Starting phenix.real_space_refine on Sun Aug 24 19:28:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tjo_41306/08_2025/8tjo_41306_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tjo_41306/08_2025/8tjo_41306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tjo_41306/08_2025/8tjo_41306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tjo_41306/08_2025/8tjo_41306.map" model { file = "/net/cci-nas-00/data/ceres_data/8tjo_41306/08_2025/8tjo_41306_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tjo_41306/08_2025/8tjo_41306_neut.cif" } resolution = 3.61 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 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= 0.029 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 1 5.49 5 S 79 5.16 5 C 13932 2.51 5 N 3979 2.21 5 O 4296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22287 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1370, 10158 Classifications: {'peptide': 1370} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 74, 'TRANS': 1295} Chain breaks: 3 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, '4HH:plan-3': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 5915 Classifications: {'peptide': 800} Link IDs: {'PTRANS': 48, 'TRANS': 751} Chain breaks: 3 Chain: "C" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1539 Classifications: {'peptide': 205} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 193} Chain breaks: 2 Chain: "D" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1568 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 14, 'TRANS': 191} Chain breaks: 2 Chain: "E" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1539 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain breaks: 2 Chain: "F" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1568 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 191} Chain breaks: 2 Time building chain proxies: 3.82, per 1000 atoms: 0.17 Number of scatterers: 22287 At special positions: 0 Unit cell: (121, 174.9, 161.7, 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 79 16.00 P 1 15.00 O 4296 8.00 N 3979 7.00 C 13932 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 39 " - pdb=" SG CYS D 109 " distance=2.04 Simple disulfide: pdb=" SG CYS D 156 " - pdb=" SG CYS D 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 100 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.03 Simple disulfide: pdb=" SG CYS F 39 " - pdb=" SG CYS F 109 " distance=2.03 Simple disulfide: pdb=" SG CYS F 156 " - pdb=" SG CYS F 216 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 839.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5398 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 30 sheets defined 33.1% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.539A pdb=" N GLU A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.750A pdb=" N PHE A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 103 removed outlier: 4.290A pdb=" N THR A 102 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 103 " --> pdb=" O GLU A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 103' Processing helix chain 'A' and resid 112 through 118 removed outlier: 4.105A pdb=" N ALA A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 137 removed outlier: 3.627A pdb=" N MET A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 167 removed outlier: 3.508A pdb=" N GLU A 166 " --> pdb=" O ARG A 163 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 167 " --> pdb=" O LEU A 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 163 through 167' Processing helix chain 'A' and resid 181 through 193 removed outlier: 4.199A pdb=" N SER A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ILE A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 206 through 221 removed outlier: 3.709A pdb=" N GLN A 217 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 247 removed outlier: 3.548A pdb=" N ASP A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 244 " --> pdb=" O MET A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 312 through 327 removed outlier: 3.726A pdb=" N GLN A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 360 Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 384 through 398 Processing helix chain 'A' and resid 481 through 497 removed outlier: 3.548A pdb=" N ARG A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 514 removed outlier: 3.546A pdb=" N GLY A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 540 Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 580 through 595 Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 601 through 607 removed outlier: 4.052A pdb=" N PHE A 605 " --> pdb=" O GLU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 645 Proline residue: A 629 - end of helix Processing helix chain 'A' and resid 657 through 666 removed outlier: 4.038A pdb=" N ALA A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 685 Processing helix chain 'A' and resid 812 through 823 Processing helix chain 'A' and resid 837 through 847 removed outlier: 3.804A pdb=" N GLY A 847 " --> pdb=" O GLU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 879 removed outlier: 3.510A pdb=" N PHE A 868 " --> pdb=" O SER A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 922 through 928 removed outlier: 3.549A pdb=" N LEU A 928 " --> pdb=" O GLU A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 972 removed outlier: 3.658A pdb=" N THR A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 995 Processing helix chain 'A' and resid 1006 through 1009 Processing helix chain 'A' and resid 1021 through 1037 removed outlier: 3.817A pdb=" N ALA A1025 " --> pdb=" O LEU A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1078 removed outlier: 3.900A pdb=" N TRP A1068 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL A1073 " --> pdb=" O GLY A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1098 removed outlier: 3.882A pdb=" N GLU A1095 " --> pdb=" O SER A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1105 Processing helix chain 'A' and resid 1151 through 1164 removed outlier: 3.792A pdb=" N GLN A1155 " --> pdb=" O GLY A1151 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A1160 " --> pdb=" O ILE A1156 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A1161 " --> pdb=" O ALA A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1178 Processing helix chain 'A' and resid 1180 through 1192 removed outlier: 3.919A pdb=" N LEU A1184 " --> pdb=" O GLY A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1214 Processing helix chain 'A' and resid 1240 through 1249 removed outlier: 3.975A pdb=" N ILE A1244 " --> pdb=" O THR A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1262 Processing helix chain 'A' and resid 1275 through 1279 Processing helix chain 'A' and resid 1285 through 1287 No H-bonds generated for 'chain 'A' and resid 1285 through 1287' Processing helix chain 'A' and resid 1288 through 1303 removed outlier: 3.717A pdb=" N ASN A1292 " --> pdb=" O TYR A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1333 removed outlier: 3.978A pdb=" N