Starting phenix.real_space_refine (version: dev) on Mon Feb 20 00:21:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agf_9617/02_2023/6agf_9617_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agf_9617/02_2023/6agf_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_9617/02_2023/6agf_9617.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agf_9617/02_2023/6agf_9617.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agf_9617/02_2023/6agf_9617_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agf_9617/02_2023/6agf_9617_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A ARG 401": "NH1" <-> "NH2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1129": "NH1" <-> "NH2" Residue "A ARG 1135": "NH1" <-> "NH2" Residue "A ARG 1337": "NH1" <-> "NH2" Residue "A TYR 1347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1454": "NH1" <-> "NH2" Residue "A PHE 1517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1554": "OD1" <-> "OD2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 1 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 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 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 chiralities: 2 Time building chain proxies: 6.75, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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: 4.92 Conformation dependent library (CDL) restraints added in 1.6 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... running ksdssp... Secondary structure from input PDB file: 54 helices and 6 sheets defined 59.8% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 121 through 128 removed outlier: 4.186A pdb=" N LYS A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 147 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 158 through 179 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 184 through 190 removed outlier: 3.534A pdb=" N LEU A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 209 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 219 through 232 removed outlier: 3.520A pdb=" N VAL A 223 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR A 229 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 243 removed outlier: 3.556A pdb=" N VAL A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 272 removed outlier: 4.192A pdb=" N LYS A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ASP A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 261 " --> pdb=" O THR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 392 through 397 removed outlier: 3.579A pdb=" N LEU A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 403 No H-bonds generated for 'chain 'A' and resid 400 through 403' Processing helix chain 'A' and resid 408 through 419 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 421 through 433 removed outlier: 4.158A pdb=" N ILE A 425 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 426 " --> pdb=" O TYR A 423 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 428 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE A 431 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 433 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 462 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) removed outlier: 3.603A pdb=" N GLU A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) 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 561 through 576 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 581 through 595 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) Processing helix chain 'A' and resid 604 through 631 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 641 through 659 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) Processing helix chain 'A' and resid 668 through 670 No H-bonds generated for 'chain 'A' and resid 668 through 670' Processing helix chain 'A' and resid 672 through 680 removed outlier: 3.712A pdb=" N ARG A 675 " --> pdb=" O ARG A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 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 703 through 726 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) Processing helix chain 'A' and resid 747 through 759 removed outlier: 3.530A pdb=" N LEU A 758 " --> pdb=" O VAL A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.991A pdb=" N ASP A 768 " --> pdb=" O GLU A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 804 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 1028 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 1031 through 1046 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 1053 through 1055 No H-bonds generated for 'chain 'A' and resid 1053 through 1055' Processing helix chain 'A' and resid 1060 through 1078 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 1081 through 1087 removed outlier: 3.520A pdb=" N VAL A1085 " --> pdb=" O LEU A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1093 No H-bonds generated for 'chain 'A' and resid 1090 through 1093' Processing helix chain 'A' and resid 1098 through 1116 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) Processing helix chain 'A' and resid 1130 through 1141 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 1144 through 1153 removed outlier: 3.554A pdb=" N VAL A1149 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1182 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 1206 through 1212 removed outlier: 4.449A pdb=" N SER A1211 " --> pdb=" O SER A1207 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A1212 " --> pdb=" O GLU A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1242 removed outlier: 3.593A pdb=" N GLN A1239 " --> pdb=" O LEU A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1246 through 1254 removed outlier: 3.528A pdb=" N ALA A1252 " --> pdb=" O ASP