Starting phenix.real_space_refine on Sat Jul 4 22:56:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m7i_23714/07_2026/7m7i_23714.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m7i_23714/07_2026/7m7i_23714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m7i_23714/07_2026/7m7i_23714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m7i_23714/07_2026/7m7i_23714.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m7i_23714/07_2026/7m7i_23714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m7i_23714/07_2026/7m7i_23714.map" } resolution = 3.4 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= 0.010 sd= 0.123 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 14957 2.51 5 N 4299 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 10 residue(s): 0.03s 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: 23965 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 7411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7411 Classifications: {'peptide': 999} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 57, 'TRANS': 941} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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': 1, 'PTRANS': 13, '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: 4.49, per 1000 atoms: 0.19 Number of scatterers: 23965 At special positions: 0 Unit cell: (108, 180, 161, 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 4299 7.00 C 14957 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.03 Simple disulfide: pdb=" SG CYS F 39 " - pdb=" SG CYS F 109 " distance=2.03 Simple disulfide: pdb=" SG CYS F 156 " - pdb=" SG CYS F 216 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 1.2 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 34 sheets defined 31.9% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'B' and resid 8 through 32 removed outlier: 3.914A pdb=" N ARG B 15 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 25 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 59 Processing helix chain 'B' and resid 112 through 119 Processing helix chain 'B' and resid 120 through 137 removed outlier: 3.616A pdb=" N LEU B 127 " --> pdb=" O GLN B 123 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 179 Processing helix chain 'B' and resid 182 through 192 removed outlier: 3.795A pdb=" N GLY B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 5.538A 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 220 Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.502A pdb=" N SER B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET B 247 " --> pdb=" O ASP B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 286 Processing helix chain 'B' and resid 312 through 328 removed outlier: 3.503A pdb=" N GLN B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 359 removed outlier: 3.566A pdb=" N ILE B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 removed outlier: 4.239A 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 385 through 398 Processing helix chain 'B' and resid 481 through 499 removed outlier: 3.567A pdb=" N ALA B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 490 " --> pdb=" O ARG B 486 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 492 " --> pdb=" O GLN B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 513 Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.593A pdb=" N LEU B 533 " --> pdb=" O GLU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 540 Processing helix chain 'B' and resid 572 through 580 removed outlier: 3.959A pdb=" N LEU B 576 " --> pdb=" O MET B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 595 Processing helix chain 'B' and resid 601 through 607 removed outlier: 4.190A pdb=" N PHE B 605 " --> pdb=" O GLU B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 616 removed outlier: 3.632A pdb=" N ASP B 616 " --> pdb=" O ARG B 612 " (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: 3.880A pdb=" N ALA B 661 " --> pdb=" O GLN B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 684 Processing helix chain 'B' and resid 700 through 708 removed outlier: 4.384A pdb=" N ALA B 706 " --> pdb=" O GLY B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 740 removed outlier: 3.896A pdb=" N VAL B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) 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 823 Processing helix chain 'B' and resid 837 through 847 removed outlier: 3.903A pdb=" N ILE B 841 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 3.789A 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: 3.604A pdb=" N VAL B 887 " --> pdb=" O ASP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 1409 through 1428 removed outlier: 3.844A 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 29 removed outlier: 3.525A pdb=" N ARG A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 114 through 119 removed outlier: 3.656A pdb=" N ALA A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 136 removed outlier: 4.048A pdb=" N MET A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 181 through 192 removed outlier: 4.160A pdb=" N SER A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.642A 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 222 removed outlier: 3.600A pdb=" N ARG A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 247 Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 315 through 327 removed outlier: 3.636A pdb=" N LEU A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 354 Processing helix chain 'A' and resid 371 through 377 removed outlier: 4.298A pdb=" N ASN A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 386 through 394 removed outlier: 3.996A pdb=" N VAL A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 498 removed outlier: 4.051A pdb=" N ARG A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ALA A 493 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 510 Processing helix chain 'A' and resid 528 through 541 removed outlier: 3.542A pdb=" N ARG A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 removed outlier: 3.718A pdb=" N SER A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 595 removed outlier: 3.839A pdb=" N ALA A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 586 " --> pdb=" O VAL A 582 " (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 601 through 608 removed outlier: 4.055A pdb=" N PHE A 605 " --> pdb=" O GLU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 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: 3.833A pdb=" N ALA A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 686 Processing helix chain 'A' and resid 700 through 708 removed outlier: 3.709A pdb=" N VAL A 704 " --> pdb=" O PRO A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 742 Processing helix chain 'A' and resid 757 through 762 removed outlier: 3.630A pdb=" N GLU A 761 " --> pdb=" O SER A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 809 removed outlier: 3.504A pdb=" N TRP A 803 " --> pdb=" O ASP A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 823 Processing helix chain 'A' and resid 836 through 845 removed outlier: 3.908A pdb=" N ALA A 840 " --> pdb=" O ILE A 836 " (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: 3.941A pdb=" N VAL A 887 " --> pdb=" O ASP A 883 " (cutoff:3.500A) removed outlier: 3.751A 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 922 through 928 Processing helix chain 'A' and resid 959 through 971 removed outlier: 