ARG A1333 " --> pdb=" O ASP A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1355 Processing helix chain 'A' and resid 1365 through 1375 removed outlier: 4.425A pdb=" N LEU A1371 " --> pdb=" O ASP A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1385 through 1390 removed outlier: 3.846A pdb=" N ARG A1390 " --> pdb=" O ASP A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1429 removed outlier: 4.016A pdb=" N LYS A1414 " --> pdb=" O PRO A1410 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG A1421 " --> pdb=" O PHE A1417 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A1422 " --> pdb=" O GLU A1418 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A1425 " --> pdb=" O ARG A1421 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1446 removed outlier: 3.995A pdb=" N LEU A1445 " --> pdb=" O ALA A1441 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A1446 " --> pdb=" O PHE A1442 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1441 through 1446' Processing helix chain 'A' and resid 1448 through 1464 removed outlier: 3.811A pdb=" N LEU A1453 " --> pdb=" O 4HH A1449 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU A1454 " --> pdb=" O LEU A1450 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A1462 " --> pdb=" O ARG A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1470 through 1475 Processing helix chain 'A' and resid 1477 through 1489 removed outlier: 3.755A pdb=" N LEU A1489 " --> pdb=" O LEU A1485 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 33 removed outlier: 3.864A pdb=" N TYR B 12 " --> pdb=" O LYS B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 112 through 118 Processing helix chain 'B' and resid 120 through 138 removed outlier: 3.813A pdb=" N GLU B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 179 Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.645A pdb=" N ALA B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 206 through 222 removed outlier: 3.786A pdb=" N LEU B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG B 220 " --> pdb=" O CYS B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 280 through 286 Processing helix chain 'B' and resid 313 through 328 Processing helix chain 'B' and resid 330 through 334 removed outlier: 4.066A pdb=" N ILE B 334 " --> pdb=" O PRO B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 360 removed outlier: 3.813A pdb=" N ILE B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'B' and resid 372 through 377 Processing helix chain 'B' and resid 379 through 383 Processing helix chain 'B' and resid 384 through 398 Processing helix chain 'B' and resid 481 through 499 Processing helix chain 'B' and resid 503 through 512 removed outlier: 3.575A pdb=" N ILE B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 542 Processing helix chain 'B' and resid 573 through 580 removed outlier: 3.606A pdb=" N LEU B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 595 removed outlier: 4.506A pdb=" N ARG B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 645 removed outlier: 3.799A pdb=" N VAL B 630 " --> pdb=" O VAL B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 667 removed outlier: 4.001A pdb=" N ILE B 660 " --> pdb=" O SER B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 686 Processing helix chain 'B' and resid 814 through 824 Processing helix chain 'B' and resid 837 through 846 removed outlier: 3.966A pdb=" N ASP B 846 " --> pdb=" O GLU B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 878 removed outlier: 3.907A pdb=" N PHE B 868 " --> pdb=" O SER B 864 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 878 " --> pdb=" O ARG B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 889 Processing helix chain 'C' and resid 91 through 95 removed outlier: 3.848A pdb=" N THR C 95 " --> pdb=" O THR C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 150 removed outlier: 3.576A pdb=" N SER D 149 " --> pdb=" O GLN D 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 removed outlier: 3.708A pdb=" N THR E 95 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing sheet with id=AA1, first strand: chain 'A' and resid 420 through 422 removed outlier: 6.110A pdb=" N LEU A 367 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY A 370 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A 336 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN A 449 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL A 299 " --> pdb=" O ASN A 449 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N HIS A 451 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR A 297 " --> pdb=" O HIS A 451 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE A 453 " --> pdb=" O ARG A 295 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA A 292 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL A 37 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU A 278 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA A 39 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 232 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ILE A 199 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL A 151 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL A 201 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL A 153 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER B 200 " --> pdb=" O ASP A 202 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL B 151 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL B 201 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL B 153 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA B 272 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N CYS B 42 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N MET B 274 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N MET B 40 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU B 276 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA B 292 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 295 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE B 453 " --> pdb=" O ARG B 295 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR B 297 " --> pdb=" O HIS B 451 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N HIS B 451 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL B 299 " --> pdb=" O ASN B 449 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN B 449 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA B 336 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY B 370 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LEU B 367 " --> pdb=" O SER B 421 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AA3, first strand: chain 'A' and resid 478 through 479 removed outlier: 3.619A pdb=" N ARG A 521 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 649 through 654 removed outlier: 7.145A pdb=" N ALA A 558 " --> pdb=" O ALA A 650 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL A 652 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE A 560 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLY A 654 " --> pdb=" O PHE A 560 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE A 562 " --> pdb=" O GLY A 654 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE A 828 " --> pdb=" O ILE A 855 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 784 through 785 removed outlier: 4.009A pdb=" N PHE A 784 " --> pdb=" O THR A 793 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 930 through 934 Processing sheet with id=AA7, first strand: chain 'A' and resid 977 through 979 removed outlier: 6.554A pdb=" N VAL A 951 " --> pdb=" O LEU A 979 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1169 through 1170 removed outlier: 3.973A pdb=" N LEU A1170 " --> pdb=" O THR A1196 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 1224 through 1225 removed outlier: 5.519A pdb=" N VAL A1224 " --> pdb=" O VAL A1271 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AB2, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AB3, first strand: chain 'B' and resid 475 through 479 removed outlier: 4.160A pdb=" N ARG B 521 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY B 550 " --> pdb=" O ARG B 521 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 560 through 561 removed outlier: 3.626A pdb=" N ILE B 855 " --> pdb=" O PHE B 828 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU B 830 " --> pdb=" O ILE B 855 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 784 through 785 removed outlier: 4.040A pdb=" N PHE B 784 " --> pdb=" O THR B 793 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 8 through 9 Processing sheet with id=AB7, first strand: chain 'C' and resid 12 through 13 removed outlier: 3.884A pdb=" N GLY C 12 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 96 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ARG C 40 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N TRP C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 172 through 173 Processing sheet with id=AB9, first strand: chain 'C' and resid 206 through 207 Processing sheet with id=AC1, first strand: chain 'D' and resid 20 through 21 removed outlier: 3.542A pdb=" N PHE D 92 " --> pdb=" O CYS D 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 28 through 29 Processing sheet with id=AC3, first strand: chain 'D' and resid 66 through 70 removed outlier: 5.654A pdb=" N LEU D 67 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU D 58 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D 69 " --> pdb=" O TRP D 56 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 8 through 9 removed outlier: 3.587A pdb=" N THR E 73 " --> pdb=" O GLN E 86 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AC6, first strand: chain 'E' and resid 62 through 64 removed outlier: 3.602A pdb=" N PHE E 52 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP E 38 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 129 through 130 removed outlier: 3.737A pdb=" N ASP E 151 " --> pdb=" O TYR E 183 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR E 183 " --> pdb=" O ASP E 151 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER E 184 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL E 176 " --> pdb=" O SER E 184 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 157 through 161 removed outlier: 3.592A pdb=" N VAL E 214 " --> pdb=" O VAL E 205 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 27 through 29 removed outlier: 4.066A pdb=" N ASP F 127 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE F 69 " --> pdb=" O TRP F 56 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU F 58 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LEU F 67 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 35 through 40 Processing sheet with id=AD2, first strand: chain 'F' and resid 152 through 155 Processing sheet with id=AD3, first strand: chain 'F' and resid 167 through 170 removed outlier: 3.960A pdb=" N LYS F 167 " --> pdb=" O THR F 219 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR F 219 " --> pdb=" O LYS F 167 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS F 216 " --> pdb=" O LYS F 229 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS F 229 " --> pdb=" O CYS F 216 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL F 218 " --> pdb=" O VAL F 227 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL F 227 " --> pdb=" O VAL F 218 " (cutoff:3.500A) 774 hydrogen bonds defined for protein. 2163 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: 3.90 Time building geometry restraints manager: 2.07 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: 3796 1.30 - 1.43: 5700 1.43 - 1.56: 13118 1.56 - 1.69: 6 1.69 - 1.82: 124 Bond restraints: 22744 Sorted by residual: bond pdb=" C GLU F 217 " pdb=" N VAL F 218 " ideal model delta sigma weight residual 1.331 1.239 0.092 1.32e-02 5.74e+03 4.87e+01 bond pdb=" CA THR F 228 " pdb=" C THR F 228 " ideal model delta sigma weight residual 1.522 1.443 0.080 1.20e-02 6.94e+03 4.41e+01 bond pdb=" C THR F 228 " pdb=" O THR F 228 " ideal model delta sigma weight residual 1.234 1.167 0.067 1.09e-02 8.42e+03 3.75e+01 bond pdb=" N THR F 228 " pdb=" CA THR F 228 " ideal model delta sigma weight residual 1.458 1.402 0.055 1.18e-02 7.18e+03 2.19e+01 bond pdb=" CA GLU F 217 " pdb=" C GLU F 217 " ideal model delta sigma weight residual 1.523 1.478 0.045 1.18e-02 7.18e+03 1.47e+01 ... (remaining 22739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.66: 30860 4.66 - 9.32: 75 9.32 - 13.98: 8 13.98 - 18.64: 0 18.64 - 23.30: 1 Bond angle restraints: 30944 Sorted by residual: angle pdb=" CB GLU F 217 " pdb=" CG GLU F 217 " pdb=" CD GLU F 217 " ideal model delta sigma weight residual 112.60 89.30 23.30 1.70e+00 3.46e-01 1.88e+02 angle pdb=" CA THR F 228 " pdb=" C THR F 228 " pdb=" O THR F 228 " ideal model delta sigma weight residual 121.28 112.11 9.17 1.07e+00 8.73e-01 7.34e+01 angle pdb=" CA THR F 228 " pdb=" CB THR F 228 " pdb=" OG1 THR F 228 " ideal model delta sigma weight residual 109.60 97.10 12.50 1.50e+00 4.44e-01 6.94e+01 angle pdb=" C GLU F 217 " pdb=" N VAL F 218 " pdb=" CA VAL F 218 " ideal model delta sigma weight residual 122.99 133.74 -10.75 1.39e+00 5.18e-01 5.99e+01 angle pdb=" O CYS F 216 " pdb=" C CYS F 216 " pdb=" N GLU F 217 " ideal model delta sigma weight residual 123.19 114.82 8.37 1.17e+00 7.31e-01 5.12e+01 ... (remaining 30939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 11857 17.94 - 35.89: 1306 35.89 - 53.83: 318 53.83 - 71.77: 62 71.77 - 89.71: 30 Dihedral angle restraints: 13573 sinusoidal: 5142 harmonic: 8431 Sorted by residual: dihedral pdb=" CB CYS F 39 " pdb=" SG CYS F 39 " pdb=" SG CYS F 109 " pdb=" CB CYS F 109 " ideal model delta sinusoidal sigma weight residual 93.00 172.29 -79.29 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" N THR F 228 " pdb=" C THR F 228 " pdb=" CA THR F 228 " pdb=" CB THR F 228 " ideal model delta harmonic sigma weight residual 123.40 108.06 15.34 0 2.50e+00 1.60e-01 3.76e+01 dihedral pdb=" CA THR B 513 " pdb=" C THR B 513 " pdb=" N GLY B 514 " pdb=" CA GLY B 514 " ideal model delta harmonic sigma weight residual -180.00 -150.95 -29.05 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 