Starting phenix.real_space_refine on Fri Mar 6 18:10:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jh7_22335/03_2026/7jh7_22335.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jh7_22335/03_2026/7jh7_22335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jh7_22335/03_2026/7jh7_22335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jh7_22335/03_2026/7jh7_22335.map" model { file = "/net/cci-nas-00/data/ceres_data/7jh7_22335/03_2026/7jh7_22335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jh7_22335/03_2026/7jh7_22335.cif" } resolution = 3.8 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= 0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 198 5.16 5 C 21508 2.51 5 N 5791 2.21 5 O 6412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33924 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2903 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Conformer: "B" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} bond proxies already assigned to first conformer: 2955 Chain: "F" Number of atoms: 5973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5973 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 28, 'TRANS': 713} Chain breaks: 3 Chain: "B" Number of atoms: 2903 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Conformer: "B" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} bond proxies already assigned to first conformer: 2955 Chain: "G" Number of atoms: 5973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5973 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 28, 'TRANS': 713} Chain breaks: 3 Chain: "C" Number of atoms: 2903 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Conformer: "B" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} bond proxies already assigned to first conformer: 2955 Chain: "H" Number of atoms: 5973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5973 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 28, 'TRANS': 713} Chain breaks: 3 Chain: "E" Number of atoms: 2903 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Conformer: "B" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} bond proxies already assigned to first conformer: 2955 Chain: "D" Number of atoms: 2903 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Conformer: "B" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} bond proxies already assigned to first conformer: 2955 Chain: "I" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "J" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.28, per 1000 atoms: 0.27 Number of scatterers: 33924 At special positions: 0 Unit cell: (144.672, 162.624, 239.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 198 16.00 P 10 15.00 Mg 5 11.99 O 6412 8.00 N 5791 7.00 C 21508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 2.0 seconds 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8168 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 54 sheets defined 53.1% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 removed outlier: 3.602A pdb=" N SER A 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.788A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.852A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 112 through 126 Processing helix chain 'A' and resid 137 through 144 removed outlier: 4.123A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.713A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.619A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 276 through 284 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.975A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.545A pdb=" N GLN A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 removed outlier: 3.637A pdb=" N GLY A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.901A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 removed outlier: 3.540A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 370 removed outlier: 3.977A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 370' Processing helix chain 'F' and resid 13 through 18 removed outlier: 3.599A pdb=" N ARG F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS F 18 " --> pdb=" O PRO F 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 13 through 18' Processing helix chain 'F' and resid 22 through 27 Processing helix chain 'F' and resid 98 through 111 removed outlier: 4.367A pdb=" N ASN F 104 " --> pdb=" O ALA F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 153 through 168 Processing helix chain 'F' and resid 183 through 198 removed outlier: 4.060A pdb=" N TYR F 194 " --> pdb=" O ARG F 190 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE F 195 " --> pdb=" O VAL F 191 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA F 196 " --> pdb=" O ILE F 192 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL F 197 " --> pdb=" O GLN F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 231 Proline residue: F 225 - end of helix Processing helix chain 'F' and resid 269 through 275 removed outlier: 3.591A pdb=" N VAL F 273 " --> pdb=" O GLU F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 291 removed outlier: 4.432A pdb=" N TYR F 287 " --> pdb=" O TYR