3.824A pdb=" N THR A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 968 " --> pdb=" O ALA A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 998 Processing helix chain 'A' and resid 1017 through 1020 Processing helix chain 'A' and resid 1021 through 1038 Processing helix chain 'A' and resid 1063 through 1075 removed outlier: 4.076A pdb=" N LEU A1067 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP A1068 " --> pdb=" O HIS A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1106 removed outlier: 3.606A pdb=" N ALA A1097 " --> pdb=" O VAL A1093 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ALA A1101 " --> pdb=" O ALA A1097 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ALA A1102 " --> pdb=" O ARG A1098 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER A1105 " --> pdb=" O ALA A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1164 removed outlier: 4.042A 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 1215 Processing helix chain 'A' and resid 1235 through 1239 removed outlier: 3.547A pdb=" N THR A1238 " --> pdb=" O THR A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1248 Processing helix chain 'A' and resid 1248 through 1263 removed outlier: 3.654A pdb=" N VAL A1252 " --> pdb=" O SER A1248 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A1254 " --> pdb=" O ALA A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1305 removed outlier: 4.280A pdb=" N GLY A1291 " --> pdb=" O GLY A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1332 Processing helix chain 'A' and resid 1340 through 1355 removed outlier: 4.466A pdb=" N ARG A1346 " --> pdb=" O GLU A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1374 removed outlier: 4.814A pdb=" N LEU A1371 " --> pdb=" O ASP A1367 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A1372 " --> pdb=" O ARG A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1385 through 1389 removed outlier: 3.815A pdb=" N ARG A1389 " --> pdb=" O ASP A1386 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'D' and resid 205 through 209 removed outlier: 3.597A pdb=" N TYR D 208 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'E' and resid 66 through 69 Processing helix chain 'E' and resid 91 through 95 removed outlier: 3.784A pdb=" N THR E 95 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 209 removed outlier: 3.599A pdb=" N TYR F 208 " --> pdb=" O LYS F 205 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 334 through 338 removed outlier: 7.585A pdb=" N GLY B 439 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL B 337 " --> pdb=" O GLY B 439 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N SER B 441 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B 296 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU B 455 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU B 294 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA B 292 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU B 276 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N MET B 40 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N MET B 274 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS B 42 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA B 272 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLY B 150 " --> pdb=" O MET B 228 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N GLY B 230 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N PHE B 152 " --> pdb=" O GLY B 230 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL B 232 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLY B 154 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE B 199 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL B 151 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL B 201 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL B 153 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 200 " --> pdb=" O ASP B 202 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLU A 278 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL A 37 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 292 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LEU A 294 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU A 455 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY A 296 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG A 437 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 336 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASP A 335 " --> pdb=" O HIS A 368 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N GLY A 370 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL A 337 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 5.795A 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: 5.772A 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: 3.606A pdb=" N PHE B 524 " --> pdb=" O TRP B 475 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 649 through 654 removed outlier: 6.241A pdb=" N ALA B 558 " --> pdb=" O PRO B 649 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA B 651 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 828 " --> pdb=" O SER B 853 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 713 through 719 removed outlier: 6.554A pdb=" N VAL B 724 " --> pdb=" O ALA B 715 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL B 717 " --> pdb=" O SER B 722 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N SER B 722 " --> pdb=" O VAL B 717 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 725 " --> pdb=" O ALA B 695 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 784 through 786 removed outlier: 4.959A pdb=" N PHE B 784 " --> pdb=" O THR B 793 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 793 " --> pdb=" O PHE B 784 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AB1, first strand: chain 'A' and resid 478 through 479 Processing sheet with id=AB2, first strand: chain 'A' and resid 649 through 654 removed outlier: 6.570A pdb=" N ALA A 558 " --> pdb=" O PRO A 649 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 651 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL A 559 " --> pdb=" O LEU A 829 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 692 through 697 removed outlier: 3.545A pdb=" N GLY A 727 " --> pdb=" O GLY A 693 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER A 722 " --> pdb=" O ASN A 718 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ALA A 726 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ILE A 714 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASP A 728 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL A 712 " --> pdb=" O ASP A 728 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 978 through 980 removed outlier: 6.069A pdb=" N LEU A 950 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A1006 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA A 952 " --> pdb=" O LEU A1006 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA A1008 " --> pdb=" O ALA A 952 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL A1003 " --> pdb=" O TRP A1044 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL A1046 " --> pdb=" O VAL A1003 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER A1005 " --> pdb=" O VAL A1046 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N GLU A1048 " --> pdb=" O SER A1005 " (cutoff:3.500A) removed outlier: 11.040A pdb=" N LEU A1007 " --> pdb=" O GLU A1048 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU A1043 " --> pdb=" O GLY A1084 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL A1086 " --> pdb=" O LEU A1043 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N THR A1045 " --> pdb=" O VAL A1086 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL A1088 " --> pdb=" O THR A1045 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N THR A1047 " --> pdb=" O VAL A1088 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU A1085 " --> pdb=" O LEU A1113 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU A1115 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASP A1087 " --> pdb=" O LEU A1115 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLN A1112 " --> pdb=" O ARG A1123 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG A1123 " --> pdb=" O GLN A1112 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N SER A1274 " --> pdb=" O TRP A1314 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1142 through 1143 removed outlier: 6.462A pdb=" N VAL A1143 " --> pdb=" O LEU A1169 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A1171 " --> pdb=" O VAL A1143 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1145 through 1146 removed outlier: 7.033A pdb=" N PHE A1225 " --> pdb=" O THR A1146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 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 13 through 14 removed outlier: 3.858A pdb=" N VAL C 14 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 97 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP C 38 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC1, first strand: chain 'C' and resid 159 through 161 removed outlier: 3.949A pdb=" N SER C 160 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN C 204 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TYR C 201 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 176 through 177 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: 6.589A pdb=" N TRP D 56 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N TYR D 70 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU D 54 " --> pdb=" O TYR D 70 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 136 through 140 removed outlier: 3.858A pdb=" N VAL D 154 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 201 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS D 156 " --> pdb=" O SER D 199 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER D 199 " --> pdb=" O CYS D 156 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N TYR D 195 " --> pdb=" O ASN D 160 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 168 through 170 removed outlier: 3.577A 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 removed outlier: 3.858A pdb=" N VAL E 14 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP E 38 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 130 through 131 removed outlier: 3.753A pdb=" N VAL E 188 " --> pdb=" O HIS E 171 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS E 171 " --> pdb=" O VAL E 188 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 159 through 161 removed outlier: 3.951A pdb=" N SER E 160 " --> pdb=" O ASN E 204 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN E 204 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR E 201 " --> pdb=" O VAL E 218 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 176 through 177 Processing sheet with id=AD4, first strand: chain 'F' and resid 21 through 22 Processing sheet with id=AD5, first strand: chain 'F' and resid 28 through 29 removed outlier: 3.761A pdb=" N GLY F 105 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU F 58 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LEU F 67 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 136 through 140 removed outlier: 3.889A pdb=" N VAL F 154 " --> pdb=" O LEU F 201 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU F 201 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N CYS F 156 " --> pdb=" O SER F 199 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER F 199 " --> pdb=" O CYS F 156 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N TYR F 195 " --> pdb=" O ASN F 160 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 168 through 170 removed outlier: 3.577A pdb=" N GLU F 217 " --> pdb=" O GLN F 169 " (cutoff:3.500A) 875 hydrogen bonds defined for protein. 2427 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: 5.99 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 15 1.20 - 1.35: 8229 1.35 - 1.51: 6470 1.51 - 1.66: 9604 1.66 - 1.81: 136 Bond restraints: 24454 Sorted by residual: bond pdb=" CG PRO B 519 " pdb=" CD PRO B 519 " ideal model delta sigma weight residual 1.503 1.040 0.463 3.40e-02 8.65e+02 1.85e+02 bond pdb=" CA SER B1449 " pdb=" CB SER B1449 " ideal model delta sigma weight residual 1.530 1.416 0.114 1.69e-02 3.50e+03 4.57e+01 bond pdb=" CA SER C 187 " pdb=" CB SER C 187 " ideal model delta sigma weight residual 1.530 1.438 0.092 1.55e-02 4.16e+03 3.52e+01 bond pdb=" N PRO B 519 " pdb=" CD PRO B 519 " ideal model delta sigma weight residual 1.473 1.543 -0.070 1.40e-02 5.10e+03 2.48e+01 bond pdb=" C LYS B 8 " pdb=" O LYS B 8 " ideal model delta sigma weight residual 1.235 1.164 0.071 1.43e-02 4.89e+03 2.46e+01 ... (remaining 24449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.49: 33161 5.49 - 10.97: 93 10.97 - 16.46: 7 16.46 - 21.95: 2 21.95 - 27.43: 3 Bond angle restraints: 33266 Sorted by residual: angle pdb=" N PRO B 519 " pdb=" CD PRO B 519 " pdb=" CG PRO B 519 " ideal model delta sigma weight residual 103.20 75.84 27.36 1.50e+00 4.44e-01 3.33e+02 angle pdb=" C THR A 233 " pdb=" CA THR A 233 " pdb=" CB THR A 233 " ideal model delta sigma weight residual 110.62 83.19 27.43 1.51e+00 4.39e-01 3.30e+02 angle pdb=" CA PRO B 519 " pdb=" CB PRO B 519 " pdb=" CG PRO B 519 " ideal model delta sigma weight residual 104.50 82.91 21.59 1.90e+00 2.77e-01 1.29e+02 angle pdb=" C ARG A 221 " pdb=" CA ARG A 221 " pdb=" CB ARG A 221 " ideal model delta sigma weight residual 110.86 92.93 17.93 1.65e+00 3.67e-01 1.18e+02 angle pdb=" CA PRO B 519 " pdb=" N PRO B 519 " pdb=" CD PRO B 519 " ideal model delta sigma weight residual 112.00 99.75 12.25 1.40e+00 5.10e-01 7.65e+01 ... (remaining 33261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13001 17.99 - 35.98: 1156 35.98 - 53.97: 332 53.97 - 71.96: 114 71.96 - 89.95: 26 Dihedral angle restraints: 14629 sinusoidal: 5561 harmonic: 9068 Sorted by residual: dihedral pdb=" CA THR D 115 " pdb=" C THR D 115 " pdb=" N PRO D 116 " pdb=" CA PRO D 116 " ideal model delta harmonic sigma weight residual 180.00 92.67 87.33 0 5.00e+00 4.00e-02 3.05e+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 92.70 87.30 0 5.00e+00 4.00e-02 3.05e+02 dihedral pdb=" C THR A 233 " pdb=" N THR A 233 " pdb=" CA THR A 233 " pdb=" CB THR A 233 " ideal model delta harmonic sigma weight residual -122.00 -88.31 -33.69 0 2.50e+00 1.60e-01 1.82e+02 ... (remaining 14626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 3351 0.091 - 0.182: 338 0.182 - 0.273: 52 0.273 - 0.364: 8 0.364 - 0.455: 5 Chirality restraints: 3754 Sorted by residual: chirality pdb=" CA THR A1310 " pdb=" N THR A1310 " pdb=" C THR A1310 " pdb=" CB THR A1310 " both_signs ideal model delta sigma weight residual False 2.53 2.98 -0.46 2.00e-01 2.50e+01 5.18e+00 chirality pdb=" CA ARG A 221 " pdb=" N ARG A 221 " pdb=" C ARG A 221 " pdb=" CB ARG A 221 " both_signs ideal model delta sigma