Starting phenix.real_space_refine on Sat Jul 4 22:22:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m7f_23711/07_2026/7m7f_23711.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m7f_23711/07_2026/7m7f_23711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m7f_23711/07_2026/7m7f_23711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m7f_23711/07_2026/7m7f_23711.map" model { file = "/net/cci-nas-00/data/ceres_data/7m7f_23711/07_2026/7m7f_23711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m7f_23711/07_2026/7m7f_23711.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.005 sd= 0.138 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 87 5.16 5 C 14960 2.51 5 N 4302 2.21 5 O 4621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23971 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 7417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7417 Classifications: {'peptide': 999} Link IDs: {'PTRANS': 57, 'TRANS': 941} Chain breaks: 1 Chain: "A" Number of atoms: 10319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 10319 Classifications: {'peptide': 1390} Link IDs: {'PTRANS': 74, 'TRANS': 1315} 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: {'PCIS': 2, 'PTRANS': 12, '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: {'PCIS': 1, 'PTRANS': 10, '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 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PN7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Time building chain proxies: 4.60, per 1000 atoms: 0.19 Number of scatterers: 23971 At special positions: 0 Unit cell: (136, 159, 149, 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 87 16.00 P 1 15.00 O 4621 8.00 N 4302 7.00 C 14960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 100 " distance=2.00 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 203 " distance=2.04 Simple disulfide: pdb=" SG CYS D 39 " - pdb=" SG CYS D 109 " distance=2.03 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=2.06 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 1.1 seconds 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5806 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 36 sheets defined 29.9% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 50 through 59 removed outlier: 3.858A pdb=" N TRP B 55 " --> pdb=" O PRO B 51 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 119 Processing helix chain 'B' and resid 120 through 136 removed outlier: 3.705A pdb=" N GLU B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 174 through 179 Processing helix chain 'B' and resid 182 through 192 removed outlier: 3.764A pdb=" N GLY B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 5.498A 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 221 Processing helix chain 'B' and resid 238 through 244 Processing helix chain 'B' and resid 280 through 286 Processing helix chain 'B' and resid 312 through 328 removed outlier: 3.586A pdb=" N GLN B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.579A pdb=" N ILE B 334 " --> pdb=" O PRO B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 359 removed outlier: 3.577A pdb=" N ILE B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 363 removed outlier: 4.032A pdb=" N ARG B 363 " --> pdb=" O GLY B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 371 through 377 removed outlier: 4.407A pdb=" N ASN B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 383 Processing helix chain 'B' and resid 384 through 398 removed outlier: 3.612A pdb=" N ILE B 389 " --> pdb=" O VAL B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 486 Processing helix chain 'B' and resid 489 through 499 Processing helix chain 'B' and resid 503 through 513 removed outlier: 3.596A pdb=" N LEU B 511 " --> pdb=" O ILE B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 580 Processing helix chain 'B' and resid 582 through 595 removed outlier: 3.562A pdb=" N LEU B 587 " --> pdb=" O PHE B 583 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 608 removed outlier: 3.899A pdb=" N PHE B 605 " --> pdb=" O GLU B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 645 Proline residue: B 629 - end of helix Processing helix chain 'B' and resid 657 through 666 removed outlier: 3.858A pdb=" N ALA B 661 " --> pdb=" O GLN B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 686 Processing helix chain 'B' and resid 700 through 708 removed outlier: 5.360A pdb=" N ALA B 706 " --> pdb=" O GLY B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 740 removed outlier: 4.194A pdb=" N VAL B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing helix chain 'B' and resid 759 through 762 Processing helix chain 'B' and resid 763 through 770 Processing helix chain 'B' and resid 799 through 807 Processing helix chain 'B' and resid 812 through 824 Processing helix chain 'B' and resid 837 through 847 removed outlier: 3.878A pdb=" N ILE B 841 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU B 842 " --> pdb=" O THR B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 878 Processing helix chain 'B' and resid 883 through 888 removed outlier: 4.019A pdb=" N VAL B 887 " --> pdb=" O ASP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 1409 through 1428 removed outlier: 3.843A pdb=" N GLU B1413 " --> pdb=" O ALA B1409 " (cutoff:3.500A) Processing helix chain 'B' and resid 1448 through 1463 Processing helix chain 'B' and resid 1470 through 1475 Processing helix chain 'B' and resid 1477 through 1488 Processing helix chain 'A' and resid 8 through 21 removed outlier: 3.654A pdb=" N ARG A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 114 through 119 removed outlier: 3.996A pdb=" N ALA A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.648A pdb=" N LEU A 175 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 176' Processing helix chain 'A' and resid 181 through 192 removed outlier: 4.190A pdb=" N SER A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 188 " --> pdb=" O ALA A 184 " (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 220 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 347 through 354 Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 481 through 489 removed outlier: 3.742A pdb=" N ARG A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 498 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 528 through 541 removed outlier: 3.624A pdb=" N ARG A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 removed outlier: 3.789A pdb=" N SER A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 595 removed outlier: 3.678A pdb=" N ALA A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N CYS A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) 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 602 through 608 Processing helix chain 'A' and resid 609 through 614 removed outlier: 3.607A pdb=" N GLU A 614 " --> pdb=" O ALA A 610 " (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 667 removed outlier: 3.638A pdb=" N ALA A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 686 Processing helix chain 'A' and resid 700 through 708 removed outlier: 3.863A pdb=" N VAL A 704 " --> pdb=" O PRO A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 809 removed outlier: 3.511A pdb=" N ARG A 809 " --> pdb=" O ARG A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 823 removed outlier: 3.533A pdb=" N ALA A 816 " --> pdb=" O ARG A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 845 removed outlier: 3.703A pdb=" N ALA A 840 " --> pdb=" O ILE A 836 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 843 " --> pdb=" O ALA A 839 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 845 " --> pdb=" O ILE A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 879 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.804A pdb=" N VAL A 887 " --> pdb=" O ASP A 883 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS A 888 " --> pdb=" O TRP A 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 883 through 888' Processing helix chain 'A' and resid 921 through 927 removed outlier: 3.676A pdb=" N VAL A 925 " --> pdb=" O GLU A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 967 removed outlier: 3.676A pdb=" N THR A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 998 Processing helix chain 'A' and resid 1021 through 1038 removed outlier: 3.535A pdb=" N ALA A1025 " --> pdb=" O LEU A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1078 removed outlier: 3.806A pdb=" N GLY A1065 " --> pdb=" O ASN A1061 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A1066 " --> pdb=" O ALA A1062 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A1067 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP A1068 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A1075 " --> pdb=" O GLY A1071 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU A1076 " --> pdb=" O ARG A1072 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A1077 " --> pdb=" O VAL A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1105 removed outlier: 3.594A pdb=" N ALA A1097 " --> pdb=" O VAL A1093 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ALA A1101 " --> pdb=" O ALA A1097 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ALA A1102 " --> pdb=" O ARG A1098 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A1105 " --> pdb=" O ALA A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1164 removed outlier: 4.199A pdb=" N ILE A1156 " --> pdb=" O VAL A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1178 Processing helix chain 'A' and resid 1180 through 1192 Processing helix chain 'A' and resid 1204 through 1214 Processing helix chain 'A' and resid 1240 through 1263 removed outlier: 6.086A pdb=" N ALA A1250 " --> pdb=" O ARG A1246 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LYS A1251 " --> pdb=" O ALA A1247 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY A1254 " --> pdb=" O ALA A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1303 removed outlier: 3.508A pdb=" N ASN A1292 " --> pdb=" O TYR A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1333 removed outlier: 3.844A pdb=" N ARG A1333 " --> pdb=" O ASP A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1354 removed outlier: 5.101A pdb=" N ARG A1346 " --> pdb=" O GLU A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1374 removed outlier: 4.808A pdb=" N LEU A1371 " --> pdb=" O ASP A1367 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A1372 " --> pdb=" O ARG A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1383 removed outlier: 3.674A pdb=" N PHE A1382 " --> pdb=" O THR A1379 " (cutoff:3.500A) Processing helix chain 'A' and resid 1385 through 1389 removed outlier: 3.565A pdb=" N ALA A1388 " --> pdb=" O ILE A1385 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG A1389 " --> pdb=" O ASP A1386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1385 through 1389' Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 91 through 95 removed outlier: 3.550A pdb=" N THR C 95 " --> pdb=" O THR C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 150 removed outlier: 3.576A pdb=" N LEU D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 209 removed outlier: 3.860A pdb=" N TYR D 208 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 Processing helix chain 'F' and resid 143 through 148 Processing helix chain 'F' and resid 205 through 209 removed outlier: 3.847A pdb=" N TYR F 208 " --> pdb=" O LYS F 205 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 336 through 338 removed outlier: 3.598A pdb=" N ALA B 336 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY B 296 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLU B 455 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU B 294 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA B 292 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU B 276 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET B 40 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N MET B 274 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N CYS B 42 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA B 272 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE B 199 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL B 151 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL B 201 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B 153 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 200 " --> pdb=" O ASP B 202 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N MET A 274 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N MET A 40 " --> pdb=" O MET A 274 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU A 276 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA A 292 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU A 294 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU A 455 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 296 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG A 437 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 336 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU A 367 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AA3, first strand: chain 'B' and resid 367 through 369 removed outlier: 5.863A pdb=" N LEU B 367 " --> pdb=" O SER B 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AA5, first strand: chain 'B' and resid 475 through 478 removed outlier: 3.730A pdb=" N PHE B 524 " --> pdb=" O TRP B 475 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 652 through 654 removed outlier: 6.797A pdb=" N VAL B 559 " --> pdb=" O LEU B 829 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 713 through 717 removed outlier: 6.485A pdb=" N VAL B 724 " --> pdb=" O ALA B 715 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 725 " --> pdb=" O ALA B 695 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AA9, first strand: chain 'A' and resid 478 through 479 Processing sheet with id=AB1, first strand: chain 'A' and resid 649 through 654 removed outlier: 7.290A pdb=" N ALA A 558 " --> pdb=" O ALA A 650 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL A 652 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE A 560 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLY A 654 " --> pdb=" O PHE A 560 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE A 562 " --> pdb=" O GLY A 654 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 559 " --> pdb=" O LEU A 829 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 695 through 697 removed outlier: 5.089A pdb=" N SER A 722 " --> pdb=" O ASN A 718 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ALA A 726 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ILE A 714 " --> pdb=" O ALA A 726 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 975 through 980 removed outlier: 3.863A pdb=" N LEU A 979 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR A 948 " --> pdb=" O GLY A1002 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LEU A1004 " --> pdb=" O THR A 948 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU A 950 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU A1006 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ALA A 952 " --> pdb=" O LEU A1006 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA A1008 " --> pdb=" O ALA A 952 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU A1007 " --> pdb=" O VAL A1046 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N GLU A1048 " --> pdb=" O LEU A1007 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU A1043 " --> pdb=" O GLY A1084 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL A1086 " --> pdb=" O LEU A1043 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR A1045 " --> pdb=" O VAL A1086 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL A1088 " --> pdb=" O