13570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2439 0.036 - 0.073: 729 0.073 - 0.109: 261 0.109 - 0.146: 64 0.146 - 0.182: 4 Chirality restraints: 3497 Sorted by residual: chirality pdb=" CA PHE A1331 " pdb=" N PHE A1331 " pdb=" C PHE A1331 " pdb=" CB PHE A1331 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CA MET A 635 " pdb=" N MET A 635 " pdb=" C MET A 635 " pdb=" CB MET A 635 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.79e-01 chirality pdb=" CA PRO B 82 " pdb=" N PRO B 82 " pdb=" C PRO B 82 " pdb=" CB PRO B 82 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 3494 not shown) Planarity restraints: 4083 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 227 " 0.024 2.00e-02 2.50e+03 5.06e-02 2.56e+01 pdb=" C VAL F 227 " -0.087 2.00e-02 2.50e+03 pdb=" O VAL F 227 " 0.034 2.00e-02 2.50e+03 pdb=" N THR F 228 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 81 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.63e+00 pdb=" N PRO B 82 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 129 " -0.039 5.00e-02 4.00e+02 5.92e-02 5.61e+00 pdb=" N PRO C 130 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 130 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 130 " -0.032 5.00e-02 4.00e+02 ... (remaining 4080 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 343 2.64 - 3.20: 20588 3.20 - 3.77: 33812 3.77 - 4.33: 43549 4.33 - 4.90: 72381 Nonbonded interactions: 170673 Sorted by model distance: nonbonded pdb=" OD1 ASP D 144 " pdb=" N GLU D 145 " model vdw 2.075 3.120 nonbonded pdb=" OG1 THR A 181 " pdb=" OD2 ASP B 202 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR B 99 " pdb=" OE2 GLU B 100 " model vdw 2.222 3.040 nonbonded pdb=" O TRP B 569 " pdb=" N GLY B 571 " model vdw 2.225 3.120 nonbonded pdb=" OG1 THR A 541 " pdb=" OD1 ASN A 543 " model vdw 2.237 3.040 ... (remaining 170668 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 'C' selection = chain 'E' } ncs_group { reference = (chain 'D' and (resid 17 through 172 or resid 178 through 231)) selection = (chain 'F' and (resid 17 through 209 or resid 215 through 231)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 9.780 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.800 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 22751 Z= 0.163 Angle : 0.689 23.300 30958 Z= 0.358 Chirality : 0.041 0.182 3497 Planarity : 0.005 0.073 4083 Dihedral : 16.357 89.714 8154 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.85 % Favored : 90.84 % Rotamer: Outliers : 2.78 % Allowed : 24.89 % Favored : 72.33 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.16), residues: 2949 helix: 1.06 (0.19), residues: 808 sheet: -0.74 (0.23), residues: 539 loop : -2.04 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 929 TYR 0.020 0.001 TYR C 152 PHE 0.017 0.001 PHE A1331 TRP 0.034 0.001 TRP B 569 HIS 0.004 0.001 HIS B 645 Details of bonding type rmsd covalent geometry : bond 0.00305 (22744) covalent geometry : angle 0.68890 (30944) SS BOND : bond 0.00281 ( 7) SS BOND : angle 0.59192 ( 14) hydrogen bonds : bond 0.18125 ( 774) hydrogen bonds : angle 6.58378 ( 2163) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 67 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.7273 (mpp) cc_final: 0.6625 (mmt) REVERT: B 240 MET cc_start: 0.8630 (mmt) cc_final: 0.7927 (mmt) REVERT: B 340 HIS cc_start: 0.7638 (OUTLIER) cc_final: 0.6819 (t-90) REVERT: D 20 MET cc_start: 0.8047 (ppp) cc_final: 0.7816 (tmm) REVERT: E 87 MET cc_start: 0.8315 (mmm) cc_final: 0.7783 (mmm) outliers start: 64 outliers final: 23 residues processed: 131 average time/residue: 0.1189 time to fit residues: 26.5082 Evaluate side-chains 79 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1314 TRP Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 52 PHE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 228 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.4980 chunk 111 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1064 HIS B 306 ASN B 340 HIS B 520 HIS B 597 HIS ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.040057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.025839 restraints weight = 227640.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.026509 restraints weight = 121347.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.026943 restraints weight = 83353.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.027177 restraints weight = 66746.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.027347 restraints weight = 58991.968| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 22751 Z= 0.206 Angle : 0.660 11.460 30958 Z= 0.332 Chirality : 0.042 0.192 3497 Planarity : 0.005 0.078 4083 Dihedral : 5.330 57.666 3289 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.55 % Favored : 91.18 % Rotamer: Outliers : 4.21 % Allowed : 21.59 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.16), residues: 2949 helix: 1.39 (0.18), residues: 867 sheet: -1.14 (0.22), residues: 612 loop : -1.97 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 929 TYR 0.012 0.001 TYR D 162 PHE 0.016 0.002 PHE A 868 TRP 0.024 0.001 TRP B 569 HIS 0.005 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00457 (22744) covalent geometry : angle 0.65977 (30944) SS BOND : bond 0.00264 ( 7) SS BOND : angle 0.82572 ( 14) hydrogen bonds : bond 0.04206 ( 774) hydrogen bonds : angle 4.81617 ( 2163) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 62 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 THR cc_start: 0.9582 (OUTLIER) cc_final: 0.9363 (p) REVERT: A 176 MET cc_start: 0.8945 (tpp) cc_final: 0.8655 (tpp) REVERT: A 635 MET cc_start: 0.7547 (mpp) cc_final: 0.6880 (mmt) REVERT: A 1051 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8899 (m) REVERT: B 340 HIS cc_start: 0.8470 (OUTLIER) cc_final: 0.7633 (t70) REVERT: C 40 ARG cc_start: 0.9396 (OUTLIER) cc_final: 0.8780 (ptm-80) REVERT: D 30 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8765 (p) REVERT: D 95 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8965 (pttm) REVERT: F 59 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8525 (tp40) REVERT: F 223 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8461 (pp) outliers start: 97 outliers final: 40 residues processed: 152 average time/residue: 0.1337 time to fit residues: 32.9689 Evaluate side-chains 104 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 56 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 784 PHE Chi-restraints excluded: chain A residue 813 PHE Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 966 ARG Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 52 PHE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 TRP Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 223 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 69 optimal weight: 8.9990 chunk 230 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 267 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 162 optimal weight: 0.4980 chunk 62 optimal weight: 10.0000 chunk 245 optimal weight: 0.9980 chunk 279 optimal weight: 0.7980 chunk 233 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN C 162 ASN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.040184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.025902 restraints weight = 226264.