weight residual False 2.51 2.94 -0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" CA THR E 101 " pdb=" N THR E 101 " pdb=" C THR E 101 " pdb=" CB THR E 101 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 3751 not shown) Planarity restraints: 4401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 30 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C LEU B 30 " -0.060 2.00e-02 2.50e+03 pdb=" O LEU B 30 " 0.022 2.00e-02 2.50e+03 pdb=" N GLU B 31 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 28 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.26e+00 pdb=" C ARG A 28 " 0.050 2.00e-02 2.50e+03 pdb=" O ARG A 28 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU A 29 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 85 " -0.015 2.00e-02 2.50e+03 2.85e-02 8.11e+00 pdb=" C LEU E 85 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU E 85 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN E 86 " -0.017 2.00e-02 2.50e+03 ... (remaining 4398 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 382 2.64 - 3.20: 21694 3.20 - 3.77: 39702 3.77 - 4.33: 55327 4.33 - 4.90: 88378 Nonbonded interactions: 205483 Sorted by model distance: nonbonded pdb=" O THR A 233 " pdb=" CB THR A 233 " model vdw 2.073 2.776 nonbonded pdb=" OG1 THR B 181 " pdb=" OD2 ASP A 202 " model vdw 2.135 3.040 nonbonded pdb=" OG SER B 182 " pdb=" OD1 ASP A 202 " model vdw 2.137 3.040 nonbonded pdb=" O LEU A 175 " pdb=" OG1 THR A 179 " model vdw 2.168 3.040 nonbonded pdb=" OG SER C 9 " pdb=" OG SER C 23 " model vdw 2.178 3.040 ... (remaining 205478 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.890 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: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.830 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 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 : 0.007 0.463 24463 Z= 0.419 Angle : 1.035 27.433 33282 Z= 0.673 Chirality : 0.060 0.455 3754 Planarity : 0.006 0.064 4401 Dihedral : 16.301 89.947 8799 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.29 % Favored : 93.62 % Rotamer: Outliers : 6.90 % Allowed : 2.79 % Favored : 90.31 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 2.21 % Twisted General : 0.03 % 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: -2.63 (0.14), residues: 3181 helix: -1.54 (0.17), residues: 896 sheet: -1.37 (0.21), residues: 588 loop : -1.99 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 24 TYR 0.023 0.002 TYR C 84 PHE 0.022 0.002 PHE C 52 TRP 0.016 0.002 TRP A 569 HIS 0.005 0.001 HIS A1226 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.41 (24454) covalent geometry : angle 1.03511 / 0.67 (33266) SS BOND : bond 0.00286 / 0.15 ( 8) SS BOND : angle 1.06796 / 0.65 ( 16) hydrogen bonds : bond 0.18341 / 12.51 ( 875) hydrogen bonds : angle 8.28926 / 5.59 ( 2427) Misc. bond : bond 0.09331 / 4.91 ( 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 656 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 485 time to evaluate : 0.798 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 THR cc_start: 0.7918 (OUTLIER) cc_final: 0.7676 (p) REVERT: B 344 THR cc_start: 0.4693 (OUTLIER) cc_final: 0.3121 (m) REVERT: B 831 VAL cc_start: 0.6713 (m) cc_final: 0.6507 (m) REVERT: B 858 LEU cc_start: 0.6839 (mt) cc_final: 0.6635 (mt) REVERT: A 43 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7870 (mmt-90) REVERT: A 1240 THR cc_start: 0.6556 (OUTLIER) cc_final: 0.6248 (p) REVERT: D 84 SER cc_start: 0.7232 (t) cc_final: 0.6927 (p) REVERT: D 187 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6885 (tp30) REVERT: E 36 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7321 (mmt) REVERT: E 74 ILE cc_start: 0.7306 (mt) cc_final: 0.7012 (tp) REVERT: E 93 GLU cc_start: 0.8084 (mp0) cc_final: 0.7681 (mp0) REVERT: F 70 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7561 (p90) REVERT: F 99 VAL cc_start: 0.7949 (OUTLIER) cc_final: 0.7560 (t) REVERT: F 114 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8239 (mp10) REVERT: F 157 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.7021 (tt) outliers start: 171 outliers final: 26 residues processed: 612 average time/residue: 0.1918 time to fit residues: 170.0075 Evaluate side-chains 247 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 612 ARG Chi-restraints excluded: chain B residue 1435 ARG Chi-restraints excluded: chain B residue 1436 VAL Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1245 GLU Chi-restraints excluded: chain A residue 1249 ARG Chi-restraints excluded: chain A residue 1302 ARG Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 82 ARG Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 82 ARG Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 157 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.0470 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B1423 HIS A 122 GLN A 123 GLN A 158 GLN A 322 GLN ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 171 HIS E 41 GLN E 171 HIS F 66 GLN F 146 GLN F 182 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.145498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.111051 restraints weight = 63483.019| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 4.47 r_work: 0.3654 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24463 Z= 0.165 Angle : 0.691 7.421 33282 Z= 0.353 Chirality : 0.044 0.248 3754 Planarity : 0.006 0.059 4401 Dihedral : 7.253 61.312 3591 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.87 % Allowed : 11.14 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 2.21 % Twisted General : 0.03 % 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: -2.29 (0.14), residues: 3181 helix: -1.04 (0.16), residues: 913 sheet: -1.31 (0.21), residues: 593 loop : -1.86 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 163 TYR 0.025 0.002 TYR A 359 PHE 0.022 0.002 PHE B 813 TRP 0.025 0.002 TRP C 161 HIS 0.007 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (24454) covalent geometry : angle 0.69070 / 0.35 (33266) SS BOND : bond 0.00282 / 0.16 ( 8) SS BOND : angle 0.59714 / 0.34 ( 16) hydrogen bonds : bond 0.04082 / 2.70 ( 875) hydrogen bonds : angle 6.21166 / 4.20 ( 2427) Misc. bond : bond 0.00728 / 0.38 ( 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 301 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 230 time to evaluate : 0.719 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: B 40 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7177 (mtp) REVERT: B 268 MET cc_start: 0.8015 (tpp) cc_final: 0.7698 (tpp) REVERT: B 609 GLU cc_start: 0.6078 (OUTLIER) cc_final: 0.5762 (tm-30) REVERT: B 1444 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6669 (tp30) REVERT: A 1322 MET cc_start: 0.6743 (tmm) cc_final: 0.6503 (tpt) REVERT: C 45 LYS cc_start: 0.5700 (OUTLIER) cc_final: 0.5445 (pptt) REVERT: C 155 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7511 (mm-30) REVERT: E 36 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7225 (mmt) REVERT: E 48 GLU cc_start: 0.7443 (tm-30) cc_final: 0.6884 (tm-30) REVERT: E 93 GLU cc_start: 0.8515 (mp0) cc_final: 0.8282 (mp0) REVERT: E 151 ASP cc_start: 0.6528 (t0) cc_final: 0.6299 (t0) outliers start: 71 outliers final: 36 residues processed: 281 average time/residue: 0.1505 time to fit residues: 66.6232 Evaluate side-chains 213 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 785 PHE Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 911 GLU Chi-restraints excluded: chain B residue 1436 VAL Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 82 ARG Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 82 ARG Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 231 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 313 optimal weight: 0.8980 chunk 290 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 174 optimal weight: 20.0000 chunk 110 optimal weight: 0.0070 chunk 235 optimal weight: 10.0000 chunk 314 optimal weight: 7.9990 overall best weight: 1.