F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 301 removed outlier: 3.874A pdb=" N LEU F 298 " --> pdb=" O LYS F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 338 removed outlier: 3.566A pdb=" N ASN F 334 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL F 338 " --> pdb=" O ASN F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 358 removed outlier: 3.734A pdb=" N ASN F 347 " --> pdb=" O SER F 343 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR F 350 " --> pdb=" O LYS F 346 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS F 358 " --> pdb=" O GLY F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 389 Processing helix chain 'F' and resid 391 through 401 removed outlier: 3.600A pdb=" N LEU F 395 " --> pdb=" O ASN F 391 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU F 396 " --> pdb=" O SER F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 448 removed outlier: 4.187A pdb=" N ALA F 428 " --> pdb=" O THR F 424 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR F 446 " --> pdb=" O ARG F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 505 removed outlier: 4.124A pdb=" N THR F 481 " --> pdb=" O CYS F 477 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU F 496 " --> pdb=" O HIS F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 525 removed outlier: 3.826A pdb=" N ALA F 519 " --> pdb=" O MET F 515 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N CYS F 520 " --> pdb=" O ASP F 516 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE F 521 " --> pdb=" O LEU F 517 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 538 removed outlier: 3.785A pdb=" N CYS F 538 " --> pdb=" O LEU F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 557 removed outlier: 3.718A pdb=" N LEU F 557 " --> pdb=" O TYR F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 592 through 597 removed outlier: 3.509A pdb=" N LYS F 596 " --> pdb=" O GLY F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 602 through 612 Processing helix chain 'F' and resid 615 through 620 Processing helix chain 'F' and resid 647 through 663 Processing helix chain 'F' and resid 685 through 696 removed outlier: 3.661A pdb=" N VAL F 689 " --> pdb=" O ASP F 685 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG F 694 " --> pdb=" O MET F 690 " (cutoff:3.500A) Processing helix chain 'F' and resid 697 through 707 removed outlier: 3.727A pdb=" N CYS F 705 " --> pdb=" O GLY F 701 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG F 706 " --> pdb=" O ILE F 702 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS F 707 " --> pdb=" O ARG F 703 " (cutoff:3.500A) Processing helix chain 'F' and resid 715 through 722 removed outlier: 3.587A pdb=" N ARG F 721 " --> pdb=" O ASP F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 737 through 747 removed outlier: 3.870A pdb=" N LEU F 745 " --> pdb=" O GLY F 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 754 No H-bonds generated for 'chain 'F' and resid 752 through 754' Processing helix chain 'F' and resid 771 through 776 removed outlier: 4.262A pdb=" N MET F 776 " --> pdb=" O LEU F 772 " (cutoff:3.500A) Processing helix chain 'F' and resid 776 through 781 Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.601A pdb=" N SER B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 63 No H-bonds generated for 'chain 'B' and resid 61 through 63' Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.788A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.853A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 Processing helix chain 'B' and resid 137 through 144 removed outlier: 4.123A pdb=" N SER B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.713A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 223 through 231 removed outlier: 3.619A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 276 through 284 Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.975A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.546A pdb=" N GLN B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 removed outlier: 3.637A pdb=" N GLY B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY B 343 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.901A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.540A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 370 removed outlier: 3.977A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 370' Processing helix chain 'G' and resid 13 through 18 removed outlier: 3.600A pdb=" N ARG G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS G 18 " --> pdb=" O PRO G 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 13 through 18' Processing helix chain 'G' and resid 22 through 27 Processing helix chain 'G' and resid 98 through 111 removed outlier: 4.366A pdb=" N ASN G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 140 Processing helix chain 'G' and resid 153 through 168 Processing helix chain 'G' and resid 183 through 198 removed outlier: 4.061A pdb=" N TYR G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE G 195 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL G 197 " --> pdb=" O GLN G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 231 Proline