Starting phenix.real_space_refine on Thu Jun 19 11:13:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tjo_41306/06_2025/8tjo_41306_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tjo_41306/06_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_41306/06_2025/8tjo_41306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tjo_41306/06_2025/8tjo_41306.map" model { file = "/net/cci-nas-00/data/ceres_data/8tjo_41306/06_2025/8tjo_41306_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tjo_41306/06_2025/8tjo_41306_neut.cif" } resolution = 3.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.029 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'ARG: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: 14.09, per 1000 atoms: 0.63 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: 5.33 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.78 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: 9.38 Time building geometry restraints manager: 6.46 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: 34.270 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: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 52.840 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.130 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.780 ------------------------------------------------------------------------------- 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 : 11.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (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 TRP 0.034 0.001 TRP B 569 HIS 0.004 0.001 HIS B 645 PHE 0.017 0.001 PHE A1331 TYR 0.020 0.001 TYR C 152 ARG 0.013 0.000 ARG A 929 Details of bonding type rmsd hydrogen bonds : bond 0.18125 ( 774) hydrogen bonds : angle 6.58378 ( 2163) SS BOND : bond 0.00281 ( 7) SS BOND : angle 0.59192 ( 14) covalent geometry : bond 0.00305 (22744) covalent geometry : angle 0.68890 (30944) *********************** 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 : 2.421 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: 0.3086 time to fit residues: 67.7773 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 : 2.427 ------------------------------------------------------------------------------- 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 250 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 151 optimal weight: 0.0370 chunk 120 optimal weight: 0.9980 chunk 232 optimal weight: 9.9990 chunk 90 optimal weight: 0.5980 chunk 141 optimal weight: 0.7980 chunk 173 optimal weight: 4.9990 chunk 269 optimal weight: 6.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1064 HIS B 597 HIS B 628 GLN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** 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 = 0.3407 r_free = 0.3407 target = 0.041568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.027417 restraints weight = 225131.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.028150 restraints weight = 118651.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.028621 restraints weight = 80671.488| |-----------------------------------------------------------------------------| r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1145 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= 0.115 Angle : 0.612 11.826 30958 Z= 0.303 Chirality : 0.041 0.163 3497 Planarity : 0.004 0.070 4083 Dihedral : 5.031 58.604 3289 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.77 % Favored : 91.96 % Rotamer: Outliers : 3.43 % Allowed : 21.16 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.16), residues: 2949 helix: 1.56 (0.18), residues: 853 sheet: -0.70 (0.23), residues: 529 loop : -2.00 (0.15), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 569 HIS 0.003 0.001 HIS A1259 PHE 0.014 0.001 PHE A 868 TYR 0.008 0.001 TYR A 930 ARG 0.005 0.000 ARG A 929 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 774) hydrogen bonds : angle 4.62862 ( 2163) SS BOND : bond 0.00222 ( 7) SS BOND : angle 0.54057 ( 14) covalent geometry : bond 0.00258 (22744) covalent geometry : angle 0.61206 (30944) *********************** 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 144 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 65 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.8858 (tpp) cc_final: 0.8556 (tpp) REVERT: A 635 MET cc_start: 0.7547 (mpp) cc_final: 0.6893 (mmt) REVERT: A 1051 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8498 (m) REVERT: D 30 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8697 (p) REVERT: D 130 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.6953 (ttp80) REVERT: E 3 GLU cc_start: 0.9063 (pt0) cc_final: 0.8732 (pt0) REVERT: F 59 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8454 (tp40) REVERT: F 110 MET cc_start: 0.7678 (mmm) cc_final: 0.7469 (tmm) outliers start: 79 outliers final: 36 residues processed: 137 average time/residue: 0.3112 time to fit residues: 71.0060 Evaluate side-chains 97 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 57 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL 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 