THR A1045 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N THR A1047 " --> pdb=" O VAL A1088 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLN A1112 " --> pdb=" O ARG A1123 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A1123 " --> pdb=" O GLN A1112 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU A1272 " --> pdb=" O VAL A1312 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP A1314 " --> pdb=" O LEU A1272 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER A1274 " --> pdb=" O TRP A1314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1145 through 1146 removed outlier: 6.783A pdb=" N PHE A1225 " --> pdb=" O THR A1146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1171 through 1172 Processing sheet with id=AB6, first strand: chain 'A' and resid 1336 through 1337 removed outlier: 4.187A pdb=" N ASP A1363 " --> pdb=" O ILE A1337 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 5 through 9 Processing sheet with id=AB8, first strand: chain 'C' and resid 12 through 14 removed outlier: 5.811A pdb=" N GLY C 12 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.676A pdb=" N TRP C 38 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 130 through 131 removed outlier: 3.554A pdb=" N GLY C 146 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 159 through 161 removed outlier: 3.722A pdb=" N SER C 160 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN C 204 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR C 201 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL C 218 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS C 207 " --> pdb=" O THR C 212 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 21 through 22 Processing sheet with id=AC4, first strand: chain 'D' and resid 28 through 29 Processing sheet with id=AC5, first strand: chain 'D' and resid 74 through 75 removed outlier: 6.450A pdb=" N TRP D 56 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR D 70 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU D 54 " --> pdb=" O TYR D 70 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 138 through 140 removed outlier: 5.559A pdb=" N SER D 153 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU D 203 " --> pdb=" O SER D 153 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL D 155 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU D 201 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU D 157 " --> pdb=" O SER D 199 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER D 199 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ASN D 159 " --> pdb=" O LEU D 197 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU D 197 " --> pdb=" O ASN D 159 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 168 through 170 removed outlier: 3.678A pdb=" N GLU D 217 " --> pdb=" O GLN D 169 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 5 through 9 Processing sheet with id=AC9, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AD1, first strand: chain 'E' and resid 36 through 41 removed outlier: 6.145A pdb=" N ARG E 40 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N TRP E 49 " --> pdb=" O ARG E 40 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 130 through 131 removed outlier: 3.564A pdb=" N GLY E 146 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 159 through 161 removed outlier: 4.339A pdb=" N TYR E 201 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL E 218 " --> pdb=" O TYR E 201 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 176 through 177 Processing sheet with id=AD5, first strand: chain 'F' and resid 21 through 22 Processing sheet with id=AD6, first strand: chain 'F' and resid 28 through 29 removed outlier: 3.838A pdb=" N GLY F 105 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU F 54 " --> pdb=" O TYR F 70 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR F 70 " --> pdb=" O LEU F 54 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP F 56 " --> pdb=" O LEU F 68 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 46 through 47 removed outlier: 3.760A pdb=" N TYR F 51 " --> pdb=" O HIS F 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 136 through 140 removed outlier: 5.612A pdb=" N LEU F 157 " --> pdb=" O SER F 199 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N SER F 199 " --> pdb=" O LEU F 157 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASN F 159 " --> pdb=" O LEU F 197 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU F 197 " --> pdb=" O ASN F 159 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER F 196 " --> pdb=" O THR F 186 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 168 through 170 removed outlier: 3.630A pdb=" N GLU F 217 " --> pdb=" O GLN F 169 " (cutoff:3.500A) 793 hydrogen bonds defined for protein. 2187 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: 4.81 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 182 1.21 - 1.36: 8217 1.36 - 1.52: 8228 1.52 - 1.67: 7697 1.67 - 1.82: 136 Bond restraints: 24460 Sorted by residual: bond pdb=" CA SER A 442 " pdb=" CB SER A 442 " ideal model delta sigma weight residual 1.532 1.304 0.228 1.58e-02 4.01e+03 2.08e+02 bond pdb=" C ARG A 43 " pdb=" O ARG A 43 " ideal model delta sigma weight residual 1.236 1.073 0.163 1.14e-02 7.69e+03 2.05e+02 bond pdb=" CA SER A 207 " pdb=" CB SER A 207 " ideal model delta sigma weight residual 1.530 1.283 0.248 1.75e-02 3.27e+03 2.00e+02 bond pdb=" C PRO B 197 " pdb=" O PRO B 197 " ideal model delta sigma weight residual 1.235 1.062 0.173 1.30e-02 5.92e+03 1.77e+02 bond pdb=" C SER A 442 " pdb=" O SER A 442 " ideal model delta sigma weight residual 1.235 1.094 0.141 1.12e-02 7.97e+03 1.59e+02 ... (remaining 24455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.41: 32940 6.41 - 12.83: 298 12.83 - 19.24: 24 19.24 - 25.66: 8 25.66 - 32.07: 3 Bond angle restraints: 33273 Sorted by residual: angle pdb=" N PRO A 162 " pdb=" CA PRO A 162 " pdb=" CB PRO A 162 " ideal model delta sigma weight residual 103.32 83.45 19.87 8.40e-01 1.42e+00 5.59e+02 angle pdb=" C GLU A 159 " pdb=" CA GLU A 159 " pdb=" CB GLU A 159 " ideal model delta sigma weight residual 110.19 78.12 32.07 1.62e+00 3.81e-01 3.92e+02 angle pdb=" C ASP B 883 " pdb=" CA ASP B 883 " pdb=" CB ASP B 883 " ideal model delta sigma weight residual 109.75 78.51 31.24 1.65e+00 3.67e-01 3.59e+02 angle pdb=" CA PHE B 266 " pdb=" CB PHE B 266 " pdb=" CG PHE B 266 " ideal model delta sigma weight residual 113.80 131.55 -17.75 1.00e+00 1.00e+00 3.15e+02 angle pdb=" C ARG A 43 " pdb=" CA ARG A 43 " pdb=" CB ARG A 43 " ideal model delta sigma weight residual 110.74 83.20 27.54 1.61e+00 3.86e-01 2.93e+02 ... (remaining 33268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.06: 13035 22.06 - 44.11: 1094 44.11 - 66.17: 461 66.17 - 88.22: 36 88.22 - 110.28: 8 Dihedral angle restraints: 14634 sinusoidal: 5566 harmonic: 9068 Sorted by residual: dihedral pdb=" CA GLU C 155 " pdb=" C GLU C 155 " pdb=" N PRO C 156 " pdb=" CA PRO C 156 " ideal model delta harmonic sigma weight residual 180.00 69.72 110.28 0 5.00e+00 4.00e-02 4.86e+02 dihedral pdb=" CA GLU E 155 " pdb=" C GLU E 155 " pdb=" N PRO E 156 " pdb=" CA PRO E 156 " ideal model delta harmonic sigma weight residual 180.00 78.77 101.23 0 5.00e+00 4.00e-02 4.10e+02 dihedral pdb=" CA THR F 115 " pdb=" C THR F 115 " pdb=" N PRO F 116 " pdb=" CA PRO F 116 " ideal model delta harmonic sigma weight residual 180.00 85.75 94.25 0 5.00e+00 4.00e-02 3.55e+02 ... (remaining 14631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 3361 0.149 - 0.297: 331 0.297 - 0.446: 49 0.446 - 0.595: 9 0.595 - 0.743: 4 Chirality restraints: 3754 Sorted by residual: chirality pdb=" CB VAL A 232 " pdb=" CA VAL A 232 " pdb=" CG1 VAL A 232 " pdb=" CG2 VAL A 232 " both_signs ideal model delta sigma weight residual False -2.63 -1.89 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CB