A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1281 removed outlier: 4.067A pdb=" N TYR A1272 " --> pdb=" O LEU A1269 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A1277 " --> pdb=" O TYR A1274 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A1278 " --> pdb=" O PHE A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1304 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 1314 through 1324 removed outlier: 4.041A pdb=" N LYS A1318 " --> pdb=" O GLU A1314 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR A1319 " --> pdb=" O GLU A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1350 No H-bonds generated for 'chain 'A' and resid 1347 through 1350' Processing helix chain 'A' and resid 1353 through 1362 removed outlier: 4.108A pdb=" N ILE A1357 " --> pdb=" O ALA A1354 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET A1360 " --> pdb=" O ILE A1357 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A1361 " --> pdb=" O THR A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1371 removed outlier: 3.858A pdb=" N MET A1370 " --> pdb=" O ASN A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1404 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 1415 through 1439 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 1447 through 1463 removed outlier: 3.858A pdb=" N ARG A1451 " --> pdb=" O PHE A1447 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA A1453 " --> pdb=" O VAL A1449 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ARG A1454 " --> pdb=" O ILE A1450 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE A1455 " --> pdb=" O ARG A1451 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY A1456 " --> pdb=" O LEU A1452 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARG A1457 " --> pdb=" O ALA A1453 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL A1458 " --> pdb=" O ARG A1454 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A1459 " --> pdb=" O ILE A1455 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG A1460 " --> pdb=" O GLY A1456 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU A1461 " --> pdb=" O ARG A1457 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE A1462 " --> pdb=" O VAL A1458 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG A1463 " --> pdb=" O LEU A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1503 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 1522 through 1531 removed outlier: 3.607A pdb=" N ILE A1527 " --> pdb=" O GLY A1523 " (cutoff:3.500A) Processing helix chain 'A' and resid 1538 through 1543 Processing helix chain 'A' and resid 1571 through 1605 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 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 155 through 190 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= A, first strand: chain 'A' and resid 279 through 282 Processing sheet with id= B, first strand: chain 'A' and resid 1187 through 1191 Processing sheet with id= C, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.187A pdb=" N GLU B 145 " --> pdb=" O ALA B 30 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 36 through 38 Processing sheet with id= E, first strand: chain 'B' and resid 138 through 144 removed outlier: 3.826A pdb=" N LEU B 71 " --> pdb=" O TRP B 57 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE B 59 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS B 69 " --> pdb=" O PHE B 59 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 126 through 128 456 hydrogen bonds defined for protein. 1254 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: 3.19 Time building geometry restraints manager: 5.24 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: 93.87 - 102.84: 85 102.84 - 111.81: 5185 111.81 - 120.77: 6601 120.77 - 129.74: 3225 129.74 - 138.71: 79 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 - 27.43: 6245 27.43 - 54.86: 287 54.86 - 82.30: 39 82.30 - 109.73: 10 109.73 - 137.16: 5 Dihedral angle restraints: 6586 sinusoidal: 2754 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 6583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1517 0.096 - 0.191: 202 0.191 - 0.287: 30 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: 131 2.63 - 3.20: 9525 3.20 - 3.76: 15919 3.76 - 4.33: 22796 4.33 - 4.90: 37142 Nonbonded interactions: 85513 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 2.520 nonbonded pdb=" O MET A1516 " pdb=" ND2 ASN A1524 " model vdw 2.213 2.520 nonbonded pdb=" NH2 ARG A 277 " pdb=" OD2 ASP A1375 " model vdw 2.230 2.520 nonbonded pdb=" O PHE A1174 " pdb=" OH TYR A1274 " model vdw 2.280 2.440 ... (remaining 85508 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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. 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: 0.650 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: 3.980 Check model and map are aligned: 0.190 Process input model: 31.450 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.100 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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= 0.893 Angle : 1.529 19.853 15175 Z= 0.806 Chirality : 0.069 0.478 1752 Planarity : 0.008 0.097 1825 Dihedral : 16.240 137.160 4088 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 % 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 *********************** 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 : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 24 residues processed: 289 average time/residue: 0.2482 time to fit residues: 99.8298 Evaluate side-chains 189 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 165 time to evaluate : 1.314 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1267 time to fit residues: 