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.026605 restraints weight = 120324.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.027063 restraints weight = 82474.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.027305 restraints weight = 65856.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.027494 restraints weight = 57978.385| |-----------------------------------------------------------------------------| r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22751 Z= 0.137 Angle : 0.602 10.603 30958 Z= 0.299 Chirality : 0.041 0.246 3497 Planarity : 0.004 0.077 4083 Dihedral : 4.882 58.816 3270 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.93 % Favored : 91.79 % Rotamer: Outliers : 4.13 % Allowed : 21.20 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.16), residues: 2949 helix: 1.61 (0.18), residues: 875 sheet: -1.13 (0.22), residues: 603 loop : -1.92 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 818 TYR 0.016 0.001 TYR E 152 PHE 0.018 0.001 PHE A1473 TRP 0.021 0.001 TRP B 569 HIS 0.004 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00312 (22744) covalent geometry : angle 0.60145 (30944) SS BOND : bond 0.00276 ( 7) SS BOND : angle 0.73945 ( 14) hydrogen bonds : bond 0.03645 ( 774) hydrogen bonds : angle 4.47778 ( 2163) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 56 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 THR cc_start: 0.9571 (OUTLIER) cc_final: 0.9350 (p) REVERT: A 176 MET cc_start: 0.9024 (tpp) cc_final: 0.8752 (tpp) REVERT: A 240 MET cc_start: 0.8851 (mmt) cc_final: 0.7017 (tpp) REVERT: A 635 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7152 (mmt) REVERT: B 340 HIS cc_start: 0.8426 (OUTLIER) cc_final: 0.7630 (t70) REVERT: C 40 ARG cc_start: 0.9378 (OUTLIER) cc_final: 0.8786 (ptm-80) REVERT: C 41 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8000 (tp-100) REVERT: D 30 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8837 (p) REVERT: F 59 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8527 (tp-100) REVERT: F 223 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8498 (pp) outliers start: 95 outliers final: 56 residues processed: 143 average time/residue: 0.1351 time to fit residues: 31.7526 Evaluate side-chains 118 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 54 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 813 PHE Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1314 TRP Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 886 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 52 PHE Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 66 GLN Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 TRP Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 167 LYS Chi-restraints excluded: chain F residue 223 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 124 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 296 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 286 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 212 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 214 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN C 86 GLN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.039861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.025617 restraints weight = 228835.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.026304 restraints weight = 120994.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.026754 restraints weight = 82930.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.027022 restraints weight = 66190.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.027171 restraints weight = 57822.894| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22751 Z= 0.142 Angle : 0.595 9.200 30958 Z= 0.295 Chirality : 0.041 0.184 3497 Planarity : 0.004 0.076 4083 Dihedral : 4.735 59.349 3263 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.24 % Favored : 91.49 % Rotamer: Outliers : 4.52 % Allowed : 20.50 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.16), residues: 2949 helix: 1.82 (0.18), residues: 864 sheet: -1.09 (0.22), residues: 606 loop : -1.93 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.011 0.001 TYR D 162 PHE 0.020 0.001 PHE C 173 TRP 0.026 0.001 TRP A 792 HIS 0.004 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00321 (22744) covalent geometry : angle 0.59420 (30944) SS BOND : bond 0.00233 ( 7) SS BOND : angle 1.12233 ( 14) hydrogen bonds : bond 0.03420 ( 774) hydrogen bonds : angle 4.32501 ( 2163) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 58 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 THR cc_start: 0.9585 (OUTLIER) cc_final: 0.9328 (p) REVERT: A 176 MET cc_start: 0.8968 (tpp) cc_final: 0.8652 (tpp) REVERT: A 465 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.6872 (ttp-110) REVERT: A 635 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7243 (mmt) REVERT: A 1051 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8826 (m) REVERT: B 340 HIS cc_start: 0.8611 (OUTLIER) cc_final: 0.7856 (t70) REVERT: C 40 ARG cc_start: 0.9320 (OUTLIER) cc_final: 0.8778 (ptm-80) REVERT: C 41 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7917 (tp-100) REVERT: C 152 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7800 (p90) REVERT: D 30 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8760 (p) REVERT: E 3 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8630 (pt0) REVERT: E 36 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8543 (mmm) REVERT: F 59 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8370 (tp-100) REVERT: F 223 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8713 (pp) outliers start: 104 outliers final: 68 residues processed: 153 average time/residue: 0.1358 time to fit residues: 33.6332 Evaluate side-chains 135 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 54 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 813 PHE Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1314 TRP Chi-restraints excluded: chain A residue 1364 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 886 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 52 PHE Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 152 TYR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 66 GLN Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 TRP Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 167 LYS Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 223 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 128 optimal weight: 1.9990 chunk 272 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 190 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 241 optimal weight: 1.9990 chunk 290 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN C 86 GLN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.042515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.024196 restraints weight = 213457.