start: 0.8889 (tpp) cc_final: 0.8680 (mmp) REVERT: A 1554 ASP cc_start: 0.8270 (t0) cc_final: 0.7780 (t0) REVERT: B 96 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8250 (mtp180) outliers start: 42 outliers final: 29 residues processed: 208 average time/residue: 0.4175 time to fit residues: 134.4349 Evaluate side-chains 205 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1200 ILE Chi-restraints excluded: chain A residue 1268 ASN Chi-restraints excluded: chain A residue 1286 THR Chi-restraints excluded: chain A residue 1304 LYS Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1440 TYR Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1489 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 95 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1602 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.151946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116809 restraints weight = 13904.464| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.71 r_work: 0.3065 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11244 Z= 0.166 Angle : 0.664 11.832 15215 Z= 0.326 Chirality : 0.042 0.200 1752 Planarity : 0.004 0.074 1825 Dihedral : 14.251 168.815 1911 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.15 % Favored : 94.70 % Rotamer: Outliers : 3.52 % Allowed : 16.21 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.44 (0.24), residues: 1301 helix: 1.17 (0.19), residues: 797 sheet: -1.44 (0.53), residues: 81 loop : -0.97 (0.33), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1097 HIS 0.004 0.001 HIS A 743 PHE 0.018 0.002 PHE B 86 TYR 0.012 0.001 TYR B 132 ARG 0.004 0.000 ARG A1257 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 4) link_NAG-ASN : angle 3.41653 ( 12) link_BETA1-4 : bond 0.00968 ( 4) link_BETA1-4 : angle 4.57299 ( 12) hydrogen bonds : bond 0.03901 ( 533) hydrogen bonds : angle 3.71651 ( 1500) SS BOND : bond 0.00641 ( 8) SS BOND : angle 2.24919 ( 16) covalent geometry : bond 0.00399 (11228) covalent geometry : angle 0.64129 (15175) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 232 VAL cc_start: 0.8771 (t) cc_final: 0.8547 (t) REVERT: A 359 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8339 (tt) REVERT: A 424 MET cc_start: 0.8531 (ttp) cc_final: 0.8328 (ttt) REVERT: A 628 LYS cc_start: 0.8302 (mttm) cc_final: 0.8089 (mtpt) REVERT: A 779 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8750 (mm) REVERT: A 1040 MET cc_start: 0.9062 (mmp) cc_final: 0.8818 (mmp) REVERT: A 1090 LYS cc_start: 0.8133 (mmpt) cc_final: 0.7857 (pttt) REVERT: A 1213 MET cc_start: 0.7914 (mmm) cc_final: 0.7686 (mmm) REVERT: A 1268 ASN cc_start: 0.8860 (OUTLIER) cc_final: 0.8488 (t0) REVERT: A 1304 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7902 (tttt) REVERT: A 1370 MET cc_start: 0.9245 (mtt) cc_final: 0.8908 (mtt) REVERT: A 1402 LEU cc_start: 0.8395 (mm) cc_final: 0.8011 (tp) REVERT: A 1405 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6464 (pp) REVERT: A 1554 ASP cc_start: 0.8391 (t0) cc_final: 0.7771 (t0) REVERT: B 96 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8208 (mtp180) outliers start: 41 outliers final: 28 residues processed: 202 average time/residue: 0.2150 time to fit residues: 63.8631 Evaluate side-chains 202 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1268 ASN Chi-restraints excluded: chain A residue 1286 THR Chi-restraints excluded: chain A residue 1304 LYS Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1440 TYR Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1489 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 83 optimal weight: 0.9980 chunk 37 optimal weight: 0.0970 chunk 125 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 121 optimal weight: 0.0980 chunk 64 optimal weight: 0.0020 chunk 112 optimal weight: 1.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1264 GLN ** A1600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1602 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.154786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120122 restraints weight = 13973.535| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.68 r_work: 0.3107 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 11244 Z= 0.112 Angle : 0.625 10.679 15215 Z= 0.304 Chirality : 0.040 0.197 1752 Planarity : 0.004 0.073 1825 Dihedral : 13.769 165.347 1911 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.07 % Favored : 94.85 % Rotamer: Outliers : 3.09 % Allowed : 16.72 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.78 (0.24), residues: 1301 helix: 1.48 (0.19), residues: 789 sheet: -1.42 (0.52), residues: 81 loop : -0.83 (0.33), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1220 HIS 0.002 0.001 HIS A 749 PHE 0.022 0.001 PHE A 805 TYR 0.009 0.001 TYR A 637 ARG 0.003 0.000 ARG A1454 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 4) link_NAG-ASN : angle 2.97038 ( 12) link_BETA1-4 : bond 0.01030 ( 4) link_BETA1-4 : angle 4.51400 ( 12) hydrogen bonds : bond 0.03425 ( 533) hydrogen bonds : angle 3.59585 ( 1500) SS BOND : bond 0.00687 ( 8) SS BOND : angle 1.95180 ( 16) covalent geometry : bond 0.00245 (11228) covalent geometry : angle 0.60331 (15175) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 198 PHE cc_start: 0.7654 (t80) cc_final: 0.6973 (t80) REVERT: A 232 VAL cc_start: 0.8746 (t) cc_final: 0.8537 (t) REVERT: A 359 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8361 (tt) REVERT: A 424 MET cc_start: 0.8550 (ttp) cc_final: 0.8341 (ttt) REVERT: A 628 LYS cc_start: 0.8317 (mttm) cc_final: 0.8111 (mtpt) REVERT: A 779 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8791 (mm) REVERT: A 