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 A residue 1272 LEU Chi-restraints excluded: chain B residue 80 PHE 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 630 VAL Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain C residue 7 VAL 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 148 LEU 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 E residue 30 THR Chi-restraints excluded: chain E residue 36 MET 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 115 THR Chi-restraints excluded: chain F residue 159 ASN 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 85 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 77 optimal weight: 0.0030 chunk 142 optimal weight: 0.8980 chunk 278 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 259 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 296 optimal weight: 7.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 ASN B 597 HIS C 41 GLN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.040096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.025844 restraints weight = 225187.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.026538 restraints weight = 119309.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.026981 restraints weight = 81853.763| |-----------------------------------------------------------------------------| r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22751 Z= 0.165 Angle : 0.612 9.026 30958 Z= 0.306 Chirality : 0.041 0.197 3497 Planarity : 0.004 0.075 4083 Dihedral : 4.776 58.825 3264 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.14 % Favored : 91.59 % Rotamer: Outliers : 3.87 % Allowed : 20.72 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.16), residues: 2949 helix: 1.66 (0.18), residues: 871 sheet: -1.04 (0.22), residues: 598 loop : -1.95 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 569 HIS 0.004 0.001 HIS B 834 PHE 0.017 0.001 PHE C 173 TYR 0.015 0.001 TYR E 152 ARG 0.004 0.000 ARG B 818 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 774) hydrogen bonds : angle 4.44411 ( 2163) SS BOND : bond 0.00266 ( 7) SS BOND : angle 0.86821 ( 14) covalent geometry : bond 0.00375 (22744) covalent geometry : angle 0.61200 (30944) *********************** 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 147 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 58 time to evaluate : 3.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.8954 (tpp) cc_final: 0.8724 (tpp) REVERT: A 240 MET cc_start: 0.8856 (mmt) cc_final: 0.7105 (tpp) REVERT: A 635 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7135 (mmt) REVERT: A 1051 VAL cc_start: 0.9182 (OUTLIER) cc_final: 0.8920 (m) REVERT: B 889 LEU cc_start: 0.9533 (tp) cc_final: 0.9320 (mt) REVERT: C 36 MET cc_start: 0.9043 (mmm) cc_final: 0.8714 (mmm) REVERT: C 40 ARG cc_start: 0.9377 (OUTLIER) cc_final: 0.8771 (ptm-80) REVERT: C 152 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.7896 (p90) REVERT: D 30 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8814 (p) REVERT: D 95 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.8860 (pttm) REVERT: D 130 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7056 (ttp80) REVERT: D 146 GLN cc_start: 0.5687 (OUTLIER) cc_final: 0.5067 (mp10) REVERT: E 3 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8608 (pt0) REVERT: F 59 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.8548 (tp-100) REVERT: F 223 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8506 (pp) outliers start: 89 outliers final: 43 residues processed: 139 average time/residue: 0.3880 time to fit residues: 90.2648 Evaluate side-chains 111 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 57 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 268 MET 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 1041 CYS Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1314 TRP 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 171 VAL Chi-restraints excluded: chain B residue 461 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 30 THR 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 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 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 146 GLN 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 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 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 115 THR Chi-restraints excluded: chain F residue 159 ASN 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 149 optimal weight: 0.8980 chunk 134 optimal weight: 7.9990 chunk 202 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 226 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 220 optimal weight: 3.9990 chunk 155 optimal weight: 0.0070 chunk 222 optimal weight: 0.7980 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 GLN C 162 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.040040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.025766 restraints weight = 228064.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.026445 restraints weight = 120516.