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.024890 restraints weight = 125829.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.025353 restraints weight = 92720.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.025574 restraints weight = 77441.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 72)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.025788 restraints weight = 69987.758| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22751 Z= 0.129 Angle : 0.579 9.806 30958 Z= 0.287 Chirality : 0.041 0.158 3497 Planarity : 0.004 0.074 4083 Dihedral : 4.691 59.782 3263 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.00 % Favored : 91.76 % Rotamer: Outliers : 4.26 % Allowed : 20.63 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.16), residues: 2949 helix: 1.92 (0.18), residues: 865 sheet: -1.07 (0.22), residues: 606 loop : -1.93 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1173 TYR 0.009 0.001 TYR C 201 PHE 0.021 0.001 PHE A 876 TRP 0.020 0.001 TRP B 569 HIS 0.004 0.001 HIS B 834 Details of bonding type rmsd covalent geometry : bond 0.00295 (22744) covalent geometry : angle 0.57893 (30944) SS BOND : bond 0.00243 ( 7) SS BOND : angle 1.01398 ( 14) hydrogen bonds : bond 0.03265 ( 774) hydrogen bonds : angle 4.25415 ( 2163) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 56 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 THR cc_start: 0.9597 (OUTLIER) cc_final: 0.9354 (p) REVERT: A 176 MET cc_start: 0.8979 (tpp) cc_final: 0.8735 (tpp) REVERT: A 465 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7048 (ttp-110) REVERT: A 635 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7131 (mmt) REVERT: A 1051 VAL cc_start: 0.8837 (OUTLIER) cc_final: 0.8572 (m) REVERT: A 1095 GLU cc_start: 0.9431 (OUTLIER) cc_final: 0.9147 (pt0) REVERT: B 340 HIS cc_start: 0.8638 (OUTLIER) cc_final: 0.7899 (t70) REVERT: C 40 ARG cc_start: 0.9324 (OUTLIER) cc_final: 0.8744 (ptm-80) REVERT: C 41 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.7959 (tp-100) REVERT: C 152 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.7728 (p90) REVERT: D 30 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8736 (p) REVERT: D 95 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.8938 (pttm) REVERT: E 3 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8647 (pt0) REVERT: F 59 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8509 (tp40) REVERT: F 223 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8764 (pp) outliers start: 98 outliers final: 69 residues processed: 145 average time/residue: 0.1370 time to fit residues: 32.3669 Evaluate side-chains 138 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 55 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 813 PHE Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1314 TRP Chi-restraints excluded: chain A residue 1364 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 886 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 52 PHE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 152 TYR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 66 GLN Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 TRP Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 167 LYS Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 223 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 29 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 288 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 657 GLN B 306 ASN B 628 GLN B 888 HIS C 41 GLN C 86 GLN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.039130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.024989 restraints weight = 229172.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.025625 restraints weight = 121715.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.026069 restraints weight = 83916.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.026330 restraints weight = 67445.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.026453 restraints weight = 59258.688| |-----------------------------------------------------------------------------| r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 22751 Z= 0.193 Angle : 0.627 10.645 30958 Z= 0.313 Chirality : 0.041 0.186 3497 Planarity : 0.004 0.078 4083 Dihedral : 4.880 59.218 3261 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.95 % Favored : 90.81 % Rotamer: Outliers : 4.21 % Allowed : 20.46 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.16), residues: 2949 helix: 1.94 (0.18), residues: 860 sheet: -1.23 (0.21), residues: 629 loop : -1.91 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1173 TYR 0.017 0.001 TYR D 162 PHE 0.024 0.002 PHE C 173 TRP 0.020 0.001 TRP B 569 HIS 0.006 0.001 HIS B 834 Details of bonding type rmsd covalent geometry : bond 0.00437 (22744) covalent geometry : angle 0.62691 (30944) SS BOND : bond 0.00294 ( 7) SS BOND : angle 0.99304 ( 14) hydrogen bonds : bond 0.03857 ( 774) hydrogen bonds : angle 4.41531 ( 2163) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 54 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 THR cc_start: 0.9597 (OUTLIER) cc_final: 0.9378 (p) REVERT: A 176 MET cc_start: 0.8972 (tpp) cc_final: 0.8717 (tpp) REVERT: A 465 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7113 (ttp-110) REVERT: A 635 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7155 (mmt) REVERT: A 648 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.9041 (pp20) REVERT: A 1051 VAL cc_start: 0.9295 (OUTLIER) cc_final: 0.9094 (m) REVERT: A 1095 GLU cc_start: 0.9365 (OUTLIER) cc_final: 0.9161 (pt0) REVERT: B 340 HIS cc_start: 0.8622 (OUTLIER) cc_final: 0.7797 (t70) REVERT: C 40 ARG cc_start: 0.9376 (OUTLIER) cc_final: 0.8870 (ptm-80) REVERT: D 30 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8758 (p) REVERT: D 95 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.8902 (pttm) REVERT: D 130 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7283 (ttp80) REVERT: E 3 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8833 (pt0) REVERT: F 59 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8526 (tp40) REVERT: F 208 TYR cc_start: 0.6684 (OUTLIER) cc_final: 0.5259 (t80) REVERT: F 223 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8725 (pp) outliers start: 97 outliers final: 64 residues processed: 142 average time/residue: 0.1432 time to fit residues: 32.4421 Evaluate side-chains 132 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 53 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 813 PHE Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1314 TRP Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 52 PHE Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 66 GLN Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 TRP Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 208 TYR Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 223 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 295 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 139 optimal weight: 0.3980 chunk 277 optimal weight: 2.9990 chunk 66 optimal weight: 40.0000 chunk 70 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 234 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.038940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.024797 restraints weight = 230990.