Starting phenix.real_space_refine on Wed Sep 25 23:33:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agf_9617/09_2024/6agf_9617_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agf_9617/09_2024/6agf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agf_9617/09_2024/6agf_9617.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agf_9617/09_2024/6agf_9617.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agf_9617/09_2024/6agf_9617_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agf_9617/09_2024/6agf_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 6.59, 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: 2.60 Conformation dependent library (CDL) restraints added in 1.3 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: 1.37 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: 3.22 Time building geometry restraints manager: 3.00 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 26.100 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.750 ------------------------------------------------------------------------------- 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 : 0.014 0.118 11228 Z= 0.899 Angle : 1.538 19.853 15175 Z= 0.806 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 *********************** 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 fitting. rotamer outliers: 59 poor density : 245 time to evaluate : 1.074 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: 0.2385 time to fit residues: 95.9979 Evaluate side-chains 194 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 166 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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: 0.0030 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: 0.6390 ------------------------------------------------------------------------------- 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 440 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11228 Z= 0.201 Angle : 0.740 12.077 15175 Z= 0.377 Chirality : 0.043 0.208 1752 Planarity : 0.006 0.073 1825 Dihedral : 19.403 169.385 1968 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.15 % Favored : 95.54 % Rotamer: Outliers : 3.86 % Allowed : 11.66 % Favored : 84.48 % 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: -2.62 (0.21), residues: 1301 helix: -1.64 (0.16), residues: 806 sheet: -1.57 (0.57), residues: 66 loop : -1.55 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 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 A1460 *********************** 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 234 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 189 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 ILE cc_start: 0.8493 (tt) cc_final: 0.8267 (tt) REVERT: A 202 MET cc_start: 0.7456 (mmp) cc_final: 0.7250 (mmm) REVERT: A 218 LEU cc_start: 0.7273 (mm) cc_final: 0.6799 (mm) REVERT: A 359 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7823 (mt) REVERT: A 424 MET cc_start: 0.7112 (ttp) cc_final: 0.6871 (ttt) REVERT: A 433 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8387 (tp) REVERT: A 604 GLU cc_start: 0.7468 (pm20) cc_final: 0.7017 (pt0) REVERT: A 1187 TYR cc_start: 0.8562 (m-10) cc_final: 0.8331 (m-80) REVERT: A 1235 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8554 (tp) REVERT: A 1370 MET cc_start: 0.8959 (mtt) cc_final: 0.8602 (mtt) REVERT: A 1405 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7062 (pp) REVERT: A 1592 MET cc_start: 0.8876 (mtm) cc_final: 0.8650 (mtp) REVERT: B 93 ASN cc_start: 0.7866 (OUTLIER) cc_final: 0.6924 (m110) REVERT: B 96 ARG cc_start: 0.8344 (mtp180) cc_final: 0.8061 (mtp180) REVERT: B 156 SER cc_start: 0.8713 (t) cc_final: 0.8496 (t) outliers start: 45 outliers final: 17 residues processed: 229 average time/residue: 0.2092 time to fit residues: 69.1015 Evaluate side-chains 181 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 667 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 1235 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 65 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 40 optimal weight: 0.2980 chunk 94 optimal weight: 6.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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** A1288 ASN B 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11228 Z= 0.273 Angle : 0.692 11.311 15175 Z= 0.354 Chirality : 0.043 0.309 1752 Planarity : 0.005 0.064 1825 Dihedral : 18.218 168.457 1925 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.07 % Favored : 94.77 % Rotamer: Outliers : 4.72 % Allowed : 13.12 % Favored : 82.16 % 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: -1.60 (0.23), residues: 1301 helix: -0.65 (0.17), residues: 814 sheet: -1.35 (0.55), residues: 71 loop : -1.55 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1246 HIS 0.005 0.001 HIS B 122 PHE 0.019 0.002 PHE B 86 TYR 0.016 0.002 TYR A 407 ARG 0.010 0.001 ARG A 222 *********************** 