6.9250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 ASN A 743 HIS A1095 ASN A1214 HIS A1288 ASN A1297 ASN ** A1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1570 ASN B 93 ASN B 135 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 11228 Z= 0.228 Angle : 0.720 12.387 15175 Z= 0.373 Chirality : 0.042 0.299 1752 Planarity : 0.006 0.075 1825 Dihedral : 14.426 130.434 1628 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.38 % Favored : 95.31 % Rotamer Outliers : 2.92 % 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: -2.92 (0.21), residues: 1301 helix: -1.87 (0.16), residues: 800 sheet: -1.68 (0.57), residues: 66 loop : -1.73 (0.29), residues: 435 *********************** 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 225 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 191 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 13 residues processed: 215 average time/residue: 0.2368 time to fit residues: 73.1224 Evaluate side-chains 171 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 158 time to evaluate : 1.362 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1121 time to fit residues: 4.5256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 20.0000 chunk 36 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 40 optimal weight: 0.0010 chunk 94 optimal weight: 10.0000 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 GLN A 559 ASN ** A1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN B 93 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 11228 Z= 0.173 Angle : 0.613 11.393 15175 Z= 0.316 Chirality : 0.040 0.211 1752 Planarity : 0.004 0.065 1825 Dihedral : 13.661 137.870 1628 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.53 % Favored : 95.16 % Rotamer Outliers : 2.57 % 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: -1.75 (0.22), residues: 1301 helix: -0.79 (0.17), residues: 807 sheet: -1.62 (0.56), residues: 71 loop : -1.52 (0.30), residues: 423 *********************** 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 210 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 180 time to evaluate : 1.367 Fit side-chains outliers start: 30 outliers final: 11 residues processed: 201 average time/residue: 0.2289 time to fit residues: 67.2057 Evaluate side-chains 169 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 158 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1030 time to fit residues: 3.8517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 62 optimal weight: 0.0170 chunk 112 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.0620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN ** A1556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1591 ASN A1602 ASN B 102 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 11228 Z= 0.199 Angle : 0.594 11.001 15175 Z= 0.307 Chirality : 0.040 0.170 1752 Planarity : 0.004 0.064 1825 Dihedral : 13.085 124.073 1628 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.61 % Favored : 95.08 % Rotamer Outliers : 1.11 % 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: -1.05 (0.23), residues: 1301 helix: -0.14 (0.18), residues: 802 sheet: -1.90 (0.54), residues: 81 loop : -1.29 (0.30), residues: 418 *********************** 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 183 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 1.400 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 182 average time/residue: 0.2279 time to fit residues: 61.1665 Evaluate side-chains 168 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 161 time to evaluate : 1.207 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1079 time to fit residues: 3.2066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 0.0020 chunk 71 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 overall best weight: 1.9192 ------------------------------------------------------------------------------- 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** A 453 GLN A1095 ASN A1524 ASN ** A1556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1602 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 11228 Z= 0.280 Angle : 0.611 10.736 15175 Z= 0.315 Chirality : 0.041 0.157 1752 Planarity : 0.004 0.063 1825 Dihedral : 12.893 112.739 1628 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.92 % Favored : 94.77 % Rotamer Outliers : 2.23 % 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: -0.81 (0.23), residues: 1301 helix: 0.05 (0.18), residues: 805 sheet: -1.86 (0.53), residues: 81 loop : -1.22 (0.30), residues: 415 *********************** 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 189 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 163 time to evaluate : 1.397 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 13 residues processed: 180 average time/residue: 0.2296 time to fit residues: 61.3899 Evaluate side-chains 171 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 158 time to evaluate : 1.347 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.1235 time to fit residues: 4.7062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 0.0050 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1524 ASN ** A1556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1600 ASN A1602 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.089 11228 Z= 0.172 Angle : 0.558 11.344 15175 Z= 0.287 Chirality : 0.039 0.149 1752 Planarity : 0.004 0.062 1825 Dihedral : 12.398 108.076 1628 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.53 % Favored : 95.23 % Rotamer Outliers : 1.46 % 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: -0.23 (0.24), residues: 1301 helix: 0.58 (0.19), residues: 785 sheet: -1.80 (0.53), residues: 81 loop : -1.03 (0.30), residues: 435 *********************** 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 