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 GLN ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN E 5 GLN E 8 GLN E 41 GLN F 66 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.147090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.102995 restraints weight = 62353.769| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 3.92 r_work: 0.3545 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24463 Z= 0.179 Angle : 0.646 10.551 33282 Z= 0.327 Chirality : 0.043 0.167 3754 Planarity : 0.005 0.060 4401 Dihedral : 5.843 59.684 3530 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.99 % Allowed : 13.65 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 2.21 % Twisted General : 0.03 % 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: -2.02 (0.14), residues: 3181 helix: -0.67 (0.17), residues: 932 sheet: -1.26 (0.20), residues: 613 loop : -1.75 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 15 TYR 0.028 0.002 TYR C 183 PHE 0.018 0.002 PHE B 813 TRP 0.022 0.002 TRP B 429 HIS 0.007 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (24454) covalent geometry : angle 0.64578 / 0.33 (33266) SS BOND : bond 0.00298 / 0.14 ( 8) SS BOND : angle 0.58618 / 0.34 ( 16) hydrogen bonds : bond 0.03592 / 2.37 ( 875) hydrogen bonds : angle 5.64434 / 3.82 ( 2427) Misc. bond : bond 0.00096 / 0.05 ( 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 250 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 176 time to evaluate : 0.833 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: B 40 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.6853 (mpp) REVERT: B 274 MET cc_start: 0.8817 (tpt) cc_final: 0.8376 (tpt) REVERT: B 583 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.6538 (m-80) REVERT: B 609 GLU cc_start: 0.5963 (OUTLIER) cc_final: 0.5735 (tm-30) REVERT: B 641 MET cc_start: 0.8596 (ttm) cc_final: 0.8308 (ttm) REVERT: B 825 TYR cc_start: 0.7708 (m-10) cc_final: 0.7507 (m-10) REVERT: B 1444 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6692 (tp30) REVERT: E 48 GLU cc_start: 0.7461 (tm-30) cc_final: 0.6940 (tm-30) REVERT: E 78 ASP cc_start: 0.6882 (m-30) cc_final: 0.6558 (t0) REVERT: E 93 GLU cc_start: 0.8598 (mp0) cc_final: 0.8334 (mp0) REVERT: E 109 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.7544 (m-80) REVERT: E 151 ASP cc_start: 0.6576 (t0) cc_final: 0.6339 (t0) REVERT: F 164 ARG cc_start: 0.8277 (ptm160) cc_final: 0.7931 (ptp-170) outliers start: 74 outliers final: 36 residues processed: 230 average time/residue: 0.1515 time to fit residues: 55.8809 Evaluate side-chains 193 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 1436 VAL Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain B residue 1463 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 82 ARG Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 231 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 253 optimal weight: 9.9990 chunk 310 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 227 optimal weight: 3.9990 chunk 292 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 chunk 156 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN A 565 GLN A 657 GLN ** A 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 GLN C 112 GLN D 74 ASN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.144283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.102417 restraints weight = 62221.947| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 4.11 r_work: 0.3474 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 24463 Z= 0.198 Angle : 0.636 8.505 33282 Z= 0.322 Chirality : 0.043 0.181 3754 Planarity : 0.005 0.055 4401 Dihedral : 5.537 58.865 3519 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.42 % Allowed : 15.14 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 2.21 % 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: -1.79 (0.15), residues: 3181 helix: -0.39 (0.17), residues: 938 sheet: -1.27 (0.20), residues: 606 loop : -1.61 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 82 TYR 0.028 0.002 TYR C 183 PHE 0.017 0.002 PHE A 781 TRP 0.020 0.001 TRP B 429 HIS 0.005 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (24454) covalent geometry : angle 0.63553 / 0.32 (33266) SS BOND : bond 0.00244 / 0.10 ( 8) SS BOND : angle 0.70091 / 0.38 ( 16) hydrogen bonds : bond 0.03381 / 2.23 ( 875) hydrogen bonds : angle 5.39250 / 3.64 ( 2427) Misc. bond : bond 0.00053 / 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 225 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 165 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 274 MET cc_start: 0.8632 (tpt) cc_final: 0.8251 (tpt) REVERT: B 477 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8623 (pp) REVERT: B 583 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6902 (m-80) REVERT: B 1444 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6830 (tp30) REVERT: A 631 MET cc_start: 0.4438 (mmm) cc_final: 0.4209 (mtp) REVERT: D 81 ASP cc_start: 0.8122 (p0) cc_final: 0.7690 (t0) REVERT: D 100 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7925 (mp0) REVERT: D 201 LEU cc_start: 0.8291 (tp) cc_final: 0.7866 (tp) REVERT: E 36 MET cc_start: 0.8236 (mmt) cc_final: 0.8018 (mmt) REVERT: E 48 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7039 (tm-30) REVERT: E 71 ARG cc_start: 0.5232 (OUTLIER) cc_final: 0.4915 (ptm160) REVERT: E 109 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7901 (t80) REVERT: E 151 ASP cc_start: 0.6622 (t0) cc_final: 0.6377 (t0) REVERT: E 155 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7188 (tp30) REVERT: F 164 ARG cc_start: 0.8276 (ptm160) cc_final: 0.7801 (ptp90) outliers start: 60 outliers final: 36 residues processed: 211 average time/residue: 0.1614 time to fit residues: 54.8895 Evaluate side-chains 193 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 1436 VAL Chi-restraints excluded: chain B residue 1463 THR Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 231 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 287 optimal weight: 0.9990 chunk 234 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 77 optimal weight: 20.