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 227 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 172 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 ILE cc_start: 0.8612 (tt) cc_final: 0.8316 (tt) REVERT: A 198 PHE cc_start: 0.7573 (t80) cc_final: 0.6898 (t80) REVERT: A 232 VAL cc_start: 0.8776 (t) cc_final: 0.8531 (t) REVERT: A 359 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8121 (tp) REVERT: A 424 MET cc_start: 0.7071 (ttp) cc_final: 0.6817 (ttt) REVERT: A 604 GLU cc_start: 0.7514 (pm20) cc_final: 0.7090 (pt0) REVERT: A 784 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7401 (mtp) REVERT: A 1187 TYR cc_start: 0.8616 (m-10) cc_final: 0.8375 (m-80) REVERT: A 1235 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8651 (tp) REVERT: A 1304 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7894 (tttt) REVERT: A 1370 MET cc_start: 0.8977 (mtt) cc_final: 0.8657 (mtt) REVERT: A 1389 ASN cc_start: 0.7571 (m-40) cc_final: 0.7240 (m110) REVERT: A 1405 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.6952 (pp) REVERT: A 1436 LEU cc_start: 0.5755 (OUTLIER) cc_final: 0.5107 (mt) REVERT: B 96 ARG cc_start: 0.8380 (mtp180) cc_final: 0.8052 (mtp180) REVERT: B 183 LYS cc_start: 0.8455 (mmtt) cc_final: 0.7848 (mtmt) outliers start: 55 outliers final: 28 residues processed: 216 average time/residue: 0.2059 time to fit residues: 65.2629 Evaluate side-chains 193 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 159 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 399 LEU Chi-restraints excluded: chain A residue 433 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 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 784 MET Chi-restraints excluded: chain A residue 1056 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 1235 LEU Chi-restraints excluded: chain A residue 1288 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 1568 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 5.9990 chunk 88 optimal weight: 0.0470 chunk 61 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 118 optimal weight: 0.2980 chunk 125 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 11228 Z= 0.160 Angle : 0.624 11.147 15175 Z= 0.315 Chirality : 0.041 0.242 1752 Planarity : 0.004 0.066 1825 Dihedral : 16.889 167.810 1921 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.69 % Favored : 95.16 % Rotamer: Outliers : 3.77 % Allowed : 14.24 % Favored : 81.99 % 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: -0.77 (0.23), residues: 1301 helix: 0.08 (0.18), residues: 808 sheet: -1.09 (0.56), residues: 71 loop : -1.39 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 156 HIS 0.003 0.001 HIS B 122 PHE 0.018 0.001 PHE A1447 TYR 0.009 0.001 TYR A1347 ARG 0.004 0.000 ARG A 222 *********************** 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 219 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 175 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 GLU cc_start: 0.7295 (tm-30) cc_final: 0.7019 (tm-30) REVERT: A 174 ILE cc_start: 0.8607 (tt) cc_final: 0.8305 (tt) REVERT: A 198 PHE cc_start: 0.7566 (t80) cc_final: 0.6958 (t80) REVERT: A 218 LEU cc_start: 0.7272 (mm) cc_final: 0.6760 (mm) REVERT: A 232 VAL cc_start: 0.8725 (t) cc_final: 0.8513 (t) REVERT: A 424 MET cc_start: 0.7136 (ttp) cc_final: 0.6871 (ttt) REVERT: A 433 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8589 (mt) REVERT: A 604 GLU cc_start: 0.7503 (pm20) cc_final: 0.7066 (pt0) REVERT: A 784 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7411 (mtp) REVERT: A 1187 TYR cc_start: 0.8598 (m-10) cc_final: 0.8390 (m-80) REVERT: A 1235 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8762 (tp) REVERT: A 1304 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7856 (tttt) REVERT: A 1370 MET cc_start: 0.8960 (mtt) cc_final: 0.8614 (mtt) REVERT: A 1405 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.6858 (pp) REVERT: A 1436 LEU cc_start: 0.5629 (OUTLIER) cc_final: 0.5036 (mt) REVERT: B 96 ARG cc_start: 0.8395 (mtp180) cc_final: 0.8026 (mtp180) REVERT: B 183 LYS cc_start: 0.8440 (mmtt) cc_final: 0.7818 (mtmt) outliers start: 44 outliers final: 21 residues processed: 211 average time/residue: 0.2184 time to fit residues: 67.5719 Evaluate side-chains 190 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 163 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 433 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1235 LEU 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 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 B residue 47 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 0.1980 chunk 71 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 107 optimal weight: 0.0020 chunk 86 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 11228 Z= 0.142 Angle : 0.588 11.052 15175 Z= 0.293 Chirality : 0.041 0.228 1752 Planarity : 0.004 0.067 1825 Dihedral : 15.616 170.868 1917 