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.025471 restraints weight = 123071.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.025907 restraints weight = 84910.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.026141 restraints weight = 67936.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.026306 restraints weight = 59949.002| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 22751 Z= 0.211 Angle : 0.643 15.543 30958 Z= 0.320 Chirality : 0.042 0.193 3497 Planarity : 0.005 0.082 4083 Dihedral : 4.943 58.282 3261 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.51 % Favored : 91.25 % Rotamer: Outliers : 4.69 % Allowed : 20.24 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.16), residues: 2949 helix: 1.89 (0.18), residues: 861 sheet: -1.19 (0.21), residues: 627 loop : -1.94 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1263 TYR 0.016 0.001 TYR D 162 PHE 0.023 0.002 PHE C 173 TRP 0.023 0.001 TRP B 569 HIS 0.008 0.001 HIS B 834 Details of bonding type rmsd covalent geometry : bond 0.00476 (22744) covalent geometry : angle 0.64231 (30944) SS BOND : bond 0.00365 ( 7) SS BOND : angle 1.06214 ( 14) hydrogen bonds : bond 0.03878 ( 774) hydrogen bonds : angle 4.47349 ( 2163) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 52 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 THR cc_start: 0.9572 (OUTLIER) cc_final: 0.9368 (p) REVERT: A 176 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8697 (tpp) REVERT: A 465 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7140 (ttp-110) REVERT: A 635 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7005 (mmt) REVERT: A 1095 GLU cc_start: 0.9377 (OUTLIER) cc_final: 0.9162 (pt0) REVERT: B 340 HIS cc_start: 0.8640 (OUTLIER) cc_final: 0.7856 (t70) REVERT: C 40 ARG cc_start: 0.9405 (OUTLIER) cc_final: 0.8908 (ptm-80) REVERT: D 30 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8799 (p) REVERT: D 95 LYS cc_start: 0.9430 (OUTLIER) cc_final: 0.8986 (pttm) REVERT: D 182 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8264 (mp10) REVERT: E 3 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8724 (pt0) REVERT: F 59 GLN cc_start: 0.9231 (OUTLIER) cc_final: 0.8606 (tp40) REVERT: F 208 TYR cc_start: 0.6717 (OUTLIER) cc_final: 0.5213 (t80) REVERT: F 223 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8714 (pp) outliers start: 108 outliers final: 70 residues processed: 151 average time/residue: 0.1443 time to fit residues: 35.2219 Evaluate side-chains 136 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 52 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 813 PHE Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1314 TRP Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 886 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 66 GLN Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 182 GLN Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 208 TYR Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 223 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 39 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 167 optimal weight: 0.0050 chunk 153 optimal weight: 0.7980 chunk 230 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 19 optimal weight: 0.0670 chunk 137 optimal weight: 0.9990 chunk 231 optimal weight: 0.8980 overall best weight: 0.5332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN A 368 HIS B 122 GLN B 306 ASN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.039640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.025509 restraints weight = 226894.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.026203 restraints weight = 119532.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.026651 restraints weight = 81602.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.026935 restraints weight = 65099.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.027079 restraints weight = 56719.101| |-----------------------------------------------------------------------------| r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22751 Z= 0.104 Angle : 0.609 14.251 30958 Z= 0.298 Chirality : 0.041 0.159 3497 Planarity : 0.004 0.077 4083 Dihedral : 4.573 59.834 3259 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.97 % Favored : 91.83 % Rotamer: Outliers : 2.91 % Allowed : 21.72 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.16), residues: 2949 helix: 2.07 (0.18), residues: 859 sheet: -1.09 (0.22), residues: 606 loop : -1.89 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1263 TYR 0.009 0.001 TYR A1294 PHE 0.017 0.001 PHE C 173 TRP 0.024 0.001 TRP B 569 HIS 0.005 0.001 HIS B 834 Details of bonding type rmsd covalent geometry : bond 0.00239 (22744) covalent geometry : angle 0.60892 (30944) SS BOND : bond 0.00284 ( 7) SS BOND : angle 1.15868 ( 14) hydrogen bonds : bond 0.02936 ( 774) hydrogen bonds : angle 4.17023 ( 2163) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 56 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7263 (ttp-110) REVERT: A 635 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.6993 (mmt) REVERT: B 340 HIS cc_start: 0.8629 (OUTLIER) cc_final: 0.7893 (t70) REVERT: B 641 MET cc_start: 0.8910 (tmm) cc_final: 0.8417 (ppp) REVERT: C 40 ARG cc_start: 0.9316 (OUTLIER) cc_final: 0.8886 (ptm-80) REVERT: D 30 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8771 (p) REVERT: D 95 LYS cc_start: 0.9435 (ptmt) cc_final: 0.8998 (pttm) REVERT: D 130 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7489 (ttp80) REVERT: E 3 GLU cc_start: 0.9164 (pt0) cc_final: 0.8760 (pt0) REVERT: F 59 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8388 (tp-100) outliers start: 67 outliers final: 44 residues processed: 115 average time/residue: 0.1430 time to fit residues: 26.8707 Evaluate side-chains 105 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 54 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 813 PHE Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1314 TRP Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 886 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 217 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 84 optimal weight: 7.9990 chunk 178 optimal weight: 0.9990 chunk 199 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 259 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 231 optimal weight: 0.2980 chunk 13 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1259 HIS B 306 ASN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.039100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.025128 restraints weight = 229217.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.025711 restraints weight = 121348.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.026106 restraints weight = 82788.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.026372 restraints weight = 65918.