190 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 173 time to evaluate : 1.658 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 187 average time/residue: 0.2146 time to fit residues: 59.1640 Evaluate side-chains 161 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 1.324 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1143 time to fit residues: 1.8529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 GLN A1524 ASN ** A1556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1602 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 11228 Z= 0.165 Angle : 0.555 10.784 15175 Z= 0.283 Chirality : 0.039 0.146 1752 Planarity : 0.004 0.068 1825 Dihedral : 12.017 105.318 1628 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.53 % Favored : 95.23 % Rotamer Outliers : 0.86 % 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: 0.10 (0.24), residues: 1301 helix: 0.86 (0.19), residues: 787 sheet: -1.61 (0.53), residues: 79 loop : -0.95 (0.30), residues: 435 *********************** 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 179 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 169 time to evaluate : 1.382 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 176 average time/residue: 0.2296 time to fit residues: 59.6455 Evaluate side-chains 162 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 158 time to evaluate : 1.328 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1129 time to fit residues: 2.6548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 ASN A1524 ASN A1602 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 11228 Z= 0.166 Angle : 0.550 10.687 15175 Z= 0.281 Chirality : 0.039 0.146 1752 Planarity : 0.004 0.066 1825 Dihedral : 11.751 105.650 1628 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.53 % Favored : 95.23 % Rotamer Outliers : 0.69 % 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: 0.28 (0.24), residues: 1301 helix: 1.01 (0.19), residues: 798 sheet: -1.60 (0.53), residues: 79 loop : -0.94 (0.31), residues: 424 *********************** 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 170 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 162 time to evaluate : 1.347 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 168 average time/residue: 0.2298 time to fit residues: 57.1286 Evaluate side-chains 159 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 156 time to evaluate : 1.332 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1295 time to fit residues: 2.4279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.0050 chunk 116 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1503 ASN A1524 ASN A1602 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 11228 Z= 0.154 Angle : 0.556 10.747 15175 Z= 0.281 Chirality : 0.039 0.178 1752 Planarity : 0.004 0.065 1825 Dihedral : 11.443 106.474 1628 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.46 % Favored : 95.39 % Rotamer Outliers : 0.26 % 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: 0.46 (0.24), residues: 1301 helix: 1.19 (0.19), residues: 798 sheet: -1.64 (0.53), residues: 81 loop : -0.90 (0.31), residues: 422 *********************** 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 173 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 1.471 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 172 average time/residue: 0.2377 time to fit residues: 59.9390 Evaluate side-chains 162 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 1.308 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1318 time to fit residues: 1.9938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1524 ASN A1600 ASN A1602 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 11228 Z= 0.186 Angle : 0.564 10.583 15175 Z= 0.287 Chirality : 0.040 0.167 1752 Planarity : 0.004 0.067 1825 Dihedral : 11.270 106.546 1628 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.77 % Favored : 95.08 % Rotamer Outliers : 0.43 % 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: 0.55 (0.24), residues: 1301 helix: 1.25 (0.19), residues: 799 sheet: -1.69 (0.53), residues: 81 loop : -0.84 (0.31), residues: 421 ********************** 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 171 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 166 time to evaluate : 1.481 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 170 average time/residue: 0.2371 time to fit residues: 59.2822 Evaluate side-chains 166 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 163 time to evaluate : 1.300 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1314 time to fit residues: 2.6171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 9.9990 chunk 95 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 103 optimal weight: 0.0980 chunk 43 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A1524 ASN A1602 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.149145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.113702 restraints weight = 14025.294| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.82 r_work: 0.3091 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 11228 Z= 0.165 Angle : 0.553 10.623 15175 Z= 0.281 Chirality : 0.039 0.162 1752 Planarity : 0.004 0.062 1825 Dihedral : 11.022 107.469 1628 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.77 % Favored : 95.16 % Rotamer Outliers : 0.34 % 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: 0.73 (0.24), residues: 1301 helix: 1.41 (0.19), residues: 798 sheet: -1.64 (0.53), residues: 81 loop : -0.80 (0.31), residues: 422 =============================================================================== Job complete usr+sys time: 2534.55 seconds wall clock time: 46 minutes 43.78 seconds (2803.78 seconds total)