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.026883 restraints weight = 82603.923| |-----------------------------------------------------------------------------| r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22751 Z= 0.139 Angle : 0.585 9.691 30958 Z= 0.290 Chirality : 0.041 0.284 3497 Planarity : 0.004 0.076 4083 Dihedral : 4.625 58.203 3262 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.87 % Favored : 91.86 % Rotamer: Outliers : 3.78 % Allowed : 20.76 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.16), residues: 2949 helix: 1.92 (0.18), residues: 860 sheet: -1.02 (0.22), residues: 602 loop : -1.90 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 792 HIS 0.004 0.001 HIS C 171 PHE 0.021 0.001 PHE C 173 TYR 0.011 0.001 TYR D 162 ARG 0.003 0.000 ARG B 818 Details of bonding type rmsd hydrogen bonds : bond 0.03307 ( 774) hydrogen bonds : angle 4.24263 ( 2163) SS BOND : bond 0.00267 ( 7) SS BOND : angle 0.71322 ( 14) covalent geometry : bond 0.00318 (22744) covalent geometry : angle 0.58452 (30944) *********************** 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 145 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 58 time to evaluate : 3.359 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: A 176 MET cc_start: 0.8966 (tpp) cc_final: 0.8625 (tpp) REVERT: A 635 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7147 (mmt) REVERT: A 1051 VAL cc_start: 0.9113 (OUTLIER) cc_final: 0.8867 (m) REVERT: B 889 LEU cc_start: 0.9611 (tp) cc_final: 0.9356 (mt) REVERT: C 36 MET cc_start: 0.9204 (mmm) cc_final: 0.8828 (mmm) REVERT: C 40 ARG cc_start: 0.9325 (OUTLIER) cc_final: 0.8690 (ptm-80) REVERT: C 152 TYR cc_start: 0.8570 (OUTLIER) cc_final: 0.7880 (p90) REVERT: D 30 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8779 (p) REVERT: D 130 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7162 (ttp80) REVERT: E 3 GLU cc_start: 0.9060 (pt0) cc_final: 0.8671 (pt0) REVERT: F 59 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8387 (tp-100) REVERT: F 223 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8645 (pp) outliers start: 87 outliers final: 51 residues processed: 137 average time/residue: 0.4338 time to fit residues: 99.4901 Evaluate side-chains 113 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 54 time to evaluate : 3.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE 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 1051 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1272 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 123 GLN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 171 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 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 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 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 200 THR 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 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 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 223 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 222 optimal weight: 1.9990 chunk 276 optimal weight: 4.9990 chunk 234 optimal weight: 10.0000 chunk 25 optimal weight: 0.0040 chunk 285 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 216 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 GLN ** D 22 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.039797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.025549 restraints weight = 228522.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.026231 restraints weight = 120747.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.026671 restraints weight = 83107.157| |-----------------------------------------------------------------------------| r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22751 Z= 0.143 Angle : 0.580 8.561 30958 Z= 0.289 Chirality : 0.041 0.181 3497 Planarity : 0.004 0.075 4083 Dihedral : 4.615 58.851 3260 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.27 % Favored : 91.45 % Rotamer: Outliers : 3.74 % Allowed : 20.37 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.16), residues: 2949 helix: 1.97 (0.18), residues: 866 sheet: -0.97 (0.22), residues: 604 loop : -1.91 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 569 HIS 0.005 0.001 HIS B 834 PHE 0.022 0.001 PHE A 876 TYR 0.010 0.001 TYR D 162 ARG 0.005 0.000 ARG A1173 Details of bonding type rmsd hydrogen bonds : bond 0.03337 ( 774) hydrogen bonds : angle 4.22581 ( 2163) SS BOND : bond 0.00226 ( 7) SS BOND : angle 1.42495 ( 14) covalent geometry : bond 0.00329 (22744) covalent geometry : angle 0.57921 (30944) *********************** 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 144 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 58 time to evaluate : 2.356 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: A 176 MET cc_start: 0.8944 (tpp) cc_final: 0.8641 (tpp) REVERT: A 465 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7076 (ttp-110) REVERT: A 635 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7112 (mmt) REVERT: A 1051 VAL cc_start: 0.9202 (OUTLIER) cc_final: 0.8984 (m) REVERT: B 176 MET cc_start: 0.9236 (tpp) cc_final: 0.9014 (tpp) REVERT: B 889 LEU cc_start: 0.9571 (tp) cc_final: 0.9325 (mt) REVERT: C 36 MET cc_start: 0.9202 (mmm) cc_final: 0.8772 (mmm) REVERT: C 40 ARG cc_start: 0.9309 (OUTLIER) cc_final: 0.8713 (ptm-80) REVERT: D 30 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8778 (p) REVERT: D 130 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7202 (ttp80) REVERT: E 3 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8676 (pt0) REVERT: E 87 MET cc_start: 0.8928 (mmm) cc_final: 0.8446 (mmp) REVERT: F 59 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8520 (tp40) REVERT: F 223 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8704 (pp) outliers start: 86 outliers final: 63 residues processed: 136 average time/residue: 0.3367 time to fit residues: 74.6899 Evaluate side-chains 127 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 55 time to evaluate : 2.453 ------------------------------------------------------------------------------- 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 111 MET 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 472 VAL Chi-restraints excluded: chain A residue 476 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 920 THR Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1047 THR 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 1272 LEU Chi-restraints excluded: chain A residue 1314 TRP 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 123 GLN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 461 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 20 LEU 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 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 119 THR 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 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 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 223 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 256 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 231 optimal weight: 3.9990 chunk 105 optimal weight: 0.4980 chunk 59 optimal weight: 8.9990 chunk 189 optimal weight: 1.9990 chunk 263 optimal weight: 0.9990 chunk 276 optimal weight: 8.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 657 GLN C 86 GLN ** D 22 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.039575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.025363 restraints weight = 227199.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.026041 restraints weight = 120662.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.026485 restraints weight = 83166.311| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22751 Z= 0.151 Angle : 0.594 10.617 30958 Z= 0.294 Chirality : 0.041 0.164 3497 Planarity : 0.004 0.075 4083 Dihedral : 4.679 59.073 3259 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.00 % Favored : 91.76 % Rotamer: Outliers : 3.74 % Allowed : 21.03 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2949 helix: 1.99 (0.18), residues: 867 sheet: -1.10 (0.21), residues: 635 loop : -1.89 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 569 HIS 0.005 0.001 HIS B 834 PHE 0.021 0.001 PHE C 173 TYR 0.012 0.001 TYR D 162 ARG 0.005 0.000 ARG A1456 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 774) hydrogen bonds : angle 4.21314 ( 2163) SS BOND : bond 0.00343 ( 7) SS BOND : angle 1.36090 ( 14) covalent geometry : bond 0.00346 (22744) covalent geometry : angle 0.59343 (30944) *********************** 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 142 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 56 time to evaluate : 2.413 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 176 MET cc_start: 0.8929 (tpp) cc_final: 0.8659 (tpp) REVERT: A 465 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7163 (ttp-110) REVERT: A 635 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7115 (mmt) REVERT: A 1051 VAL cc_start: 0.9243 (OUTLIER) cc_final: 0.9028 (m) REVERT: B 889 LEU cc_start: 0.9552 (tp) cc_final: 0.9294 (mt) REVERT: C 36 MET cc_start: 0.9173 (mmm) cc_final: 0.8727 (mmm) REVERT: C 40 ARG cc_start: 0.9348 (OUTLIER) cc_final: 0.8725 (ptm-80) REVERT: C 152 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.7898 (p90) REVERT: D 30 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8778 (p) REVERT: D 95 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.8910 (pttm) REVERT: D 130 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7338 (ttp80) REVERT: D 146 GLN cc_start: 0.5536 (OUTLIER) cc_final: 0.4977 (mp10) REVERT: E 3 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8698 (pt0) REVERT: E 87 MET cc_start: 0.8953 (mmm) cc_final: 0.8528 (mmp) REVERT: F 59 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8522 (tp-100) REVERT: F 223 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8727 (pp) outliers start: 86 outliers final: 64 residues processed: 133 average time/residue: 0.3410 time to fit residues: 73.6246 Evaluate side-chains 131 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 55 time to evaluate : 2.691 ------------------------------------------------------------------------------- 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 