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.84 % Favored : 95.00 % Rotamer: Outliers : 3.77 % Allowed : 15.01 % Favored : 81.22 % 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: 0.08 (0.24), residues: 1301 helix: 0.81 (0.19), residues: 786 sheet: -0.77 (0.56), residues: 69 loop : -1.07 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1220 HIS 0.003 0.001 HIS A 368 PHE 0.018 0.001 PHE A 805 TYR 0.015 0.001 TYR A 637 ARG 0.005 0.000 ARG A1454 *********************** 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 225 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 181 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 PHE cc_start: 0.7592 (t80) cc_final: 0.7008 (t80) REVERT: A 232 VAL cc_start: 0.8676 (t) cc_final: 0.8449 (t) REVERT: A 359 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8081 (tt) REVERT: A 424 MET cc_start: 0.7103 (ttp) cc_final: 0.6824 (ttt) REVERT: A 441 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8400 (mt) REVERT: A 1109 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8606 (mt) REVERT: A 1187 TYR cc_start: 0.8563 (m-10) cc_final: 0.8295 (m-80) REVERT: A 1304 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7793 (tttt) REVERT: A 1362 LEU cc_start: 0.8114 (mt) cc_final: 0.7829 (mt) REVERT: A 1370 MET cc_start: 0.9006 (mtt) cc_final: 0.8621 (mtt) REVERT: A 1405 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6802 (pp) REVERT: A 1436 LEU cc_start: 0.5758 (OUTLIER) cc_final: 0.5112 (mt) REVERT: A 1554 ASP cc_start: 0.7725 (t0) cc_final: 0.7329 (t0) REVERT: B 96 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8017 (mtp180) REVERT: B 183 LYS cc_start: 0.8427 (mmtt) cc_final: 0.7783 (mtmt) outliers start: 44 outliers final: 22 residues processed: 217 average time/residue: 0.2051 time to fit residues: 65.3339 Evaluate side-chains 193 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 164 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 441 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 667 VAL Chi-restraints excluded: chain A residue 697 VAL 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 1194 THR Chi-restraints excluded: chain A residue 1200 ILE 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 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 42 optimal weight: 0.9980 chunk 113 optimal weight: 0.0020 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 104 optimal weight: 0.3980 chunk 58 optimal weight: 0.0170 chunk 10 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 overall best weight: 0.3026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN A1602 ASN B 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 11228 Z= 0.138 Angle : 0.571 10.980 15175 Z= 0.287 Chirality : 0.040 0.216 1752 Planarity : 0.004 0.069 1825 Dihedral : 14.893 168.012 1913 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.69 % Favored : 95.23 % Rotamer: Outliers : 3.43 % Allowed : 15.35 % Favored : 81.22 % 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: 0.49 (0.24), residues: 1301 helix: 1.15 (0.19), residues: 790 sheet: -0.77 (0.57), residues: 71 loop : -0.92 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1220 HIS 0.002 0.001 HIS B 122 PHE 0.021 0.001 PHE A1447 TYR 0.009 0.001 TYR A1581 ARG 0.004 0.000 ARG A1454 *********************** 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 221 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 181 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 PHE cc_start: 0.7584 (t80) cc_final: 0.6985 (t80) REVERT: A 232 VAL cc_start: 0.8680 (t) cc_final: 0.8461 (t) REVERT: A 359 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8174 (tt) REVERT: A 424 MET cc_start: 0.7019 (ttp) cc_final: 0.6735 (ttt) REVERT: A 1187 TYR cc_start: 0.8484 (m-10) cc_final: 0.8240 (m-80) REVERT: A 1304 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7782 (tttt) REVERT: A 1362 LEU cc_start: 0.8205 (mt) cc_final: 0.7901 (mt) REVERT: A 1370 MET cc_start: 0.8962 (mtt) cc_final: 0.8597 (mtt) REVERT: A 1405 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6664 (pp) REVERT: A 1436 LEU cc_start: 0.5780 (OUTLIER) cc_final: 0.5183 (mt) REVERT: A 1554 ASP cc_start: 0.7535 (t0) cc_final: 0.7238 (t0) REVERT: A 1593 TYR cc_start: 0.8304 (m-10) cc_final: 0.7778 (m-80) REVERT: B 96 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8045 (mtp180) outliers start: 40 outliers final: 20 residues processed: 214 average time/residue: 0.2085 time to fit residues: 65.8444 Evaluate side-chains 191 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 166 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 667 VAL Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1200 ILE 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 1436 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 61 GLN Chi-restraints excluded: chain B residue 96 ARG 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 121 