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 217 GLN B 556 GLN ** A 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 207 HIS F 74 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.138629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.098398 restraints weight = 62389.729| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.50 r_work: 0.3510 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24463 Z= 0.154 Angle : 0.599 9.178 33282 Z= 0.302 Chirality : 0.042 0.169 3754 Planarity : 0.005 0.056 4401 Dihedral : 5.266 55.581 3510 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.95 % Allowed : 15.26 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 2.21 % 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: -0.27 (0.17), residues: 945 sheet: -1.30 (0.20), residues: 604 loop : -1.56 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1412 TYR 0.017 0.002 TYR F 162 PHE 0.015 0.001 PHE B 266 TRP 0.018 0.001 TRP A1159 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (24454) covalent geometry : angle 0.59945 / 0.30 (33266) SS BOND : bond 0.00220 / 0.09 ( 8) SS BOND : angle 0.59563 / 0.33 ( 16) hydrogen bonds : bond 0.03180 / 2.11 ( 875) hydrogen bonds : angle 5.21159 / 3.52 ( 2427) Misc. bond : bond 0.00069 / 0.04 ( 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 232 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 159 time to evaluate : 0.855 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: B 274 MET cc_start: 0.8684 (tpt) cc_final: 0.8213 (tpt) REVERT: B 357 GLU cc_start: 0.8732 (tp30) cc_final: 0.8515 (tp30) REVERT: B 477 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8632 (pp) REVERT: B 1444 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6801 (tp30) REVERT: A 1028 LEU cc_start: 0.8376 (mt) cc_final: 0.8117 (tp) REVERT: A 1034 MET cc_start: 0.5328 (OUTLIER) cc_final: 0.4361 (mpp) REVERT: A 1322 MET cc_start: 0.5997 (tpt) cc_final: 0.5738 (tpt) REVERT: C 201 TYR cc_start: 0.7138 (OUTLIER) cc_final: 0.5782 (m-80) REVERT: D 81 ASP cc_start: 0.8001 (p0) cc_final: 0.7763 (t0) REVERT: D 100 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7965 (mp0) REVERT: D 167 LYS cc_start: 0.8446 (tttt) cc_final: 0.8159 (tppt) REVERT: D 201 LEU cc_start: 0.8268 (tp) cc_final: 0.7826 (tp) REVERT: E 5 GLN cc_start: 0.7998 (mp-120) cc_final: 0.7664 (mp10) REVERT: E 48 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7013 (tm-30) REVERT: E 71 ARG cc_start: 0.5249 (OUTLIER) cc_final: 0.4852 (ptm160) REVERT: E 76 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6698 (ptm160) REVERT: E 109 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7762 (t80) REVERT: E 151 ASP cc_start: 0.6496 (t0) cc_final: 0.6256 (t0) REVERT: E 155 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7064 (tp30) REVERT: F 114 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8650 (mp10) REVERT: F 164 ARG cc_start: 0.8032 (ptm160) cc_final: 0.7647 (ptp90) outliers start: 73 outliers final: 46 residues processed: 217 average time/residue: 0.1451 time to fit residues: 50.9198 Evaluate side-chains 205 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 152 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 1436 VAL Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain B residue 1463 THR Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 231 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 271 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 chunk 173 optimal weight: 0.9990 chunk 316 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 317 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 HIS A 248 ASN ** A 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.139311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.099462 restraints weight = 62697.910| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 3.53 r_work: 0.3437 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24463 Z= 0.132 Angle : 0.576 9.235 33282 Z= 0.291 Chirality : 0.042 0.164 3754 Planarity : 0.005 0.051 4401 Dihedral : 5.123 52.524 3510 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.58 % Allowed : 16.35 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 2.21 % 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: -1.58 (0.15), residues: 3181 helix: -0.19 (0.17), residues: 959 sheet: -1.19 (0.20), residues: 599 loop : -1.49 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 117 TYR 0.023 0.001 TYR B 825 PHE 0.014 0.001 PHE B 266 TRP 0.016 0.001 TRP A 642 HIS 0.004 0.001 HIS A1334 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (24454) covalent geometry : angle 0.57633 / 0.29 (33266) SS BOND : bond 0.00201 / 0.08 ( 8) SS BOND : angle 0.55197 / 0.31 ( 16) hydrogen bonds : bond 0.03023 / 2.01 ( 875) hydrogen bonds : angle 5.09490 / 3.45 ( 2427) Misc. bond : bond 0.00048 / 0.03 ( 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 226 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 162 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 MET cc_start: 0.8716 (mmm) cc_final: 0.8310 (tpt) REVERT: B 274 MET cc_start: 0.8737 (tpt) cc_final: 0.8216 (tpt) REVERT: B 357 GLU cc_start: 0.8908 (tp30) cc_final: 0.8618 (tp30) REVERT: B 477 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8577 (pp) REVERT: B 1444 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6706 (tp30) REVERT: A 631 MET cc_start: 0.4041 (mmm) cc_final: 0.3732 (ttt) REVERT: A 1028 LEU cc_start: 0.8406 (mt) cc_final: 0.8130 (tp) REVERT: A 1034 MET cc_start: 0.5415 (OUTLIER) cc_final: 0.4605 (mpp) REVERT: A 1322 MET cc_start: 0.6104 (tpt) cc_final: 0.5474 (tpt) REVERT: C 84 TYR cc_start: 0.7196 (m-80) cc_final: 0.6900 (m-10) REVERT: D 81 ASP cc_start: 0.8161 (p0) cc_final: 0.7789 (t0) REVERT: D 100 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7778 (mp0) REVERT: D 167 LYS cc_start: 0.8574 (tttt) cc_final: 0.8174 (tppt) REVERT: D 201 LEU cc_start: 0.8234 (tp) cc_final: 0.7804 (tp) REVERT: E 48 GLU cc_start: 0.7592 (tm-30) cc_final: 0.6936 (tm-30) REVERT: E 71 ARG cc_start: 0.5398 (OUTLIER) cc_final: 0.4942 (ptm160) REVERT: E 109 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: E 151 ASP cc_start: 0.6665 (t0) cc_final: 0.6402 (t0) REVERT: F 164 ARG cc_start: 0.8270 (ptm160) cc_final: 0.7870 (ptp90) outliers start: 64 outliers final: 44 residues processed: 212 average time/residue: 0.1480 time to fit residues: 50.7299 Evaluate side-chains 200 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 1436 VAL Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain B residue 1463 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 148 LYS Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 231 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 72 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 239 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 chunk 206 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 315 optimal weight: 5.9990 chunk 221 optimal weight: 8.9990 chunk 16 optimal weight: 0.0270 chunk 58 optimal weight: 6.9990 overall best weight: 2.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 904 GLN ** A 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 171 HIS F 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.136001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.095268 restraints weight = 61641.007| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.74 r_work: 0.3427 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 24463 Z= 0.266 Angle : 0.655 9.316 33282 Z= 0.331 Chirality : 0.044 0.179 3754 Planarity : 0.005 0.073 4401 Dihedral : 5.276 52.417 3510 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.62 % Allowed : 16.75 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 2.21 % 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: -1.55 (0.15), residues: 3181 helix: -0.13 (0.17), residues: 962 sheet: -1.30 (0.21), residues: 603 loop : -1.44 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 76 TYR 0.020 0.002 TYR C 109 PHE 0.023 0.002 PHE A1273 TRP 0.015 0.001 TRP A 55 HIS 0.011 0.001 HIS A 645 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.27 (24454) covalent geometry : angle 0.65520 / 0.33 (33266) SS BOND : bond 0.00307 / 0.13 ( 