residue: G 225 - end of helix Processing helix chain 'G' and resid 269 through 275 removed outlier: 3.591A pdb=" N VAL G 273 " --> pdb=" O GLU G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 291 removed outlier: 4.432A pdb=" N TYR G 287 " --> pdb=" O TYR G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 301 removed outlier: 3.874A pdb=" N LEU G 298 " --> pdb=" O LYS G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 338 removed outlier: 3.565A pdb=" N ASN G 334 " --> pdb=" O MET G 330 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL G 338 " --> pdb=" O ASN G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 343 through 358 removed outlier: 3.734A pdb=" N ASN G 347 " --> pdb=" O SER G 343 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR G 350 " --> pdb=" O LYS G 346 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS G 358 " --> pdb=" O GLY G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 379 through 389 Processing helix chain 'G' and resid 391 through 401 removed outlier: 3.600A pdb=" N LEU G 395 " --> pdb=" O ASN G 391 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU G 396 " --> pdb=" O SER G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 448 removed outlier: 4.187A pdb=" N ALA G 428 " --> pdb=" O THR G 424 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR G 446 " --> pdb=" O ARG G 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 505 removed outlier: 4.125A pdb=" N THR G 481 " --> pdb=" O CYS G 477 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU G 496 " --> pdb=" O HIS G 492 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 525 removed outlier: 3.825A pdb=" N ALA G 519 " --> pdb=" O MET G 515 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N CYS G 520 " --> pdb=" O ASP G 516 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE G 521 " --> pdb=" O LEU G 517 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 538 removed outlier: 3.785A pdb=" N CYS G 538 " --> pdb=" O LEU G 534 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 557 removed outlier: 3.718A pdb=" N LEU G 557 " --> pdb=" O TYR G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 592 through 598 removed outlier: 3.509A pdb=" N LYS G 596 " --> pdb=" O GLY G 592 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS G 598 " --> pdb=" O LEU G 594 " (cutoff:3.500A) Processing helix chain 'G' and resid 602 through 612 Processing helix chain 'G' and resid 615 through 620 Processing helix chain 'G' and resid 646 through 663 Processing helix chain 'G' and resid 685 through 696 removed outlier: 3.660A pdb=" N VAL G 689 " --> pdb=" O ASP G 685 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG G 694 " --> pdb=" O MET G 690 " (cutoff:3.500A) Processing helix chain 'G' and resid 697 through 707 removed outlier: 3.727A pdb=" N CYS G 705 " --> pdb=" O GLY G 701 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG G 706 " --> pdb=" O ILE G 702 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS G 707 " --> pdb=" O ARG G 703 " (cutoff:3.500A) Processing helix chain 'G' and resid 715 through 722 removed outlier: 3.586A pdb=" N ARG G 721 " --> pdb=" O ASP G 717 " (cutoff:3.500A) Processing helix chain 'G' and resid 737 through 747 removed outlier: 3.870A pdb=" N LEU G 745 " --> pdb=" O GLY G 741 " (cutoff:3.500A) Processing helix chain 'G' and resid 752 through 754 No H-bonds generated for 'chain 'G' and resid 752 through 754' Processing helix chain 'G' and resid 771 through 776 removed outlier: 4.262A pdb=" N MET G 776 " --> pdb=" O LEU G 772 " (cutoff:3.500A) Processing helix chain 'G' and resid 776 through 781 Processing helix chain 'C' and resid 56 through 60 removed outlier: 3.602A pdb=" N SER C 60 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 63 No H-bonds generated for 'chain 'C' and resid 61 through 63' Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.788A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.852A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 137 through 144 removed outlier: 4.124A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.713A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 205 through 216 Processing helix chain 'C' and resid 223 through 231 removed outlier: 3.620A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 276 through 284 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.974A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.546A pdb=" N GLN C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 347 removed outlier: 3.637A pdb=" N GLY C 342 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.901A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.539A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 370 removed outlier: 3.977A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 370' Processing helix chain 'H' and resid 13 through 18 removed outlier: 3.598A pdb=" N ARG H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS H 18 " --> pdb=" O PRO H 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 13 through 18' Processing helix chain 'H' and resid 22 through 27 Processing helix chain 'H' and resid 98 through 111 removed outlier: 4.366A