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN A1366 ASN A1556 ASN A1602 ASN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 11228 Z= 0.170 Angle : 0.588 10.713 15175 Z= 0.292 Chirality : 0.041 0.217 1752 Planarity : 0.004 0.070 1825 Dihedral : 14.525 166.814 1913 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.30 % Favored : 95.62 % Rotamer: Outliers : 2.83 % Allowed : 16.30 % 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: 0.65 (0.24), residues: 1301 helix: 1.28 (0.19), residues: 793 sheet: -0.74 (0.58), residues: 71 loop : -0.88 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1220 HIS 0.003 0.001 HIS A 749 PHE 0.020 0.001 PHE A 805 TYR 0.014 0.001 TYR A 637 ARG 0.003 0.000 ARG A1454 *********************** 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 206 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 173 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 PHE cc_start: 0.7669 (t80) cc_final: 0.6815 (t80) REVERT: A 232 VAL cc_start: 0.8667 (t) cc_final: 0.8445 (t) REVERT: A 359 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8125 (tt) REVERT: A 424 MET cc_start: 0.7151 (ttp) cc_final: 0.6875 (ttt) REVERT: A 1187 TYR cc_start: 0.8531 (m-10) cc_final: 0.8297 (m-80) REVERT: A 1362 LEU cc_start: 0.8257 (mt) cc_final: 0.7970 (mt) REVERT: A 1370 MET cc_start: 0.9023 (mtt) cc_final: 0.8683 (mtt) REVERT: A 1405 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6679 (pp) REVERT: A 1436 LEU cc_start: 0.5897 (OUTLIER) cc_final: 0.5226 (mt) REVERT: A 1554 ASP cc_start: 0.7576 (t0) cc_final: 0.7289 (t0) REVERT: B 96 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8022 (mtp180) outliers start: 33 outliers final: 25 residues processed: 201 average time/residue: 0.2129 time to fit residues: 62.4751 Evaluate side-chains 198 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 169 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 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 667 VAL Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1200 ILE Chi-restraints excluded: chain A residue 1286 THR 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 1440 TYR Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1489 LEU Chi-restraints excluded: chain A residue 1568 CYS 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 50 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 ASN A1602 ASN B 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 11228 Z= 0.251 Angle : 0.635 10.330 15175 Z= 0.319 Chirality : 0.042 0.207 1752 Planarity : 0.004 0.072 1825 Dihedral : 14.266 167.420 1913 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.07 % Favored : 94.77 % Rotamer: Outliers : 3.60 % Allowed : 15.78 % Favored : 80.62 % 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: 0.55 (0.24), residues: 1301 helix: 1.26 (0.19), residues: 789 sheet: -1.35 (0.53), residues: 81 loop : -0.91 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 173 HIS 0.004 0.001 HIS A 743 PHE 0.025 0.002 PHE A1447 TYR 0.018 0.002 TYR A 637 ARG 0.004 0.001 ARG A1257 *********************** 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 210 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 168 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 202 MET cc_start: 0.7174 (mmp) cc_final: 0.6936 (mmm) REVERT: A 359 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8085 (mt) REVERT: A 424 MET cc_start: 0.7196 (ttp) cc_final: 0.6960 (ttt) REVERT: A 1304 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7882 (tttt) REVERT: A 1370 MET cc_start: 0.8973 (mtt) cc_final: 0.8617 (mtt) REVERT: A 1405 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6736 (pp) REVERT: A 1554 ASP cc_start: 0.7771 (t0) cc_final: 0.7371 (t0) REVERT: B 96 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8113 (mtp180) outliers start: 42 outliers final: 25 residues processed: 202 average time/residue: 0.2049 time to fit residues: 60.4690 Evaluate side-chains 190 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 161 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 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 667 VAL Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 795 ASN 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 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 1568 CYS Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 61 GLN 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 109 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A1602 ASN B 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11228 Z= 0.197 Angle : 0.613 10.519 15175 Z= 0.306 Chirality : 0.041 0.200 1752 Planarity : 0.004 0.074 1825 Dihedral : 13.977 166.222 1911 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.46 % Favored : 95.39 % Rotamer: Outliers : 3.09 % Allowed : 16.81 % Favored : 80.10 % 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: 0.73 (0.24), residues: 1301 helix: 1.43 (0.19), residues: 784 