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 920 THR Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1051 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 63 ASP Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR 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 134 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 461 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 52 PHE Chi-restraints excluded: chain C residue 91 LYS 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 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 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 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 223 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 95 optimal weight: 0.0060 chunk 100 optimal weight: 7.9990 chunk 282 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 286 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.039371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.025189 restraints weight = 229694.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.025867 restraints weight = 122010.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.026294 restraints weight = 83812.073| |-----------------------------------------------------------------------------| r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22751 Z= 0.157 Angle : 0.597 12.916 30958 Z= 0.295 Chirality : 0.041 0.206 3497 Planarity : 0.004 0.077 4083 Dihedral : 4.667 58.641 3259 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.48 % Favored : 91.29 % Rotamer: Outliers : 3.87 % Allowed : 20.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.16), residues: 2949 helix: 2.01 (0.18), residues: 867 sheet: -1.11 (0.21), residues: 637 loop : -1.88 (0.16), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 569 HIS 0.006 0.001 HIS B 834 PHE 0.021 0.001 PHE C 173 TYR 0.012 0.001 TYR D 162 ARG 0.003 0.000 ARG B 818 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 774) hydrogen bonds : angle 4.23898 ( 2163) SS BOND : bond 0.00289 ( 7) SS BOND : angle 1.00962 ( 14) covalent geometry : bond 0.00358 (22744) covalent geometry : angle 0.59672 (30944) *********************** 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 144 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 55 time to evaluate : 2.385 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 176 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8698 (tpp) REVERT: A 465 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7174 (ttp-110) REVERT: A 635 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7146 (mmt) REVERT: B 340 HIS cc_start: 0.8529 (OUTLIER) cc_final: 0.7688 (t-90) REVERT: B 889 LEU cc_start: 0.9576 (tp) cc_final: 0.9309 (mt) REVERT: C 36 MET cc_start: 0.9149 (mmm) cc_final: 0.8656 (mmm) REVERT: C 40 ARG cc_start: 0.9342 (OUTLIER) cc_final: 0.8850 (ptm-80) REVERT: C 87 MET cc_start: 0.9031 (pmm) cc_final: 0.8561 (pmm) REVERT: D 30 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8755 (p) REVERT: D 95 LYS cc_start: 0.9442 (OUTLIER) cc_final: 0.8959 (pttm) REVERT: D 130 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7352 (ttp80) REVERT: E 3 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8759 (pt0) REVERT: E 87 MET cc_start: 0.8962 (mmm) cc_final: 0.8579 (mmp) REVERT: F 59 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8518 (tp-100) REVERT: F 208 TYR cc_start: 0.6647 (OUTLIER) cc_final: 0.5199 (t80) REVERT: F 223 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8710 (pp) outliers start: 89 outliers final: 64 residues processed: 134 average time/residue: 0.3386 time to fit residues: 73.5274 Evaluate side-chains 131 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 55 time to evaluate : 2.690 ------------------------------------------------------------------------------- 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 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 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 920 THR Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1041 CYS 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 63 ASP Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR 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 134 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 461 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 52 PHE Chi-restraints excluded: chain C residue 91 LYS 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 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 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 158 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 218 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 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 208 TYR 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 21 optimal weight: 2.9990 chunk 294 optimal weight: 5.9990 chunk 91 optimal weight: 0.1980 chunk 249 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 888 HIS C 5 GLN ** D 22 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.039102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.024923 restraints weight = 230374.