pdb=" N ASN H 104 " --> pdb=" O ALA H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 140 Processing helix chain 'H' and resid 153 through 168 Processing helix chain 'H' and resid 183 through 198 removed outlier: 4.060A pdb=" N TYR H 194 " --> pdb=" O ARG H 190 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE H 195 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA H 196 " --> pdb=" O ILE H 192 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL H 197 " --> pdb=" O GLN H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 231 Proline residue: H 225 - end of helix Processing helix chain 'H' and resid 269 through 275 removed outlier: 3.590A pdb=" N VAL H 273 " --> pdb=" O GLU H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 291 removed outlier: 4.432A pdb=" N TYR H 287 " --> pdb=" O TYR H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 301 removed outlier: 3.874A pdb=" N LEU H 298 " --> pdb=" O LYS H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 338 removed outlier: 3.565A pdb=" N ASN H 334 " --> pdb=" O MET H 330 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL H 338 " --> pdb=" O ASN H 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 343 through 358 removed outlier: 3.734A pdb=" N ASN H 347 " --> pdb=" O SER H 343 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR H 350 " --> pdb=" O LYS H 346 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS H 358 " --> pdb=" O GLY H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 389 Processing helix chain 'H' and resid 391 through 401 removed outlier: 3.599A pdb=" N LEU H 395 " --> pdb=" O ASN H 391 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU H 396 " --> pdb=" O SER H 392 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 448 removed outlier: 4.186A pdb=" N ALA H 428 " --> pdb=" O THR H 424 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR H 446 " --> pdb=" O ARG H 442 " (cutoff:3.500A) Processing helix chain 'H' and resid 472 through 505 removed outlier: 4.125A pdb=" N THR H 481 " --> pdb=" O CYS H 477 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU H 496 " --> pdb=" O HIS H 492 " (cutoff:3.500A) Processing helix chain 'H' and resid 514 through 525 removed outlier: 3.826A pdb=" N ALA H 519 " --> pdb=" O MET H 515 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N CYS H 520 " --> pdb=" O ASP H 516 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE H 521 " --> pdb=" O LEU H 517 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 538 removed outlier: 3.785A pdb=" N CYS H 538 " --> pdb=" O LEU H 534 " (cutoff:3.500A) Processing helix chain 'H' and resid 544 through 557 removed outlier: 3.718A pdb=" N LEU H 557 " --> pdb=" O TYR H 553 " (cutoff:3.500A) Processing helix chain 'H' and resid 592 through 597 removed outlier: 3.509A pdb=" N LYS H 596 " --> pdb=" O GLY H 592 " (cutoff:3.500A) Processing helix chain 'H' and resid 602 through 612 Processing helix chain 'H' and resid 615 through 620 Processing helix chain 'H' and resid 647 through 663 Processing helix chain 'H' and resid 685 through 696 removed outlier: 3.660A pdb=" N VAL H 689 " --> pdb=" O ASP H 685 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG H 694 " --> pdb=" O MET H 690 " (cutoff:3.500A) Processing helix chain 'H' and resid 697 through 707 removed outlier: 3.727A pdb=" N CYS H 705 " --> pdb=" O GLY H 701 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG H 706 " --> pdb=" O ILE H 702 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS H 707 " --> pdb=" O ARG H 703 " (cutoff:3.500A) Processing helix chain 'H' and resid 715 through 722 removed outlier: 3.587A pdb=" N ARG H 721 " --> pdb=" O ASP H 717 " (cutoff:3.500A) Processing helix chain 'H' and resid 737 through 747 removed outlier: 3.870A pdb=" N LEU H 745 " --> pdb=" O GLY H 741 " (cutoff:3.500A) Processing helix chain 'H' and resid 752 through 754 No H-bonds generated for 'chain 'H' and resid 752 through 754' Processing helix chain 'H' and resid 771 through 776 removed outlier: 4.262A pdb=" N MET H 776 " --> pdb=" O LEU H 772 " (cutoff:3.500A) Processing helix chain 'H' and resid 776 through 781 Processing helix chain 'E' and resid 56 through 60 removed outlier: 3.603A pdb=" N SER E 60 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 63 No H-bonds generated for 'chain 'E' and resid 61 through 63' Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.787A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.853A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 112 through 126 Processing helix chain 'E' and resid 137 through 144 removed outlier: 4.123A pdb=" N SER E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.713A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 204 No H-bonds generated for 'chain 'E' and resid 202 through 204' Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 223 through 231 removed outlier: 3.620A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 262 Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'E' and resid 276 through 284 Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.975A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.546A pdb=" N