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.026520 restraints weight = 57919.153| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22751 Z= 0.175 Angle : 0.631 14.268 30958 Z= 0.310 Chirality : 0.041 0.179 3497 Planarity : 0.004 0.078 4083 Dihedral : 4.656 59.559 3258 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.65 % Favored : 91.15 % Rotamer: Outliers : 2.65 % Allowed : 21.63 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.16), residues: 2949 helix: 2.05 (0.18), residues: 862 sheet: -1.08 (0.22), residues: 600 loop : -1.87 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1263 TYR 0.013 0.001 TYR D 162 PHE 0.019 0.001 PHE C 173 TRP 0.021 0.001 TRP B 569 HIS 0.006 0.001 HIS B 834 Details of bonding type rmsd covalent geometry : bond 0.00398 (22744) covalent geometry : angle 0.63042 (30944) SS BOND : bond 0.00288 ( 7) SS BOND : angle 1.25226 ( 14) hydrogen bonds : bond 0.03446 ( 774) hydrogen bonds : angle 4.30016 ( 2163) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 53 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7129 (ttp-110) REVERT: A 635 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7090 (mmt) REVERT: A 1034 MET cc_start: 0.9407 (pmm) cc_final: 0.9174 (pmm) REVERT: B 340 HIS cc_start: 0.8462 (OUTLIER) cc_final: 0.7714 (t70) REVERT: B 641 MET cc_start: 0.8953 (tmm) cc_final: 0.8464 (ppp) REVERT: C 40 ARG cc_start: 0.9386 (OUTLIER) cc_final: 0.8954 (ptm-80) REVERT: D 30 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8863 (p) REVERT: D 95 LYS cc_start: 0.9387 (ptmt) cc_final: 0.9075 (pttm) REVERT: D 130 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7424 (ttp80) REVERT: E 3 GLU cc_start: 0.9060 (pt0) cc_final: 0.8718 (pt0) REVERT: F 59 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8679 (tp-100) outliers start: 61 outliers final: 50 residues processed: 110 average time/residue: 0.1447 time to fit residues: 26.2682 Evaluate side-chains 110 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 53 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 813 PHE Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1314 TRP Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 886 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 66 GLN Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 217 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 117 optimal weight: 0.9990 chunk 239 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 23 optimal weight: 0.0060 chunk 135 optimal weight: 0.0870 chunk 296 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN D 146 GLN ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.039554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.025505 restraints weight = 227500.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.026159 restraints weight = 118199.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.026601 restraints weight = 81067.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.026865 restraints weight = 64524.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.026967 restraints weight = 56758.278| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22751 Z= 0.111 Angle : 0.606 13.812 30958 Z= 0.295 Chirality : 0.041 0.167 3497 Planarity : 0.004 0.075 4083 Dihedral : 4.473 59.375 3258 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.63 % Favored : 92.17 % Rotamer: Outliers : 2.65 % Allowed : 21.59 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.16), residues: 2949 helix: 2.05 (0.18), residues: 867 sheet: -1.04 (0.21), residues: 625 loop : -1.90 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1263 TYR 0.010 0.001 TYR A1294 PHE 0.017 0.001 PHE C 173 TRP 0.023 0.001 TRP B 569 HIS 0.005 0.001 HIS B 834 Details of bonding type rmsd covalent geometry : bond 0.00259 (22744) covalent geometry : angle 0.60570 (30944) SS BOND : bond 0.00268 ( 7) SS BOND : angle 1.04905 ( 14) hydrogen bonds : bond 0.02967 ( 774) hydrogen bonds : angle 4.14848 ( 2163) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 54 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7130 (mmt) REVERT: A 1034 MET cc_start: 0.9410 (pmm) cc_final: 0.9183 (pmm) REVERT: B 340 HIS cc_start: 0.8474 (OUTLIER) cc_final: 0.7758 (t70) REVERT: B 641 MET cc_start: 0.8936 (tmm) cc_final: 0.8411 (ppp) REVERT: C 40 ARG cc_start: 0.9351 (OUTLIER) cc_final: 0.8948 (ptm-80) REVERT: D 30 THR cc_start: 0.9095 (OUTLIER) cc_final: 0.8867 (p) REVERT: D 95 LYS cc_start: 0.9392 (ptmt) cc_final: 0.9084 (pttm) REVERT: E 3 GLU cc_start: 0.9063 (pt0) cc_final: 0.8482 (pt0) REVERT: F 59 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8507 (tp-100) outliers start: 61 outliers final: 52 residues processed: 110 average time/residue: 0.1223 time to fit residues: 22.5975 Evaluate side-chains 110 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 53 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 813 PHE Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1314 TRP Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 688 MET Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 886 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 66 GLN Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 217 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 38 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 chunk 257 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 259 optimal weight: 0.9980 chunk 119 optimal weight: 7.9990 chunk 269 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN D 146 GLN ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.038605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.024567 restraints weight = 229168.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.025106 restraints weight = 124927.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.025483 restraints weight = 87139.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.025732 restraints weight = 70201.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.025849 restraints weight = 62135.530| |-----------------------------------------------------------------------------| r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 22751 Z= 0.237 Angle : 0.681 14.041 30958 Z= 0.334 Chirality : 0.042 0.181 3497 Planarity : 0.005 0.080 4083 Dihedral : 4.768 59.842 3258 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.33 % Favored : 90.44 % Rotamer: Outliers : 3.04 % Allowed : 21.29 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.16), residues: 2949 helix: 2.01 (0.18), residues: 861 sheet: -1.01 (0.22), residues: 593 loop : -1.93 (0.16), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 607 TYR 0.018 0.001 TYR D 162 PHE 0.023 0.002 PHE C 173 TRP 0.022 0.001 TRP B 569 HIS 0.008 0.001 HIS B 834 Details of bonding type rmsd covalent geometry : bond 0.00533 (22744) covalent geometry : angle 0.68049 (30944) SS BOND : bond 0.00351 ( 7) SS BOND : angle 1.40127 ( 14) hydrogen bonds : bond 0.03896 ( 774) hydrogen bonds : angle 4.44204 ( 2163) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4242.93 seconds wall clock time: 73 minutes 40.65 seconds (4420.65 seconds total)