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.025582 restraints weight = 122012.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.026022 restraints weight = 84142.848| |-----------------------------------------------------------------------------| r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 22751 Z= 0.177 Angle : 0.614 10.345 30958 Z= 0.305 Chirality : 0.041 0.189 3497 Planarity : 0.004 0.081 4083 Dihedral : 4.700 58.761 3259 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.68 % Favored : 91.12 % Rotamer: Outliers : 3.87 % Allowed : 20.59 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2949 helix: 1.96 (0.18), residues: 871 sheet: -1.11 (0.21), residues: 618 loop : -1.88 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 569 HIS 0.007 0.001 HIS B 834 PHE 0.022 0.001 PHE C 173 TYR 0.014 0.001 TYR D 162 ARG 0.007 0.000 ARG A1263 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 774) hydrogen bonds : angle 4.32408 ( 2163) SS BOND : bond 0.00313 ( 7) SS BOND : angle 1.11941 ( 14) covalent geometry : bond 0.00404 (22744) covalent geometry : angle 0.61361 (30944) *********************** 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 143 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 54 time to evaluate : 2.411 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 176 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8703 (tpp) REVERT: A 465 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7263 (ttp-110) REVERT: A 635 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.6986 (mmt) REVERT: A 1051 VAL cc_start: 0.9224 (OUTLIER) cc_final: 0.9016 (m) REVERT: B 340 HIS cc_start: 0.8591 (OUTLIER) cc_final: 0.7786 (t-90) REVERT: B 641 MET cc_start: 0.8975 (tmm) cc_final: 0.8549 (ppp) REVERT: C 36 MET cc_start: 0.9180 (mmm) cc_final: 0.8680 (mmm) REVERT: C 40 ARG cc_start: 0.9325 (OUTLIER) cc_final: 0.8832 (ptm-80) REVERT: C 87 MET cc_start: 0.9026 (pmm) cc_final: 0.8572 (pmm) REVERT: D 30 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8752 (p) REVERT: D 95 LYS cc_start: 0.9453 (OUTLIER) cc_final: 0.8969 (pttm) REVERT: D 130 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7400 (ttp80) REVERT: D 146 GLN cc_start: 0.5709 (OUTLIER) cc_final: 0.4963 (mp10) REVERT: E 3 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8896 (pt0) REVERT: E 87 MET cc_start: 0.9024 (mmm) cc_final: 0.8675 (mmp) REVERT: F 59 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8486 (tp40) REVERT: F 208 TYR cc_start: 0.6721 (OUTLIER) cc_final: 0.5212 (t80) REVERT: F 221 GLN cc_start: 0.9590 (OUTLIER) cc_final: 0.9364 (pm20) REVERT: F 223 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8742 (pp) outliers start: 89 outliers final: 62 residues processed: 133 average time/residue: 0.3378 time to fit residues: 73.0644 Evaluate side-chains 130 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 53 time to evaluate : 2.395 ------------------------------------------------------------------------------- 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 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 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 920 THR Chi-restraints excluded: chain A residue 967 GLU 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 1272 LEU Chi-restraints excluded: chain A residue 1314 TRP Chi-restraints excluded: chain B residue 35 VAL 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 111 MET Chi-restraints excluded: chain B residue 119 VAL 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 461 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 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 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 185 VAL Chi-restraints excluded: chain D residue 200 THR 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 158 THR Chi-restraints excluded: chain E residue 218 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 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 208 TYR Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 221 GLN Chi-restraints excluded: chain F residue 223 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 285 optimal weight: 0.2980 chunk 8 optimal weight: 7.9990 chunk 260 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 233 optimal weight: 8.9990 chunk 291 optimal weight: 3.9990 chunk 239 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 193 optimal weight: 0.9980 chunk 253 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN B 122 GLN ** D 22 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.039618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.025470 restraints weight = 227553.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.026162 restraints weight = 120361.