GLN E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 347 removed outlier: 3.637A pdb=" N GLY E 342 " --> pdb=" O SER E 338 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY E 343 " --> pdb=" O VAL E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 356 removed outlier: 3.901A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TRP E 356 " --> pdb=" O GLN E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 removed outlier: 3.540A pdb=" N GLU E 364 " --> pdb=" O GLN E 360 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA E 365 " --> pdb=" O GLU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 370 removed outlier: 3.977A pdb=" N VAL E 370 " --> pdb=" O PRO E 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 367 through 370' Processing helix chain 'D' and resid 56 through 60 removed outlier: 3.602A pdb=" N SER D 60 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.788A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.853A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 Processing helix chain 'D' and resid 137 through 144 removed outlier: 4.124A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.713A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 223 through 231 removed outlier: 3.620A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 263 through 267 Processing helix chain 'D' and resid 276 through 284 Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.976A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.546A pdb=" N GLN D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 347 removed outlier: 3.637A pdb=" N GLY D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY D 343 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 356 removed outlier: 3.901A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.540A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 370 removed outlier: 3.977A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 367 through 370' Processing helix chain 'I' and resid 63 through 196 removed outlier: 3.767A pdb=" N UNK I 93 " --> pdb=" O UNK I 89 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N UNK I 97 " --> pdb=" O UNK I 93 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N UNK I 106 " --> pdb=" O UNK I 102 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N UNK I 114 " --> pdb=" O UNK I 110 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N UNK I 162 " --> pdb=" O UNK I 158 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N UNK I 163 " --> pdb=" O UNK I 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 196 removed outlier: 4.145A pdb=" N UNK J 110 " --> pdb=" O UNK J 106 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N UNK J 111 " --> pdb=" O UNK J 107 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N UNK J 129 " --> pdb=" O UNK J 125 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N UNK J 131 " --> pdb=" O UNK J 127 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N UNK J 138 " --> pdb=" O UNK J 134 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N UNK J 139 " --> pdb=" O UNK J 135 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N UNK J 141 " --> pdb=" O UNK J 137 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N UNK J 142 " --> pdb=" O UNK J 138 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N UNK J 143 " --> pdb=" O UNK J 139 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N UNK J 152 " --> pdb=" O UNK J 148 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N UNK J 195 " --> pdb=" O UNK J 191 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N UNK J 196 " --> pdb=" O UNK J 192 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.537A pdb=" N GLY A 20 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 132 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.588A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 177 through 178 removed outlier: 5.847A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 165 through 166 Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 240 Processing sheet with id=AA6, first strand: chain 'F' and resid 70 through 72 Processing sheet with id=AA7, first strand: chain 'F' and resid 115 through 118 removed outlier: 3.574A pdb=" N PHE F 121 " --> pdb=" O SER F 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 258 through 263 removed outlier: 4.160A pdb=" N ILE F 250 " --> pdb=" O ILE F 457 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE F 462 " --> pdb=" O ILE F 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 232 through 233 Processing sheet with id=AB1, first strand: chain 'F' and resid 365 through 366 Processing sheet with id=AB2, first strand: chain 'F' and resid 403 through 406 Processing sheet with id=AB3, first strand: chain 'F' and resid 563 through 564 removed outlier: 3.588A pdb=" N PHE F 577 " --> pdb=" O TYR F 588 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 598 through 599 removed outlier: 3.901A pdb=" N GLN F 645 " --> pdb=" O ASP F 599 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 711 through 714 removed outlier: 3.750A pdb=" N PHE F 764 " --> pdb=" O LYS F 757 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS F 757 " --> pdb=" O PHE F 764 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.537A pdb=" N GLY B 20 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET B 132 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.587A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 177 through 178 removed outlier: 5.847A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 165 through 166 Processing sheet with id=AC1, first strand: chain 'B' and resid 238 through 240 Processing sheet with id=AC2, first strand: chain 'G' and resid 70 through 72 Processing sheet with id=AC3, first strand: chain 'G' and resid 115 through 118 removed outlier: 3.574A pdb=" N PHE G 121 " --> pdb=" O SER G 118 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 258 through 263 removed outlier: 4.162A pdb=" N ILE G 250 " --> pdb=" O ILE G 457 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE G 462 " --> pdb=" O ILE G 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 232 through 233 Processing sheet with id=AC6, first strand: chain 'G' and resid 365 through 366 Processing sheet with id=AC7, first strand: chain 'G' and resid 403 through 406 Processing sheet with id=AC8, first strand: chain 'G' and resid 563 through 564 removed outlier: 3.588A pdb=" N PHE G 577 " --> pdb=" O TYR G 588 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 711 through 714 removed outlier: 3.749A pdb=" N PHE G 764 " --> pdb=" O LYS G 757 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS G 757 " --> pdb=" O PHE G 764 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 8 through 9 removed outlier: 6.570A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET C 132 " --> pdb=" O ILE C 357 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 18 through 19 removed outlier: 3.785A pdb=" N ALA C 29 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.587A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 177 through 178 removed outlier: 5.848A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 165 through 166 Processing sheet with id=AD6, first strand: chain 'C' and resid 238 through 240 Processing sheet with id=AD7, first strand: chain 'H' and resid 70 through 72 Processing sheet with id=AD8, first strand: chain 'H' and resid 115 through 118 removed outlier: 3.574A pdb=" N PHE H 121 " --> pdb=" O SER H 118 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 258 through 263 removed outlier: 4.154A pdb=" N ILE H 250 " --> pdb=" O ILE H 457 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE H 462 " --> pdb=" O ILE H 176 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 232 through 233 Processing sheet with id=AE2, first strand: chain 'H' and resid 365 through 366 Processing sheet with id=AE3, first strand: chain 'H' and resid 403 through 406 Processing sheet with id=AE4, first strand: chain 'H' and resid 563 through 564 removed outlier: 3.588A pdb=" N PHE H 577 " --> pdb=" O TYR H 588 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 598 through 599 removed outlier: 4.074A pdb=" N GLN H 645 " --> pdb=" O ASP H 599 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 711 through 714 removed outlier: 3.750A pdb=" N PHE H 764 " --> pdb=" O LYS H 757 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS H 757 " --> pdb=" O PHE H 764 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 8 through 9 removed outlier: 6.569A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET E 132 " --> pdb=" O ILE E 357 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 17 through 18 removed outlier: 3.733A pdb=" N PHE E 31 " --> pdb=" O VAL E 17 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.587A pdb=" N ARG E 37 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 177 through 178 removed outlier: 5.848A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 165 through 166 Processing sheet with id=AF3, first strand: chain 'E' and resid 238 through 240 Processing sheet with id=AF4, first strand: chain 'D' and resid 20 through 21 removed outlier: 3.537A pdb=" N GLY D 20 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET D 132 " --> pdb=" O ILE D 357 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 17 through 18 Processing sheet with id=AF6, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.587A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 177 through 178 removed outlier: 5.847A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 165 through 166 Processing sheet with id=AF9, first strand: chain 'D' and resid 238 through 240 1508 hydrogen bonds defined for protein. 