1040 MET cc_start: 0.9021 (mmp) cc_final: 0.8782 (mmp) REVERT: A 1090 LYS cc_start: 0.8092 (mmpt) cc_final: 0.7809 (pttt) REVERT: A 1213 MET cc_start: 0.7869 (mmm) cc_final: 0.7650 (mmm) REVERT: A 1268 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8441 (t0) REVERT: A 1304 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7902 (tttt) REVERT: A 1370 MET cc_start: 0.9273 (mtt) cc_final: 0.8939 (mtt) REVERT: A 1402 LEU cc_start: 0.8375 (mm) cc_final: 0.8001 (tp) REVERT: A 1405 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6446 (pp) REVERT: A 1554 ASP cc_start: 0.8286 (t0) cc_final: 0.7786 (t0) REVERT: B 96 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8240 (mtp180) outliers start: 36 outliers final: 25 residues processed: 206 average time/residue: 0.2127 time to fit residues: 64.7226 Evaluate side-chains 199 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1268 ASN Chi-restraints excluded: chain A residue 1286 THR Chi-restraints excluded: chain A residue 1304 LYS Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1440 TYR Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1489 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 96 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 95 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 29 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1600 ASN A1602 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.152646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116645 restraints weight = 13930.294| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.96 r_work: 0.3043 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11244 Z= 0.157 Angle : 0.660 11.238 15215 Z= 0.322 Chirality : 0.042 0.197 1752 Planarity : 0.004 0.075 1825 Dihedral : 13.750 164.918 1911 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.53 % Favored : 94.31 % Rotamer: Outliers : 3.00 % Allowed : 16.98 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.69 (0.24), residues: 1301 helix: 1.39 (0.19), residues: 795 sheet: -1.37 (0.53), residues: 81 loop : -0.90 (0.33), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1097 HIS 0.004 0.001 HIS A 743 PHE 0.027 0.002 PHE A1447 TYR 0.012 0.001 TYR A1270 ARG 0.005 0.000 ARG A1135 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 4) link_NAG-ASN : angle 3.27266 ( 12) link_BETA1-4 : bond 0.00920 ( 4) link_BETA1-4 : angle 4.58279 ( 12) hydrogen bonds : bond 0.03821 ( 533) hydrogen bonds : angle 3.69078 ( 1500) SS BOND : bond 0.00625 ( 8) SS BOND : angle 2.07535 ( 16) covalent geometry : bond 0.00374 (11228) covalent geometry : angle 0.63772 (15175) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: A 359 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8495 (tp) REVERT: A 628 LYS cc_start: 0.8336 (mttm) cc_final: 0.8115 (mtpt) REVERT: A 779 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8779 (mm) REVERT: A 1040 MET cc_start: 0.9102 (mmp) cc_final: 0.8862 (mmp) REVERT: A 1090 LYS cc_start: 0.8167 (mmpt) cc_final: 0.7846 (pttt) REVERT: A 1213 MET cc_start: 0.7834 (mmm) cc_final: 0.7582 (mmm) REVERT: A 1268 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8555 (t0) REVERT: A 1304 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7905 (tttt) REVERT: A 1370 MET cc_start: 0.9254 (mtt) cc_final: 0.8902 (mtt) REVERT: A 1402 LEU cc_start: 0.8373 (mm) cc_final: 0.7976 (tp) REVERT: A 1405 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6387 (pp) REVERT: B 96 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8255 (mtp180) outliers start: 35 outliers final: 29 residues processed: 199 average time/residue: 0.2242 time to fit residues: 65.1942 Evaluate side-chains 200 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1268 ASN Chi-restraints excluded: chain A residue 1286 THR Chi-restraints excluded: chain A residue 1304 LYS Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1440 TYR Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1489 LEU Chi-restraints excluded: chain A residue 1600 ASN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 119 optimal weight: 0.0980 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 86 optimal weight: 0.0000 chunk 79 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1600 ASN A1602 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.152335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117392 restraints weight = 13847.315| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.70 r_work: 0.3062 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.159 11244 Z= 0.185 Angle : 0.952 59.192 15215 Z= 0.536 Chirality : 0.041 0.194 1752 Planarity : 0.004 0.075 1825 Dihedral : 13.747 164.886 1911 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.53 % Favored : 94.31 % Rotamer: Outliers : 2.74 % Allowed : 17.50 % Favored : 79.76 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.67 (0.24), residues: 1301 helix: 1.37 (0.19), residues: 795 sheet: -1.37 (0.53), residues: 81 loop : -0.90 (0.33), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1097 HIS 0.003 0.001 HIS A 749 PHE 0.020 0.001 PHE A 805 TYR 0.012 0.001 TYR A1270 ARG 0.004 0.000 ARG A1257 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 4) link_NAG-ASN : angle 3.25587 ( 12) link_BETA1-4 : bond 0.00827 ( 4) link_BETA1-4 : angle 4.62153 ( 12) hydrogen bonds : bond 0.03797 ( 533) hydrogen bonds : angle 3.69446 ( 1500) SS BOND : bond 0.03165 ( 8) SS BOND : angle 5.53136 ( 16) covalent geometry : bond 0.00397 (11228) covalent geometry : angle 0.92240 (15175) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7559.71 seconds wall clock time: 135 minutes 56.87 seconds (8156.87 seconds total)