8) SS BOND : angle 0.64389 / 0.38 ( 16) hydrogen bonds : bond 0.03285 / 2.18 ( 875) hydrogen bonds : angle 5.14682 / 3.48 ( 2427) Misc. bond : bond 0.00042 / 0.02 ( 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 224 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 159 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8629 (mp) REVERT: B 274 MET cc_start: 0.8803 (tpt) cc_final: 0.8290 (tpt) REVERT: B 357 GLU cc_start: 0.8854 (tp30) cc_final: 0.8612 (tp30) REVERT: B 477 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8633 (pp) REVERT: A 631 MET cc_start: 0.4123 (mmm) cc_final: 0.3662 (ttt) REVERT: A 635 MET cc_start: 0.6366 (mmt) cc_final: 0.5472 (mmt) REVERT: A 1034 MET cc_start: 0.5473 (OUTLIER) cc_final: 0.4637 (mpp) REVERT: A 1322 MET cc_start: 0.5940 (tpt) cc_final: 0.5670 (tpt) REVERT: D 81 ASP cc_start: 0.8150 (p0) cc_final: 0.7865 (t0) REVERT: D 167 LYS cc_start: 0.8600 (tttt) cc_final: 0.8342 (tppt) REVERT: D 201 LEU cc_start: 0.8217 (tp) cc_final: 0.7765 (tp) REVERT: E 41 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: E 48 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7138 (tm-30) REVERT: E 71 ARG cc_start: 0.5883 (OUTLIER) cc_final: 0.5340 (ptm160) REVERT: E 109 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.8020 (t80) REVERT: E 151 ASP cc_start: 0.6527 (t0) cc_final: 0.6290 (t0) REVERT: F 114 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8623 (mp10) REVERT: F 164 ARG cc_start: 0.8123 (ptm160) cc_final: 0.7509 (ttp-170) outliers start: 65 outliers final: 44 residues processed: 211 average time/residue: 0.1493 time to fit residues: 51.0782 Evaluate side-chains 200 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 149 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 1436 VAL Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain B residue 1463 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 64 TYR Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 148 LYS Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 231 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 47 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 182 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 187 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 556 GLN B 904 GLN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 HIS ** A1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN F 66 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.143825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.100549 restraints weight = 62110.352| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 4.33 r_work: 0.3462 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24463 Z= 0.130 Angle : 0.581 9.868 33282 Z= 0.292 Chirality : 0.042 0.154 3754 Planarity : 0.005 0.056 4401 Dihedral : 5.138 50.927 3510 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.10 % Allowed : 17.16 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 2.21 % 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: -1.45 (0.15), residues: 3181 helix: -0.00 (0.17), residues: 965 sheet: -1.22 (0.21), residues: 589 loop : -1.42 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 117 TYR 0.017 0.001 TYR B 825 PHE 0.035 0.001 PHE B 784 TRP 0.017 0.001 TRP A 55 HIS 0.004 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (24454) covalent geometry : angle 0.58084 / 0.29 (33266) SS BOND : bond 0.00195 / 0.08 ( 8) SS BOND : angle 0.59045 / 0.33 ( 16) hydrogen bonds : bond 0.02935 / 1.94 ( 875) hydrogen bonds : angle 5.04456 / 3.42 ( 2427) Misc. bond : bond 0.00028 / 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 219 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 167 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8582 (mp) REVERT: B 240 MET cc_start: 0.8070 (tpp) cc_final: 0.7634 (tpp) REVERT: B 274 MET cc_start: 0.8796 (tpt) cc_final: 0.8365 (tpt) REVERT: B 357 GLU cc_start: 0.8821 (tp30) cc_final: 0.8587 (tp30) REVERT: B 477 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8647 (pp) REVERT: B 830 GLU cc_start: 0.5872 (mt-10) cc_final: 0.5601 (tt0) REVERT: A 274 MET cc_start: 0.8466 (mtm) cc_final: 0.8209 (mtp) REVERT: A 391 MET cc_start: 0.7986 (tpp) cc_final: 0.7768 (mmt) REVERT: A 631 MET cc_start: 0.4312 (mmm) cc_final: 0.3810 (ttt) REVERT: A 1034 MET cc_start: 0.5403 (OUTLIER) cc_final: 0.4555 (mpp) REVERT: A 1322 MET cc_start: 0.6012 (tpt) cc_final: 0.5703 (tpt) REVERT: C 84 TYR cc_start: 0.7153 (m-80) cc_final: 0.6896 (m-10) REVERT: D 81 ASP cc_start: 0.8133 (p0) cc_final: 0.7795 (t0) REVERT: D 100 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8245 (mp0) REVERT: D 103 ASP cc_start: 0.8500 (m-30) cc_final: 0.8216 (m-30) REVERT: D 117 ARG cc_start: 0.5099 (mmm160) cc_final: 0.4742 (mmm160) REVERT: D 167 LYS cc_start: 0.8526 (tttt) cc_final: 0.8225 (tppt) REVERT: D 201 LEU cc_start: 0.8203 (tp) cc_final: 0.7763 (tp) REVERT: E 48 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7152 (tm-30) REVERT: E 71 ARG cc_start: 0.5888 (OUTLIER) cc_final: 0.5161 (ptm160) REVERT: E 109 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.7793 (m-80) REVERT: E 151 ASP cc_start: 0.6649 (t0) cc_final: 0.6381 (t0) REVERT: F 164 ARG cc_start: 0.8293 (ptm160) cc_final: 0.7705 (ttp-110) outliers start: 52 outliers final: 40 residues processed: 210 average time/residue: 0.1473 time to fit residues: 49.7629 Evaluate side-chains 201 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 556 GLN Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain B residue 1463 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 148 LYS Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 231 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 316 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 171 optimal weight: 30.0000 chunk 87 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 185 optimal weight: 10.0000 chunk 264 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN F 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.142727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.099468 restraints weight = 61846.976| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 4.38 r_work: 0.3434 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24463 Z= 0.173 Angle : 0.608 10.643 33282 Z= 0.305 Chirality : 0.043 0.177 3754 Planarity : 0.005 0.056 4401 Dihedral : 5.119 50.613 3508 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.26 % Allowed : 17.40 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 2.21 % 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: -1.38 (0.15), residues: 3181 helix: 0.05 (0.17), residues: 969 sheet: -1.21 (0.21), residues: 617 loop : -1.35 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 117 TYR 0.020 0.002 TYR C 109 PHE 0.032 0.002 PHE B 784 TRP 0.016 0.001 TRP A 55 HIS 0.004 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (24454) covalent geometry : angle 0.60751 / 0.31 (33266) SS BOND : bond 0.00221 / 0.08 ( 8) SS BOND : angle 0.62126 / 0.34 ( 16) hydrogen bonds : bond 0.03016 / 1.99 ( 875) hydrogen bonds : angle 5.02781 / 3.41 ( 2427) Misc. bond : bond 0.00017 / 0.01 ( 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 214 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 158 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 MET cc_start: 0.8710 (mmm) cc_final: 0.8271 (tpt) REVERT: B 214 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8528 (mp) REVERT: B 274 MET cc_start: 