VAL B 385 " pdb=" CA VAL B 385 " pdb=" CG1 VAL B 385 " pdb=" CG2 VAL B 385 " both_signs ideal model delta sigma weight residual False -2.63 -1.97 -0.66 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA ARG A1303 " pdb=" N ARG A1303 " pdb=" C ARG A1303 " pdb=" CB ARG A1303 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.40e+00 ... (remaining 3751 not shown) Planarity restraints: 4402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A1301 " 0.050 2.00e-02 2.50e+03 1.05e-01 1.10e+02 pdb=" C GLN A1301 " -0.181 2.00e-02 2.50e+03 pdb=" O GLN A1301 " 0.070 2.00e-02 2.50e+03 pdb=" N ARG A1302 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 96 " -0.031 2.00e-02 2.50e+03 6.06e-02 3.67e+01 pdb=" C ALA E 96 " 0.105 2.00e-02 2.50e+03 pdb=" O ALA E 96 " -0.038 2.00e-02 2.50e+03 pdb=" N VAL E 97 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 266 " -0.046 2.00e-02 2.50e+03 4.32e-02 3.26e+01 pdb=" CG PHE B 266 " 0.100 2.00e-02 2.50e+03 pdb=" CD1 PHE B 266 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE B 266 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE B 266 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 266 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 266 " -0.010 2.00e-02 2.50e+03 ... (remaining 4399 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 58 2.38 - 3.01: 13611 3.01 - 3.64: 37730 3.64 - 4.27: 61223 4.27 - 4.90: 99572 Nonbonded interactions: 212194 Sorted by model distance: nonbonded pdb=" O GLU A 159 " pdb=" CB GLU A 159 " model vdw 1.751 2.752 nonbonded pdb=" O ARG A 43 " pdb=" CB ARG A 43 " model vdw 1.811 2.752 nonbonded pdb=" O PRO B 902 " pdb=" CB PRO B 902 " model vdw 1.948 2.752 nonbonded pdb=" N THR C 101 " pdb=" OG1 THR C 101 " model vdw 1.954 2.496 nonbonded pdb=" O ARG C 102 " pdb=" CB ARG C 102 " model vdw 2.022 2.752 ... (remaining 212189 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.030 Process input model: 20.410 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 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 : 0.012 0.248 24469 Z= 0.894 Angle : 1.707 32.071 33289 Z= 1.172 Chirality : 0.095 0.743 3754 Planarity : 0.009 0.139 4402 Dihedral : 18.866 110.281 8804 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.55 % Favored : 91.35 % Rotamer: Outliers : 16.06 % Allowed : 5.61 % Favored : 78.33 % Cbeta Deviations : 2.20 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.66 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.26 (0.13), residues: 3181 helix: -3.24 (0.13), residues: 915 sheet: -2.66 (0.19), residues: 555 loop : -2.64 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 21 TYR 0.040 0.003 TYR E 99 PHE 0.100 0.004 PHE B 266 TRP 0.066 0.004 TRP A 642 HIS 0.015 0.002 HIS F 220 Details of bonding type rmsd/Z covalent geometry : bond 0.01232 / 0.89 (24460) covalent geometry : angle 1.70729 / 1.17 (33273) SS BOND : bond 0.01511 / 1.04 ( 8) SS BOND : angle 1.93924 / 1.06 ( 16) hydrogen bonds : bond 0.20411 / 13.39 ( 793) hydrogen bonds : angle 9.71168 / 6.64 ( 2187) Misc. bond : bond 0.09350 / 4.92 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 398 poor density : 335 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 SER cc_start: 0.8020 (OUTLIER) cc_final: 0.7755 (p) REVERT: B 123 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7979 (mt0) REVERT: B 197 PRO cc_start: 0.8852 (OUTLIER) cc_final: 0.8566 (Cg_exo) REVERT: B 268 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6917 (ttp) REVERT: B 391 MET cc_start: 0.7959 (mmm) cc_final: 0.7478 (mmp) REVERT: B 865 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.5942 (tp) REVERT: B 901 TYR cc_start: 0.8235 (t80) cc_final: 0.7847 (t80) REVERT: A 43 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8084 (mpt180) REVERT: A 62 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7614 (ttm170) REVERT: A 124 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.6995 (ptp-170) REVERT: A 391 MET cc_start: 0.7403 (mmt) cc_final: 0.7182 (mmt) REVERT: A 601 GLU cc_start: 0.2165 (OUTLIER) cc_final: 0.1771 (mm-30) REVERT: A 631 MET cc_start: 0.4097 (mmm) cc_final: 0.3779 (mtt) REVERT: A 694 MET cc_start: 0.3212 (mmm) cc_final: 0.2917 (mmm) REVERT: A 703 GLU cc_start: 0.2588 (OUTLIER) cc_final: 0.2216 (pm20) REVERT: A 745 ARG cc_start: 0.1269 (OUTLIER) cc_final: 0.1001 (ptt180) REVERT: A 799 ASP cc_start: 0.3297 (OUTLIER) cc_final: 0.2644 (p0) REVERT: A 841 ILE cc_start: 0.6422 (OUTLIER) cc_final: 0.6191 (mm) REVERT: A 1300 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.7075 (mt0) REVERT: C 106 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7680 (tp) REVERT: C 108 ASP cc_start: 0.6897 (OUTLIER) cc_final: 0.6577 (m-30) REVERT: E 34 TYR cc_start: 0.7364 (m-80) cc_final: 0.7154 (m-80) REVERT: E 97 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8769 (t) REVERT: F 127 ASP cc_start: 0.6655 (m-30) cc_final: 0.6418 (m-30) outliers start: 398 outliers final: 82 residues processed: 643 average time/residue: 0.2059 time to fit residues: 198.3506 Evaluate side-chains 331 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 232 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 197 PRO Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 581 PRO Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 797 GLU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 859 ARG Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 162 PRO Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 465 ARG Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 683 ARG Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 977 ARG Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1179 ASP Chi-restraints excluded: chain A residue 1188 LEU Chi-restraints excluded: chain A residue 1194 ARG Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1249 ARG Chi-restraints excluded: chain A residue 1300 GLN Chi-restraints excluded: chain A residue 1330 ARG Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 84 TYR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 217 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.0870 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 213 HIS B 657 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 GLN ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 ASN ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 ASN C 206 ASN D 49 ASN D 180 ASN ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.199392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.171022 restraints weight = 31997.031| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 1.49 r_work: 0.3679 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24469 Z= 0.168 Angle : 0.716 8.947 33289 Z= 0.369 Chirality : 0.045 0.234 3754 Planarity : 0.007 0.133 4402 Dihedral : 10.041 84.275 3715 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.53 % Favored : 94.34 % Rotamer: Outliers : 4.76 % Allowed : 12.87 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.66 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.13), residues: 3181 helix: -2.12 (0.15), residues: 937 sheet: -2.19 (0.19), residues: 571 loop : -2.22 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 721 TYR 0.023 0.002 TYR E 183 PHE 0.033 0.002 PHE A1369 TRP 0.035 0.002 TRP A 642 HIS 0.008 0.001 HIS A1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (24460) covalent geometry : angle 0.71542 / 0.37 (33273) SS BOND : bond 0.00479 / 0.21 ( 8) SS BOND : angle 1.37586 / 0.84 ( 16) hydrogen bonds : bond 0.04155 / 2.79 ( 793) hydrogen bonds : angle 6.72237 / 4.61 ( 2187) Misc. bond : bond 0.00065 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 270 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 VAL cc_start: 0.8149 (t) cc_final: 0.7912 (t) REVERT: B 112 SER cc_start: 0.8444 (OUTLIER) cc_final: 0.8213 (p) REVERT: B 123 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7914 (mt0) REVERT: B 159 GLU cc_start: 0.6730 (pm20) cc_final: 0.6526 (pm20) REVERT: B 209 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8871 (mt) REVERT: B 243 ASP cc_start: 0.7505 (m-30) cc_final: 0.7237 (m-30) REVERT: B 268 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7043 (mtm) REVERT: B 659 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.5886 (mm-30) REVERT: B 785 PHE cc_start: 0.6062 (OUTLIER) cc_final: 0.5689 (t80) REVERT: B 802 TYR cc_start: 0.6009 (t80) cc_final: 0.5744 (t80) REVERT: B 834 HIS cc_start: 0.7437 (t70) cc_final: 0.7108 (t70) REVERT: A 601 GLU cc_start: 0.2127 (OUTLIER) cc_final: 0.1858 (mm-30) REVERT: A 631 MET cc_start: 0.4460 (mmm) cc_final: 0.4099 (mtt) REVERT: A 799 ASP cc_start: 0.4100 (OUTLIER) cc_final: 0.3402 (p0) REVERT: A 1138 LYS cc_start: 0.7428 (mmpt) cc_final: 0.7181 (mmpt) REVERT: C 106 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8210 (tp) REVERT: D 145 GLU cc_start: 0.6796 (pp20) cc_final: 0.6296 (pt0) REVERT: E 112 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7597 (pm20) REVERT: F 195 TYR cc_start: 0.7687 (m-80) cc_final: 0.6782 (m-10) outliers start: 118 outliers final: 59 residues processed: 367 average time/residue: 0.1761 time to fit residues: 101.9347 Evaluate side-chains 292 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 223 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 785 PHE Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1463 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 1111 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1179 ASP Chi-restraints excluded: chain A residue 1188 LEU Chi-restraints excluded: chain A residue 1249 ARG Chi-restraints excluded: chain A residue 1330 ARG Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 231 PHE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 185 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 287 optimal weight: 0.6980 chunk 60 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 174 optimal weight: 20.0000 chunk 110 optimal weight: 0.3980 chunk 235 optimal weight: 0.3980 chunk 314 optimal weight: 3.9990 chunk 302 optimal weight: 0.9980 chunk 241 optimal weight: 4.9990 chunk 249 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 375 ASN B 794 GLN B 856 HIS A 378 HIS A 459 GLN A 628 GLN A 776 HIS ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 HIS ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1376 GLN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN E 171 HIS ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.196009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.163207 restraints weight = 31578.089| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 1.60 r_work: 0.3514 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 24469 Z= 0.207 Angle : 0.674 7.783 33289 Z= 0.348 Chirality : 0.044 0.194 3754 Planarity : 0.007 0.104 4402 Dihedral : 7.846 62.322 3592 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.24 % Allowed : 15.66 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.66 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.14), residues: 3181 helix: -1.64 (0.16), residues: 942 sheet: -1.97 (0.20), residues: 560 loop : -1.95 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 721 TYR 0.016 0.002 TYR E 183 PHE 0.032 0.002 PHE A 266 TRP 0.030 0.002 TRP F 170 HIS 0.006 0.001 HIS A1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (24460) covalent geometry : angle 0.67385 / 0.35 (33273) SS BOND : bond 0.00441 / 0.23 ( 8) SS BOND : angle 0.85473 / 0.49 ( 16) hydrogen bonds : bond 0.03841 / 2.60 ( 793) hydrogen bonds : angle 6.20881 / 4.25 ( 2187) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 241 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8123 (mt0) REVERT: B 268 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7599 (ttp) REVERT: B 350 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8378 (mp) REVERT: B 659 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.6255 (mm-30) REVERT: B 785 PHE cc_start: 0.6568 (OUTLIER) cc_final: 0.6057 (t80) REVERT: B 818 ARG cc_start: 0.7345 (mtt-85) cc_final: 0.6821 (ptp-110) REVERT: B 834 HIS cc_start: 0.7993 (t70) cc_final: 0.7359 (t70) REVERT: B 852 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5900 (mm) REVERT: B 901 TYR cc_start: 0.8346 (t80) cc_final: 0.7825 (t80) REVERT: A 500 PRO cc_start: 0.8055 (Cg_endo) cc_final: 0.7760 (Cg_exo) REVERT: A 631 MET cc_start: 0.4192 (mmm) cc_final: 0.3670 (mtt) REVERT: A 1273 PHE cc_start: 0.7881 (m-80) cc_final: 0.7415 (t80) REVERT: A 1376 GLN cc_start: 0.6858 (OUTLIER) cc_final: 0.6613 (pm20) REVERT: C 106 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8373 (tp) REVERT: D 108 TYR cc_start: 0.8813 (m-80) cc_final: 0.8550 (m-80) REVERT: D 139 ILE cc_start: 0.7997 (tp) cc_final: 0.7627 (tp) REVERT: D 145 GLU cc_start: 0.7173 (pp20) cc_final: 0.6650 (pp20) REVERT: E 112 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7861 (pm20) REVERT: F 154 VAL cc_start: 0.6928 (OUTLIER) cc_final: 0.6548 (p) REVERT: F 195 TYR cc_start: 0.8014 (m-80) cc_final: 0.7357 (m-10) REVERT: F 217 GLU cc_start: 0.8321 (pm20) cc_final: 0.7732 (pm20) outliers start: 105 outliers final: 58 residues processed: 326 average time/residue: 0.1671 time to fit residues: 87.3393 Evaluate side-chains 282 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 214 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 785 PHE Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1413 GLU Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1463 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 826 ARG Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 1111 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1337 ILE Chi-restraints excluded: chain A residue 1376 GLN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 231 PHE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 196 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 274 optimal weight: 6.9990 chunk 71 optimal weight: 30.0000 chunk 225 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 315 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1423 HIS A 81 HIS A 368 HIS A 459 GLN A 520 HIS A 756 HIS ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 ASN A1376 GLN E 171 HIS ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.193253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.159673 restraints weight = 31664.297| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 1.65 r_work: 0.3462 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 24469 Z= 0.274 Angle : 0.704 8.795 33289 Z= 0.360 Chirality : 0.045 0.178 3754 Planarity : 0.006 0.100 4402 Dihedral : 7.012 58.741 3555 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.28 % Allowed : 16.71 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.66 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.14), residues: 3181 helix: -1.45 (0.16), residues: 938 sheet: -1.94 (0.19), residues: 592 loop : -1.81 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 721 TYR 0.017 0.002 TYR D 51 PHE 0.029 0.002 PHE A 54 TRP 0.032 0.002 TRP F 170 HIS 0.007 0.001 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.27 (24460) covalent geometry : angle 0.70394 / 0.36 (33273) SS BOND : bond 0.00445 / 0.24 ( 8) SS BOND : angle 1.01929 / 0.58 ( 16) hydrogen bonds : bond 0.03742 / 2.54 ( 793) hydrogen bonds : angle 6.14557 / 4.23 ( 2187) Misc. bond : bond 0.00061 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 237 time to evaluate : 0.894 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: B 268 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7673 (ttp) REVERT: B 350 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8411 (mp) REVERT: B 785 PHE cc_start: 0.6820 (OUTLIER) cc_final: 0.6278 (t80) REVERT: B 834 HIS cc_start: 0.8026 (t70) cc_final: 0.7396 (t70) REVERT: B 852 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6262 (mm) REVERT: A 87 SER cc_start: 0.8385 (OUTLIER) cc_final: 0.8036 (t) REVERT: A 266 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8488 (p90) REVERT: A 500 PRO cc_start: 0.8409 (Cg_endo) cc_final: 0.8158 (Cg_exo) REVERT: A 560 PHE cc_start: 0.7010 (m-80) cc_final: 0.6360 (t80) REVERT: A 642 TRP cc_start: 0.6082 (OUTLIER) cc_final: 0.3122 (m-90) REVERT: A 1111 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6941 (m-30) REVERT: D 108 TYR cc_start: 0.8922 (m-80) cc_final: 0.8653 (m-80) REVERT: D 139 ILE cc_start: 0.8169 (tp) cc_final: 0.7802 (tp) REVERT: D 217 GLU cc_start: 0.7223 (pp20) cc_final: 0.6652 (pp20) REVERT: E 33 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.6613 (t0) REVERT: E 86 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.6733 (mm110) REVERT: E 112 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7917 (pm20) REVERT: F 110 MET cc_start: 0.8564 (tpp) cc_final: 0.8319 (mmm) REVERT: F 217 GLU cc_start: 0.8328 (pm20) cc_final: 0.7497 (pm20) outliers start: 106 outliers final: 68 residues processed: 321 average time/residue: 0.1645 time to fit residues: 85.1385 Evaluate side-chains 298 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 219 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 405 HIS Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 785 PHE Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1413 GLU Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 642 TRP Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 843 GLU Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 930 TYR Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1111 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 231 PHE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 196 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 97 optimal weight: 6.9990 chunk 285 optimal weight: 10.0000 chunk 270 optimal weight: 6.9990 chunk 304 optimal weight: 0.3980 chunk 76 optimal weight: 5.9990 chunk 263 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 794 GLN A 459 GLN ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.196461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.167116 restraints weight = 31321.217| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 1.50 r_work: 0.3617 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24469 Z= 0.150 Angle : 0.607 8.047 33289 Z= 0.312 Chirality : 0.042 0.170 3754 Planarity : 0.006 0.100 4402 Dihedral : 6.418 58.293 3540 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.47 % Allowed : 18.04 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.66 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.14), residues: 3181 helix: -1.05 (0.16), residues: 945 sheet: -1.77 (0.20), residues: 602 loop : -1.68 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 721 TYR 0.021 0.001 TYR E 183 PHE 0.023 0.002 PHE A1369 TRP 0.023 0.001 TRP A1125 HIS 0.007 0.001 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (24460) covalent geometry : angle 0.60735 / 0.31 (33273) SS BOND : bond 0.00207 / 0.10 ( 8) SS BOND : angle 0.57864 / 0.35 ( 16) hydrogen bonds : bond 0.03290 / 2.21 ( 793) hydrogen bonds : angle 5.74920 / 3.94 ( 2187) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 234 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 268 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7266 (ttp) REVERT: B 350 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8364 (mp) REVERT: B 785 PHE cc_start: 0.6432 (OUTLIER) cc_final: 0.6014 (t80) REVERT: B 802 TYR cc_start: 0.6202 (t80) cc_final: 0.5987 (t80) REVERT: B 834 HIS cc_start: 0.7609 (t70) cc_final: 0.7296 (t70) REVERT: B 901 TYR cc_start: 0.8344 (t80) cc_final: 0.7654 (t80) REVERT: A 87 SER cc_start: 0.8191 (OUTLIER) cc_final: 0.7866 (t) REVERT: A 266 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.8373 (p90) REVERT: A 500 PRO cc_start: 0.8277 (Cg_endo) cc_final: 0.8057 (Cg_exo) REVERT: A 560 PHE cc_start: 0.6889 (m-80) cc_final: 0.6569 (t80) REVERT: A 642 TRP cc_start: 0.6083 (OUTLIER) cc_final: 0.3293 (m-90) REVERT: A 992 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: A 1285 LEU cc_start: 0.7129 (mp) cc_final: 0.6894 (mt) REVERT: A 1334 HIS cc_start: 0.5668 (p-80) cc_final: 0.5267 (p90) REVERT: C 183 TYR cc_start: 0.6810 (m-80) cc_final: 0.6545 (m-80) REVERT: D 108 TYR cc_start: 0.8814 (m-80) cc_final: 0.8465 (m-80) REVERT: D 139 ILE cc_start: 0.8053 (tp) cc_final: 0.7619 (tp) REVERT: D 145 GLU cc_start: 0.6783 (pp20) cc_final: 0.6263 (pt0) REVERT: D 217 GLU cc_start: 0.6914 (pp20) cc_final: 0.6366 (pp20) REVERT: E 33 ASP cc_start: 0.7105 (m-30) cc_final: 0.6602 (t0) REVERT: E 82 ILE cc_start: 0.7200 (tp) cc_final: 0.6753 (tp) REVERT: E 112 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7881 (pm20) REVERT: F 25 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7354 (tt) REVERT: F 217 GLU cc_start: 0.7719 (pm20) cc_final: 0.7128 (pm20) outliers start: 86 outliers final: 50 residues processed: 306 average time/residue: 0.1509 time to fit residues: 76.6083 Evaluate side-chains 277 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 218 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 785 PHE Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 1413 GLU Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 642 TRP Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 930 TYR Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 231 PHE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 185 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 111 optimal weight: 0.8980 chunk 258 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 91 optimal weight: 0.0970 chunk 297 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 chunk 162 optimal weight: 5.9990 chunk 14 optimal weight: 0.2980 chunk 112 optimal weight: 0.4980 chunk 161 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 449 ASN ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.198064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.165469 restraints weight = 31579.835| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 1.60 r_work: 0.3554 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24469 Z= 0.128 Angle : 0.584 8.037 33289 Z= 0.299 Chirality : 0.042 0.161 3754 Planarity : 0.006 0.103 4402 Dihedral : 5.959 55.376 3532 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.31 % Allowed : 18.52 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.66 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.15), residues: 3181 helix: -0.76 (0.17), residues: 954 sheet: -1.54 (0.20), residues: 595 loop : -1.58 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 721 TYR 0.024 0.001 TYR E 183 PHE 0.023 0.002 PHE A1369 TRP 0.040 0.001 TRP A1125 HIS 0.008 0.001 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (24460) covalent geometry : angle 0.58437 / 0.30 (33273) SS BOND : bond 0.00184 / 0.08 ( 8) SS BOND : angle 0.45037 / 0.26 ( 16) hydrogen bonds : bond 0.03042 / 2.05 ( 793) hydrogen bonds : angle 5.53948 / 3.80 ( 2187) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 241 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 LEU cc_start: 0.8940 (mt) cc_final: 0.8729 (pt) REVERT: B 350 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8335 (mp) REVERT: B 785 PHE cc_start: 0.6861 (OUTLIER) cc_final: 0.6500 (t80) REVERT: B 802 TYR cc_start: 0.7019 (t80) cc_final: 0.6646 (t80) REVERT: B 834 HIS cc_start: 0.7862 (t70) cc_final: 0.7317 (t70) REVERT: A 87 SER cc_start: 0.8064 (OUTLIER) cc_final: 0.7742 (t) REVERT: A 124 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.5508 (ptm-80) REVERT: A 126 MET cc_start: 0.8595 (mmm) cc_final: 0.8380 (mmt) REVERT: A 163 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8137 (mtt180) REVERT: A 266 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.8298 (p90) REVERT: A 302 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7648 (t0) REVERT: A 500 PRO cc_start: 0.8348 (Cg_endo) cc_final: 0.8139 (Cg_exo) REVERT: A 642 TRP cc_start: 0.6120 (OUTLIER) cc_final: 0.3184 (m-90) REVERT: A 992 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: A 1334 HIS cc_start: 0.5909 (p-80) cc_final: 0.5482 (p90) REVERT: C 183 TYR cc_start: 0.6942 (m-80) cc_final: 0.6483 (m-80) REVERT: D 108 TYR cc_start: 0.8783 (m-80) cc_final: 0.8410 (m-80) REVERT: D 139 ILE cc_start: 0.8138 (tp) cc_final: 0.7771 (tp) REVERT: D 217 GLU cc_start: 0.7239 (pp20) cc_final: 0.6523 (pp20) REVERT: E 33 ASP cc_start: 0.6812 (m-30) cc_final: 0.6336 (t0) REVERT: E 82 ILE cc_start: 0.7203 (tp) cc_final: 0.6710 (tp) REVERT: E 112 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7865 (pm20) REVERT: E 206 ASN cc_start: 0.7053 (p0) cc_final: 0.6575 (p0) REVERT: F 25 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7249 (tt) REVERT: F 217 GLU cc_start: 0.8129 (pm20) cc_final: 0.7281 (pm20) outliers start: 82 outliers final: 56 residues processed: 303 average time/residue: 0.1604 time to fit residues: 79.2115 Evaluate side-chains 282 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 215 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 785 PHE Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 1413 GLU Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 642 TRP Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 231 PHE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 152 TYR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 185 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 107 optimal weight: 0.6980 chunk 293 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 262 optimal weight: 0.0040 chunk 78 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 159 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 794 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.204125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.176959 restraints weight = 30813.135| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 1.38 r_work: 0.4005 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3920 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24469 Z= 0.176 Angle : 0.618 14.762 33289 Z= 0.313 Chirality : 0.043 0.197 3754 Planarity : 0.006 0.092 4402 Dihedral : 5.821 54.364 3526 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.47 % Allowed : 18.52 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.66 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.15), residues: 3181 helix: -0.67 (0.17), residues: 959 sheet: -1.52 (0.20), residues: 609 loop : -1.46 (0.16), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 721 TYR 0.023 0.002 TYR F 195 PHE 0.042 0.002 PHE B 244 TRP 0.054 0.002 TRP A1125 HIS 0.007 0.001 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (24460) covalent geometry : angle 0.61816 / 0.31 (33273) SS BOND : bond 0.00290 / 0.14 ( 8) SS BOND : angle 0.56884 / 0.32 ( 16) hydrogen bonds : bond 0.03165 / 2.13 ( 793) hydrogen bonds : angle 5.49798 / 3.78 ( 2187) Misc. bond : bond 0.00026 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 227 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 350 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8372 (mp) REVERT: A 87 SER cc_start: 0.7813 (OUTLIER) cc_final: 0.7607 (t) REVERT: A 124 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.5567 (ptm-80) REVERT: A 302 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7576 (t0) REVERT: A 642 TRP cc_start: 0.5629 (OUTLIER) cc_final: 0.3068 (m-90) REVERT: D 108 TYR cc_start: 0.8610 (m-80) cc_final: 0.8364 (m-80) REVERT: D 139 ILE cc_start: 0.7727 (tp) cc_final: 0.7292 (tp) REVERT: D 145 GLU cc_start: 0.4972 (pp20) cc_final: 0.4325 (pp20) REVERT: D 217 GLU cc_start: 0.6023 (pp20) cc_final: 0.5817 (pp20) REVERT: E 112 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7581 (pm20) outliers start: 86 outliers final: 64 residues processed: 295 average time/residue: 0.1527 time to fit residues: 73.4745 Evaluate side-chains 283 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 213 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 1413 GLU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 642 TRP Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 231 PHE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 152 TYR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 109 CYS Chi-restraints excluded: chain F residue 185 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 73 optimal weight: 50.0000 chunk 168 optimal weight: 40.0000 chunk 223 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 132 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 182 optimal weight: 0.5980 chunk 279 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 GLN ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN E 171 HIS ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.205020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.177850 restraints weight = 30710.343| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 1.40 r_work: 0.4032 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3979 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 24469 Z= 0.186 Angle : 0.627 10.085 33289 Z= 0.318 Chirality : 0.043 0.195 3754 Planarity : 0.006 0.089 4402 Dihedral : 5.725 54.368 3522 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.35 % Allowed : 18.85 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.66 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.15), residues: 3181 helix: -0.63 (0.17), residues: 963 sheet: -1.42 (0.20), residues: 603 loop : -1.46 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 721 TYR 0.014 0.002 TYR D 162 PHE 0.020 0.002 PHE B 266 TRP 0.058 0.002 TRP A1125 HIS 0.007 0.001 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (24460) covalent geometry : angle 0.62674 / 0.32 (33273) SS BOND : bond 0.00250 / 0.12 ( 8) SS BOND : angle 0.56508 / 0.33 ( 16) hydrogen bonds : bond 0.03101 / 2.09 ( 793) hydrogen bonds : angle 5.48260 / 3.78 ( 2187) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 220 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.7337 (tmm) cc_final: 0.6252 (tmm) REVERT: B 350 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8403 (mp) REVERT: B 391 MET cc_start: 0.8089 (mmm) cc_final: 0.7500 (mmp) REVERT: A 87 SER cc_start: 0.7814 (OUTLIER) cc_final: 0.7599 (t) REVERT: A 124 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.5575 (ptm-80) REVERT: A 502 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7330 (mt0) REVERT: A 642 TRP cc_start: 0.5421 (OUTLIER) cc_final: 0.2901 (m-90) REVERT: A 1285 LEU cc_start: 0.5672 (mp) cc_final: 0.5357 (mt) REVERT: D 108 TYR cc_start: 0.8619 (m-80) cc_final: 0.8375 (m-80) REVERT: D 139 ILE cc_start: 0.7645 (tp) cc_final: 0.7227 (tp) REVERT: E 112 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7626 (pm20) outliers start: 83 outliers final: 63 residues processed: 281 average time/residue: 0.1571 time to fit residues: 72.1340 Evaluate side-chains 276 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 207 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 1413 GLU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 502 GLN Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 642 TRP Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1339 MET Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 231 PHE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 109 CYS Chi-restraints excluded: chain F residue 185 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 121 optimal weight: 0.9990 chunk 301 optimal weight: 0.0980 chunk 38 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 142 optimal weight: 0.0040 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 264 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 HIS A 597 HIS ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.195612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3635 r_free = 0.3635 target = 0.128971 restraints weight = 31677.651| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.52 r_work: 0.3286 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24469 Z= 0.125 Angle : 0.597 10.473 33289 Z= 0.304 Chirality : 0.042 0.216 3754 Planarity : 0.006 0.084 4402 Dihedral : 5.566 54.838 3522 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.78 % Allowed : 19.81 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.15), residues: 3181 helix: -0.43 (0.17), residues: 965 sheet: -1.39 (0.20), residues: 634 loop : -1.40 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 221 TYR 0.017 0.001 TYR F 195 PHE 0.019 0.002 PHE A1369 TRP 0.062 0.002 TRP A1125 HIS 0.005 0.001 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (24460) covalent geometry : angle 0.59698 / 0.30 (33273) SS BOND : bond 0.00211 / 0.12 ( 8) SS BOND : angle 0.37567 / 0.23 ( 16) hydrogen bonds : bond 0.02919 / 1.97 ( 793) hydrogen bonds : angle 5.30611 / 3.65 ( 2187) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 224 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 350 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7879 (mp) REVERT: B 391 MET cc_start: 0.8586 (mmm) cc_final: 0.8157 (mmp) REVERT: B 562 PHE cc_start: 0.7383 (m-80) cc_final: 0.7043 (m-80) REVERT: B 802 TYR cc_start: 0.7211 (t80) cc_final: 0.6739 (t80) REVERT: B 820 LEU cc_start: 0.5575 (OUTLIER) cc_final: 0.5367 (mm) REVERT: A 87 SER cc_start: 0.8249 (OUTLIER) cc_final: 0.7711 (t) REVERT: A 124 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.5215 (ptm-80) REVERT: A 302 ASP cc_start: 0.8074 (t0) cc_final: 0.7846 (t0) REVERT: A 635 MET cc_start: 0.4636 (ttt) cc_final: 0.4423 (ttt) REVERT: A 642 TRP cc_start: 0.5777 (OUTLIER) cc_final: 0.2980 (m-90) REVERT: A 1322 MET cc_start: 0.3104 (ttm) cc_final: 0.2709 (ttm) REVERT: D 108 TYR cc_start: 0.8947 (m-80) cc_final: 0.8579 (m-80) REVERT: D 139 ILE cc_start: 0.8129 (tp) cc_final: 0.7840 (tp) REVERT: D 145 GLU cc_start: 0.7452 (pp20) cc_final: 0.6965 (pp20) REVERT: E 93 GLU cc_start: 0.7498 (pp20) cc_final: 0.6730 (mp0) outliers start: 69 outliers final: 56 residues processed: 274 average time/residue: 0.1411 time to fit residues: 62.9651 Evaluate side-chains 272 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 211 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 1413 GLU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 642 TRP Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1339 MET Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 152 TYR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 85 optimal weight: 4.9990 chunk 25 optimal weight: 0.3980 chunk 243 optimal weight: 3.9990 chunk 313 optimal weight: 0.0970 chunk 219 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 60 optimal weight: 0.0470 chunk 213 optimal weight: 20.0000 chunk 242 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1334 HIS C 178 GLN D 159 ASN E 171 HIS ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 ASN ** F 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.196325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 116)---------------| | r_work = 0.3667 r_free = 0.3667 target = 0.130540 restraints weight = 31661.310| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 3.45 r_work: 0.3295 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 24469 Z= 0.122 Angle : 0.595 14.613 33289 Z= 0.301 Chirality : 0.042 0.203 3754 Planarity : 0.006 0.078 4402 Dihedral : 5.369 55.618 3519 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.66 % Allowed : 19.90 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.15), residues: 3181 helix: -0.34 (0.17), residues: 970 sheet: -1.27 (0.20), residues: 635 loop : -1.33 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 221 TYR 0.022 0.001 TYR E 84 PHE 0.016 0.001 PHE A 785 TRP 0.051 0.001 TRP A1125 HIS 0.006 0.001 HIS A1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (24460) covalent geometry : angle 0.59497 / 0.30 (33273) SS BOND : bond 0.00181 / 0.10 ( 8) SS BOND : angle 0.52290 / 0.34 ( 16) hydrogen bonds : bond 0.02853 / 1.94 ( 793) hydrogen bonds : angle 5.17693 / 3.57 ( 2187) Misc. bond : bond 0.00006 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 225 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6339 (tmm) cc_final: 0.6117 (tmm) REVERT: B 176 MET cc_start: 0.7620 (tmm) cc_final: 0.6678 (tmm) REVERT: B 350 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7882 (mp) REVERT: B 562 PHE cc_start: 0.7460 (m-80) cc_final: 0.7179 (m-80) REVERT: B 802 TYR cc_start: 0.7111 (t80) cc_final: 0.6663 (t80) REVERT: A 87 SER cc_start: 0.8223 (OUTLIER) cc_final: 0.7595 (t) REVERT: A 124 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.5198 (ptm-80) REVERT: A 302 ASP cc_start: 0.8080 (t0) cc_final: 0.7720 (t0) REVERT: A 312 ASN cc_start: 0.6048 (m-40) cc_final: 0.5657 (m-40) REVERT: A 642 TRP cc_start: 0.5740 (OUTLIER) cc_final: 0.2907 (m-90) REVERT: A 1068 TRP cc_start: 0.7930 (m100) cc_final: 0.7600 (m100) REVERT: A 1285 LEU cc_start: 0.6982 (mt) cc_final: 0.6637 (mp) REVERT: C 86 GLN cc_start: 0.7084 (tp40) cc_final: 0.6610 (tp40) REVERT: D 108 TYR cc_start: 0.8904 (m-80) cc_final: 0.8539 (m-80) REVERT: D 139 ILE cc_start: 0.8097 (tp) cc_final: 0.7808 (tp) REVERT: D 145 GLU cc_start: 0.7427 (pp20) cc_final: 0.6908 (pp20) REVERT: E 93 GLU cc_start: 0.7606 (pp20) cc_final: 0.6840 (mp0) REVERT: F 100 GLU cc_start: 0.7415 (pm20) cc_final: 0.7170 (pm20) REVERT: F 130 ARG cc_start: 0.7775 (ptm-80) cc_final: 0.7468 (ptm-80) outliers start: 66 outliers final: 57 residues processed: 274 average time/residue: 0.1514 time to fit residues: 68.5113 Evaluate side-chains 276 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 215 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 1413 GLU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 642 TRP Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1339 MET Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 152 TYR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 203 CYS Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 109 CYS Chi-restraints excluded: chain F residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 242 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 286 optimal weight: 3.9990 chunk 228 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 316 optimal weight: 0.0030 chunk 166 optimal weight: 7.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1334 HIS E 171 HIS ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.196310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3642 r_free = 0.3642 target = 0.129402 restraints weight = 31592.684| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 3.57 r_work: 0.3295 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24469 Z= 0.129 Angle : 0.603 17.248 33289 Z= 0.303 Chirality : 0.042 0.211 3754 Planarity : 0.006 0.081 4402 Dihedral : 5.352 55.524 3519 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.78 % Allowed : 19.77 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.15), residues: 3181 helix: -0.30 (0.17), residues: 973 sheet: -1.21 (0.20), residues: 632 loop : -1.29 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 221 TYR 0.014 0.001 TYR D 162 PHE 0.016 0.002 PHE A 785 TRP 0.053 0.002 TRP A1125 HIS 0.006 0.001 HIS A1334 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (24460) covalent geometry : angle 0.60292 / 0.30 (33273) SS BOND : bond 0.00187 / 0.10 ( 8) SS BOND : angle 0.50109 / 0.31 ( 16) hydrogen bonds : bond 0.02858 / 1.93 ( 793) hydrogen bonds : angle 5.16103 / 3.57 ( 2187) Misc. bond : bond 0.00001 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7120.59 seconds wall clock time: 122 minutes 46.19 seconds (7366.19 seconds total)