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.026605 restraints weight = 82414.474| |-----------------------------------------------------------------------------| r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22751 Z= 0.112 Angle : 0.600 16.310 30958 Z= 0.293 Chirality : 0.041 0.180 3497 Planarity : 0.004 0.076 4083 Dihedral : 4.412 59.023 3257 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.07 % Favored : 91.73 % Rotamer: Outliers : 2.61 % Allowed : 21.76 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.16), residues: 2949 helix: 2.01 (0.18), residues: 873 sheet: -0.95 (0.22), residues: 621 loop : -1.87 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 569 HIS 0.005 0.001 HIS B 834 PHE 0.017 0.001 PHE C 173 TYR 0.010 0.001 TYR A1294 ARG 0.005 0.000 ARG A1263 Details of bonding type rmsd hydrogen bonds : bond 0.02930 ( 774) hydrogen bonds : angle 4.09702 ( 2163) SS BOND : bond 0.00286 ( 7) SS BOND : angle 1.11710 ( 14) covalent geometry : bond 0.00260 (22744) covalent geometry : angle 0.59979 (30944) *********************** 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 116 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 56 time to evaluate : 2.358 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: A 176 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8772 (tpp) REVERT: A 465 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7286 (ttp-110) REVERT: A 635 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7047 (mmt) REVERT: A 1051 VAL cc_start: 0.9172 (OUTLIER) cc_final: 0.8950 (m) REVERT: B 340 HIS cc_start: 0.8520 (OUTLIER) cc_final: 0.7668 (t-90) REVERT: B 641 MET cc_start: 0.8917 (tmm) cc_final: 0.8431 (ppp) REVERT: C 36 MET cc_start: 0.9158 (mmm) cc_final: 0.8746 (mmm) REVERT: C 40 ARG cc_start: 0.9300 (OUTLIER) cc_final: 0.8847 (ptm-80) REVERT: C 87 MET cc_start: 0.9000 (pmm) cc_final: 0.8498 (pmm) REVERT: D 30 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8808 (p) REVERT: D 95 LYS cc_start: 0.9440 (ptmt) cc_final: 0.9007 (pttm) REVERT: D 130 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.7565 (ttp80) REVERT: E 3 GLU cc_start: 0.9122 (pt0) cc_final: 0.8626 (pt0) REVERT: F 59 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8350 (tp-100) REVERT: F 221 GLN cc_start: 0.9599 (OUTLIER) cc_final: 0.9251 (pm20) REVERT: F 223 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8661 (pp) outliers start: 60 outliers final: 44 residues processed: 108 average time/residue: 0.3296 time to fit residues: 58.5385 Evaluate side-chains 108 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 53 time to evaluate : 2.361 ------------------------------------------------------------------------------- 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 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 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 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 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 171 VAL Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 688 MET 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 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 227 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 53 ILE 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 23 SER 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 217 GLU Chi-restraints excluded: chain F residue 221 GLN Chi-restraints excluded: chain F residue 223 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.2148 > 50: distance: 14 - 59: 20.088 distance: 44 - 49: 3.987 distance: 49 - 50: 14.280 distance: 50 - 51: 6.160 distance: 50 - 53: 5.964 distance: 51 - 52: 4.668 distance: 51 - 56: 6.856 distance: 53 - 54: 10.709 distance: 53 - 55: 6.178 distance: 56 - 57: 3.244 distance: 57 - 58: 18.889 distance: 57 - 60: 15.228 distance: 58 - 59: 31.653 distance: 58 - 64: 8.465 distance: 60 - 61: 13.607 distance: 61 - 62: 11.380 distance: 61 - 63: 7.801 distance: 64 - 65: 4.131 distance: 65 - 66: 12.506 distance: 65 - 68: 4.435 distance: 66 - 67: 30.086 distance: 66 - 72: 7.078 distance: 68 - 69: 13.664 distance: 68 - 70: 17.507 distance: 69 - 71: 12.010 distance: 72 - 73: 8.600 distance: 73 - 74: 9.243 distance: 73 - 76: 20.046 distance: 74 - 75: 13.311 distance: 74 - 81: 20.839 distance: 76 - 77: 28.849 distance: 77 - 78: 18.165 distance: 78 - 79: 21.431 distance: 79 - 80: 20.053 distance: 81 - 82: 7.612 distance: 82 - 83: 11.883 distance: 82 - 85: 5.470 distance: 83 - 84: 15.562 distance: 83 - 92: 13.055 distance: 85 - 86: 20.931 distance: 87 - 88: 3.946 distance: 89 - 90: 6.293 distance: 89 - 91: 3.057 distance: 92 - 93: 3.870 distance: 93 - 94: 17.724 distance: 93 - 96: 25.441 distance: 94 - 95: 18.313 distance: 94 - 99: 23.027 distance: 96 - 97: 14.020 distance: 96 - 98: 16.288 distance: 99 - 100: 18.509 distance: 100 - 101: 7.879 distance: 100 - 103: 14.887 distance: 101 - 102: 30.628 distance: 101 - 106: 22.191 distance: 103 - 104: 18.709 distance: 103 - 105: 26.185 distance: 106 - 107: 16.905 distance: 107 - 108: 17.536 distance: 107 - 110: 14.722 distance: 108 - 109: 26.732 distance: 108 - 111: 9.625 distance: 111 - 112: 5.326 distance: 112 - 113: 14.722 distance: 112 - 115: 4.433 distance: 113 - 114: 24.441 distance: 113 - 116: 8.253 distance: 116 - 117: 8.161 distance: 116 - 122: 24.495 distance: 117 - 118: 9.328 distance: 117 - 120: 13.221 distance: 118 - 119: 15.616 distance: 118 - 123: 6.777 distance: 120 - 121: 21.766 distance: 121 - 122: 9.807