0.8760 (tpt) cc_final: 0.8322 (tpt) REVERT: B 357 GLU cc_start: 0.8937 (tp30) cc_final: 0.8668 (tp30) REVERT: B 395 MET cc_start: 0.8657 (mtp) cc_final: 0.8360 (ttm) REVERT: B 477 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8656 (pp) REVERT: B 830 GLU cc_start: 0.5916 (mt-10) cc_final: 0.5578 (tt0) REVERT: A 391 MET cc_start: 0.8145 (tpp) cc_final: 0.7922 (mmt) REVERT: A 631 MET cc_start: 0.4233 (mmm) cc_final: 0.3753 (ttt) REVERT: A 1034 MET cc_start: 0.5357 (OUTLIER) cc_final: 0.4551 (mpp) REVERT: A 1155 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7151 (tp-100) REVERT: A 1322 MET cc_start: 0.6137 (tpt) cc_final: 0.5834 (tpt) REVERT: C 84 TYR cc_start: 0.7505 (m-80) cc_final: 0.7208 (m-10) REVERT: D 81 ASP cc_start: 0.8228 (p0) cc_final: 0.7793 (t0) REVERT: D 100 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8156 (mp0) REVERT: D 103 ASP cc_start: 0.8525 (m-30) cc_final: 0.8270 (m-30) REVERT: D 117 ARG cc_start: 0.5119 (mmm160) cc_final: 0.4864 (mmm160) REVERT: D 167 LYS cc_start: 0.8712 (tttt) cc_final: 0.8366 (tppt) REVERT: D 201 LEU cc_start: 0.8184 (tp) cc_final: 0.7756 (tp) REVERT: E 48 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7226 (tm-30) REVERT: E 71 ARG cc_start: 0.6079 (OUTLIER) cc_final: 0.5269 (ptm160) REVERT: E 109 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.7907 (t80) REVERT: F 164 ARG cc_start: 0.8248 (ptm160) cc_final: 0.7682 (ttp-170) outliers start: 56 outliers final: 43 residues processed: 206 average time/residue: 0.1346 time to fit residues: 45.3179 Evaluate side-chains 198 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 149 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain B residue 1463 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1155 GLN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 64 TYR Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 148 LYS Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 231 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 204 optimal weight: 0.5980 chunk 312 optimal weight: 0.3980 chunk 264 optimal weight: 0.9990 chunk 193 optimal weight: 20.0000 chunk 306 optimal weight: 5.9990 chunk 141 optimal weight: 0.0980 chunk 208 optimal weight: 0.2980 chunk 171 optimal weight: 10.0000 chunk 301 optimal weight: 5.9990 chunk 292 optimal weight: 1.9990 chunk 156 optimal weight: 30.0000 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 657 GLN A 904 GLN A1349 GLN ** A1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 88 ASN F 66 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.141804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.099555 restraints weight = 63385.598| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 3.95 r_work: 0.3537 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24463 Z= 0.112 Angle : 0.578 9.759 33282 Z= 0.290 Chirality : 0.042 0.214 3754 Planarity : 0.005 0.057 4401 Dihedral : 5.005 51.508 3508 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.98 % Allowed : 17.80 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 2.21 % 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: -1.29 (0.15), residues: 3181 helix: 0.16 (0.17), residues: 972 sheet: -1.07 (0.21), residues: 600 loop : -1.38 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 117 TYR 0.021 0.001 TYR D 70 PHE 0.033 0.001 PHE B 784 TRP 0.017 0.001 TRP A 55 HIS 0.005 0.001 HIS A1334 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (24454) covalent geometry : angle 0.57790 / 0.29 (33266) SS BOND : bond 0.00203 / 0.10 ( 8) SS BOND : angle 0.56440 / 0.33 ( 16) hydrogen bonds : bond 0.02812 / 1.86 ( 875) hydrogen bonds : angle 4.93612 / 3.35 ( 2427) Misc. bond : bond 0.00019 / 0.01 ( 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 220 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 171 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 MET cc_start: 0.8739 (mmm) cc_final: 0.8390 (tpt) REVERT: B 274 MET cc_start: 0.8876 (tpt) cc_final: 0.8340 (tpt) REVERT: B 357 GLU cc_start: 0.9061 (tp30) cc_final: 0.8656 (tp30) REVERT: B 477 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8615 (pp) REVERT: B 830 GLU cc_start: 0.5841 (mt-10) cc_final: 0.5365 (tt0) REVERT: A 144 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8251 (mt) REVERT: A 631 MET cc_start: 0.4160 (mmm) cc_final: 0.3857 (ttt) REVERT: A 1034 MET cc_start: 0.5068 (OUTLIER) cc_final: 0.4380 (mpp) REVERT: A 1155 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7120 (tp40) REVERT: A 1322 MET cc_start: 0.6456 (tpt) cc_final: 0.6168 (tpt) REVERT: C 84 TYR cc_start: 0.7468 (m-80) cc_final: 0.7206 (m-10) REVERT: D 81 ASP cc_start: 0.8232 (p0) cc_final: 0.7881 (t0) REVERT: D 100 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8224 (mp0) REVERT: D 103 ASP cc_start: 0.8433 (m-30) cc_final: 0.8122 (m-30) REVERT: D 167 LYS cc_start: 0.8829 (tttt) cc_final: 0.8282 (tppt) REVERT: D 201 LEU cc_start: 0.8160 (tp) cc_final: 0.7732 (tp) REVERT: E 48 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7092 (tm-30) REVERT: E 109 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.7786 (m-80) REVERT: E 151 ASP cc_start: 0.6842 (t0) cc_final: 0.6294 (t0) REVERT: F 71 LEU cc_start: 0.8963 (mt) cc_final: 0.8585 (mt) REVERT: F 164 ARG cc_start: 0.8569 (ptm160) cc_final: 0.7980 (ttp-110) outliers start: 49 outliers final: 41 residues processed: 211 average time/residue: 0.1517 time to fit residues: 51.3802 Evaluate side-chains 198 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 152 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain B residue 1463 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1155 GLN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 148 LYS Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 231 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.9980 chunk 237 optimal weight: 0.9980 chunk 83 optimal weight: 0.0030 chunk 100 optimal weight: 3.9990 chunk 304 optimal weight: 0.0980 chunk 65 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 238 optimal weight: 7.9990 chunk 231 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 192 optimal weight: 0.0980 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.142112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.100211 restraints weight = 62844.315| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 4.28 r_work: 0.3539 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24463 Z= 0.110 Angle : 0.576 15.432 33282 Z= 0.289 Chirality : 0.042 0.164 3754 Planarity : 0.005 0.053 4401 Dihedral : 4.896 53.263 3508 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.02 % Allowed : 17.88 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 2.21 % 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: -1.18 (0.15), residues: 3181 helix: 0.25 (0.17), residues: 975 sheet: -0.99 (0.21), residues: 612 loop : -1.32 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 117 TYR 0.019 0.001 TYR F 162 PHE 0.031 0.001 PHE B 784 TRP 0.066 0.002 TRP C 161 HIS 0.004 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (24454) covalent geometry : angle 0.57578 / 0.29 (33266) SS BOND : bond 0.00211 / 0.11 ( 8) SS BOND : angle 0.48068 / 0.28 ( 16) hydrogen bonds : bond 0.02778 / 1.85 ( 875) hydrogen bonds : angle 4.89939 / 3.33 ( 2427) Misc. bond : bond 0.00013 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6200.94 seconds wall clock time: 106 minutes 48.64 seconds (6408.64 seconds total)