sheet: -1.39 (0.53), residues: 81 loop : -0.82 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 156 HIS 0.003 0.001 HIS A 749 PHE 0.021 0.001 PHE A 805 TYR 0.010 0.001 TYR B 119 ARG 0.003 0.000 ARG A1454 *********************** 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 202 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 166 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 232 VAL cc_start: 0.8706 (t) cc_final: 0.8441 (t) REVERT: A 359 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8098 (tt) REVERT: A 424 MET cc_start: 0.7168 (ttp) cc_final: 0.6930 (ttt) REVERT: A 1304 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7893 (tttt) REVERT: A 1370 MET cc_start: 0.8991 (mtt) cc_final: 0.8638 (mtt) REVERT: A 1405 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6749 (pp) REVERT: A 1433 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7233 (tt) REVERT: A 1554 ASP cc_start: 0.7719 (t0) cc_final: 0.7349 (t0) REVERT: B 96 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8054 (mtp180) outliers start: 36 outliers final: 28 residues processed: 196 average time/residue: 0.2258 time to fit residues: 65.3109 Evaluate side-chains 195 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 162 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 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 630 ILE Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1200 ILE 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 1433 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 1568 CYS Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 61 GLN 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 75 optimal weight: 0.6980 chunk 58 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1602 ASN B 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 11228 Z= 0.148 Angle : 0.590 10.680 15175 Z= 0.294 Chirality : 0.040 0.193 1752 Planarity : 0.004 0.074 1825 Dihedral : 13.576 162.833 1911 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.53 % Favored : 95.39 % Rotamer: Outliers : 2.66 % Allowed : 17.24 % Favored : 80.10 % 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: 1.03 (0.24), residues: 1301 helix: 1.72 (0.19), residues: 781 sheet: -1.37 (0.53), residues: 81 loop : -0.78 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1220 HIS 0.002 0.001 HIS A 749 PHE 0.030 0.001 PHE A1447 TYR 0.010 0.001 TYR A1581 ARG 0.005 0.000 ARG B 60 ********************** 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 197 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 166 time to evaluate : 1.292 Fit side-chains revert: symmetry clash REVERT: A 232 VAL cc_start: 0.8703 (t) cc_final: 0.8446 (t) REVERT: A 359 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8104 (tt) REVERT: A 424 MET cc_start: 0.7134 (ttp) cc_final: 0.6884 (ttt) REVERT: A 783 LEU cc_start: 0.8949 (mt) cc_final: 0.8713 (mm) REVERT: A 1304 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7842 (tttt) REVERT: A 1370 MET cc_start: 0.9034 (mtt) cc_final: 0.8679 (mtt) REVERT: A 1405 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6707 (pp) REVERT: A 1433 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7262 (tt) REVERT: A 1554 ASP cc_start: 0.7526 (t0) cc_final: 0.7211 (t0) REVERT: B 96 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7997 (mtp180) outliers start: 31 outliers final: 23 residues processed: 193 average time/residue: 0.2120 time to fit residues: 59.4798 Evaluate side-chains 190 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 162 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 667 VAL Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1200 ILE 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 1433 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 1568 CYS 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 31 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 43 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1602 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.154051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.119087 restraints weight = 13743.040| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.72 r_work: 0.3116 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11228 Z= 0.157 Angle : 0.586 10.618 15175 Z= 0.293 Chirality : 0.040 0.190 1752 Planarity : 0.004 0.073 1825 Dihedral : 13.288 160.218 1911 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.54 % Rotamer: Outliers : 2.66 % Allowed : 17.32 % 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: 1.19 (0.24), residues: 1301 helix: 1.85 (0.19), residues: 781 sheet: -1.32 (0.53), residues: 81 loop : -0.70 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1220 HIS 0.002 0.001 HIS A 749 PHE 0.020 0.001 PHE A 805 TYR 0.010 0.001 TYR A1581 ARG 0.003 0.000 ARG B 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2605.56 seconds wall clock time: 47 minutes 3.34 seconds (2823.34 seconds total)