4146 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: 8.17 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7277 1.33 - 1.45: 7642 1.45 - 1.57: 19343 1.57 - 1.69: 10 1.69 - 1.81: 347 Bond restraints: 34619 Sorted by residual: bond pdb=" C LYS E 18 " pdb=" O LYS E 18 " ideal model delta sigma weight residual 1.236 1.206 0.030 1.19e-02 7.06e+03 6.33e+00 bond pdb=" C LYS C 18 " pdb=" O LYS C 18 " ideal model delta sigma weight residual 1.235 1.207 0.029 1.14e-02 7.69e+03 6.27e+00 bond pdb=" CA LYS E 18 " pdb=" C LYS E 18 " ideal model delta sigma weight residual 1.523 1.493 0.029 1.23e-02 6.61e+03 5.64e+00 bond pdb=" CB GLN G 288 " pdb=" CG GLN G 288 " ideal model delta sigma weight residual 1.520 1.449 0.071 3.00e-02 1.11e+03 5.60e+00 bond pdb=" CB GLN H 288 " pdb=" CG GLN H 288 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.51e+00 ... (remaining 34614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 45735 2.78 - 5.57: 942 5.57 - 8.35: 119 8.35 - 11.13: 59 11.13 - 13.92: 3 Bond angle restraints: 46858 Sorted by residual: angle pdb=" N ILE H 457 " pdb=" CA ILE H 457 " pdb=" C ILE H 457 " ideal model delta sigma weight residual 109.34 95.42 13.92 2.08e+00 2.31e-01 4.48e+01 angle pdb=" N ILE F 457 " pdb=" CA ILE F 457 " pdb=" C ILE F 457 " ideal model delta sigma weight residual 109.34 95.46 13.88 2.08e+00 2.31e-01 4.45e+01 angle pdb=" N ILE G 457 " pdb=" CA ILE G 457 " pdb=" C ILE G 457 " ideal model delta sigma weight residual 109.34 95.51 13.83 2.08e+00 2.31e-01 4.42e+01 angle pdb=" N ALA H 136 " pdb=" CA ALA H 136 " pdb=" C ALA H 136 " ideal model delta sigma weight residual 111.07 116.77 -5.70 1.07e+00 8.73e-01 2.84e+01 angle pdb=" N ALA G 136 " pdb=" CA ALA G 136 " pdb=" C ALA G 136 " ideal model delta sigma weight residual 111.07 116.77 -5.70 1.07e+00 8.73e-01 2.84e+01 ... (remaining 46853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.98: 20400 24.98 - 49.96: 490 49.96 - 74.95: 26 74.95 - 99.93: 11 99.93 - 124.91: 5 Dihedral angle restraints: 20932 sinusoidal: 8249 harmonic: 12683 Sorted by residual: dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 64.91 -124.91 1 2.00e+01 2.50e-03 3.77e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 64.84 -124.84 1 2.00e+01 2.50e-03 3.77e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 64.84 -124.83 1 2.00e+01 2.50e-03 3.77e+01 ... (remaining 20929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 4435 0.079 - 0.158: 682 0.158 - 0.238: 55 0.238 - 0.317: 18 0.317 - 0.396: 7 Chirality restraints: 5197 Sorted by residual: chirality pdb=" CB ILE G 580 " pdb=" CA ILE G 580 " pdb=" CG1 ILE G 580 " pdb=" CG2 ILE G 580 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" CB ILE H 580 " pdb=" CA ILE H 580 " pdb=" CG1 ILE H 580 " pdb=" CG2 ILE H 580 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CB ILE F 580 " pdb=" CA ILE F 580 " pdb=" CG1 ILE F 580 " pdb=" CG2 ILE F 580 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 5194 not shown) Planarity restraints: 6060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU F 88 " -0.014 2.00e-02 2.50e+03 2.96e-02 8.78e+00 pdb=" CD GLU F 88 " 0.051 2.00e-02 2.50e+03 pdb=" OE1 GLU F 88 " -0.018 2.00e-02 2.50e+03 pdb=" OE2 GLU F 88 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU G 88 " -0.014 2.00e-02 2.50e+03 2.95e-02 8.73e+00 pdb=" CD GLU G 88 " 0.051 2.00e-02 2.50e+03 pdb=" OE1 GLU G 88 " -0.018 2.00e-02 2.50e+03 pdb=" OE2 GLU G 88 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 88 " -0.014 2.00e-02 2.50e+03 2.95e-02 8.68e+00 pdb=" CD GLU H 88 " 0.051 2.00e-02 2.50e+03 pdb=" OE1 GLU H 88 " -0.018 2.00e-02 2.50e+03 pdb=" OE2 GLU H 88 " -0.018 2.00e-02 2.50e+03 ... (remaining 6057 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 117 2.47 - 3.08: 21537 3.08 - 3.69: 53398 3.69 - 4.29: 77573 4.29 - 4.90: 124833 Nonbonded interactions: 277458 Sorted by model distance: nonbonded pdb=" OD1 ASP C 157 " pdb=" O3' ADP C 401 " model vdw 1.864 3.040 nonbonded pdb=" OD1 ASN C 12 " pdb=" CE MET C 119 " model vdw 1.901 3.460 nonbonded pdb=" OG SER C 14 " pdb=" CA GLY C 158 " model vdw 1.939 3.440 nonbonded pdb=" OD1 ASP E 157 " pdb=" O3' ADP E 401 " model vdw 1.945 3.040 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 1.995 2.170 ... (remaining 277453 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: 0.09 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 46 or resid 48 through 402)) selection = (chain 'B' and (resid 5 through 46 or resid 48 through 402)) selection = (chain 'C' and (resid 5 through 46 or resid 48 through 402)) selection = (chain 'D' and (resid 5 through 46 or resid 48 through 402)) selection = (chain 'E' and (resid 5 through 46 or resid 48 through 402)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 34.480 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 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 : 0.006 0.071 34619 Z= 0.284 Angle : 1.030 13.916 46858 Z= 0.548 Chirality : 0.059 0.396 5197 Planarity : 0.008 0.057 6060 Dihedral : 10.791 124.912 12764 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.43 % Allowed : 2.48 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.13 (0.11), residues: 4052 helix: -3.19 (0.08), residues: 1641 sheet: -3.21 (0.19), residues: 534 loop : -1.99 (0.13), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 116 TYR 0.037 0.004 TYR A 294 PHE 0.037 0.004 PHE C 262 TRP 0.044 0.005 TRP D 340 HIS 0.016 0.003 HIS F 492 Details of bonding type rmsd covalent geometry : bond 0.00643 (34619) covalent geometry : angle 1.02992 (46858) hydrogen bonds : bond 0.17004 ( 1508) hydrogen bonds : angle 9.38696 ( 4146) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1155 time to evaluate : 1.170 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 SER cc_start: 0.9060 (t) cc_final: 0.8803 (p) REVERT: A 57 GLU cc_start: 0.7283 (tt0) cc_final: 0.7014 (tt0) REVERT: A 82 MET cc_start: 0.8796 (tpt) cc_final: 0.8183 (tpp) REVERT: A 132 MET cc_start: 0.9020 (ppp) cc_final: 0.8503 (ppp) REVERT: A 180 LEU cc_start: 0.8826 (tt) cc_final: 0.8418 (tp) REVERT: A 191 LYS cc_start: 0.7534 (ttmt) cc_final: 0.7266 (ttpp) REVERT: A 291 LYS cc_start: 0.8432 (tttt) cc_final: 0.7998 (ttpp) REVERT: A 296 ASN cc_start: 0.8693 (m-40) cc_final: 0.8315 (m-40) REVERT: A 320 LEU cc_start: 0.9071 (mt) cc_final: 0.8772 (mt) REVERT: A 325 MET cc_start: 0.8877 (tpp) cc_final: 0.8488 (tpp) REVERT: A 328 LYS cc_start: 0.7876 (tttt) cc_final: 0.7456 (tptm) REVERT: A 330 ILE cc_start: 0.8964 (mp) cc_final: 0.8702 (mm) REVERT: F 63 THR cc_start: 0.4276 (t) cc_final: 0.3663 (m) REVERT: F 99 PRO cc_start: 0.6655 (Cg_endo) cc_final: 0.6431 (Cg_exo) REVERT: F 177 THR cc_start: 0.6903 (m) cc_final: 0.6656 (m) REVERT: F 239 ASP cc_start: 0.8459 (m-30) cc_final: 0.7865 (t70) REVERT: F 272 ARG cc_start: 0.7168 (tpp-160) cc_final: 0.6002 (tpt170) REVERT: F 422 TYR cc_start: 0.7358 (m-80) cc_final: 0.5237 (m-10) REVERT: F 478 ILE cc_start: 0.8811 (mm) cc_final: 0.8548 (mm) REVERT: F 484 LYS cc_start: 0.8247 (tptt) cc_final: 0.7830 (ttmt) REVERT: F 488 PHE cc_start: 0.8026 (t80) cc_final: 0.7806 (t80) REVERT: F 506 ILE cc_start: 0.7011 (mm) cc_final: 0.6634 (mm) REVERT: F 580 ILE cc_start: 0.7499 (tt) cc_final: 0.6981 (pt) REVERT: F 614 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6186 (tp) REVERT: F 653 GLU cc_start: 0.7702 (tp30) cc_final: 0.7319 (tp30) REVERT: F 673 ILE cc_start: 0.8183 (pt) cc_final: 0.7665 (pt) REVERT: F 700 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7334 (mm-30) REVERT: F 776 MET cc_start: 0.4449 (ttm) cc_final: 0.4219 (mtm) REVERT: B 60 SER cc_start: 0.8907 (t) cc_final: 0.8663 (t) REVERT: B 78 ASN cc_start: 0.8088 (t0) cc_final: 0.7742 (t0) REVERT: B 91 TYR cc_start: 0.8442 (m-80) cc_final: 0.8177 (m-80) REVERT: B 136 ILE cc_start: 0.8206 (mt) cc_final: 0.7920 (tt) REVERT: B 157 ASP cc_start: 0.7179 (t0) cc_final: 0.6859 (t0) REVERT: B 203 THR cc_start: 0.7889 (p) cc_final: 0.7625 (t) REVERT: B 205 GLU cc_start: 0.7111 (mp0) cc_final: 0.6431 (mp0) REVERT: B 263 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7764 (mm110) REVERT: B 291 LYS cc_start: 0.8893 (tttt) cc_final: 0.7850 (mptt) REVERT: B 326 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7704 (tmtt) REVERT: G 282 ASP cc_start: 0.7171 (t0) cc_final: 0.6921 (t0) REVERT: G 345 GLU cc_start: 0.7626 (pp20) cc_final: 0.6863 (tt0) REVERT: G 370 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7210 (mt-10) REVERT: G 417 VAL cc_start: 0.8566 (p) cc_final: 0.8352 (p) REVERT: G 429 LYS cc_start: 0.7390 (ptpt) cc_final: 0.7149 (ptpp) REVERT: G 478 ILE cc_start: 0.7245 (mm) cc_final: 0.6976 (mm) REVERT: G 482 ASN cc_start: 0.6352 (m-40) cc_final: 0.6097 (m110) REVERT: G 487 GLN cc_start: 0.7899 (tp-100) cc_final: 0.7696 (tp40) REVERT: G 691 HIS cc_start: 0.6862 (t70) cc_final: 0.6505 (t-170) REVERT: G 710 PRO cc_start: 0.8111 (Cg_endo) cc_final: 0.7810 (Cg_exo) REVERT: G 765 PHE cc_start: 0.6776 (m-80) cc_final: 0.6471 (m-80) REVERT: G 778 ASP cc_start: 0.7137 (m-30) cc_final: 0.6835 (m-30) REVERT: C 191 LYS cc_start: 0.7984 (ttmt) cc_final: 0.7714 (ttmm) REVERT: C 215 LYS cc_start: 0.8894 (mttm) cc_final: 0.8541 (mttm) REVERT: C 291 LYS cc_start: 0.7346 (tttt) cc_final: 0.7103 (tttt) REVERT: C 328 LYS cc_start: 0.7832 (tttt) cc_final: 0.7305 (tptt) REVERT: C 351 THR cc_start: 0.8477 (p) cc_final: 0.8110 (t) REVERT: H 155 PHE cc_start: 0.6350 (m-10) cc_final: 0.5889 (m-10) REVERT: H 163 GLN cc_start: 0.6618 (tp40) cc_final: 0.6403 (tp40) REVERT: H 357 MET cc_start: 0.7258 (mmm) cc_final: 0.7035 (mtt) REVERT: H 451 GLN cc_start: 0.6455 (mp-120) cc_final: 0.6174 (mp-120) REVERT: H 536 GLU cc_start: 0.8351 (pp20) cc_final: 0.7799 (pp20) REVERT: H 657 LYS cc_start: 0.7365 (tmtm) cc_final: 0.6783 (tptp) REVERT: H 690 MET cc_start: 0.5738 (mmm) cc_final: 0.5501 (mmm) REVERT: H 702 ILE cc_start: 0.8169 (mm) cc_final: 0.7882 (mm) REVERT: H 762 LYS cc_start: 0.7130 (mttt) cc_final: 0.6927 (mttt) REVERT: E 53 TYR cc_start: 0.7764 (m-80) cc_final: 0.7408 (m-80) REVERT: E 113 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7719 (tppt) REVERT: E 127 PHE cc_start: 0.7683 (m-80) cc_final: 0.7355 (m-80) REVERT: E 155 SER cc_start: 0.8215 (t) cc_final: 0.7738 (m) REVERT: E 258 PRO cc_start: 0.7337 (Cg_endo) cc_final: 0.6687 (Cg_exo) REVERT: E 296 ASN cc_start: 0.8431 (m-40) cc_final: 0.8075 (m-40) REVERT: E 316 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6653 (mm-30) REVERT: E 354 GLN cc_start: 0.7312 (pt0) cc_final: 0.7094 (pt0) REVERT: E 363 ASP cc_start: 0.8023 (m-30) cc_final: 0.7603 (m-30) REVERT: D 9 VAL cc_start: 0.8914 (t) cc_final: 0.8691 (t) REVERT: D 16 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8360 (mp) REVERT: D 50 LYS cc_start: 0.8765 (mtmm) cc_final: 0.8447 (mtpt) REVERT: D 54 VAL cc_start: 0.8555 (m) cc_final: 0.7931 (m) REVERT: D 91 TYR cc_start: 0.8248 (m-80) cc_final: 0.7958 (m-10) REVERT: D 118 LYS cc_start: 0.7743 (tptt) cc_final: 0.7235 (ttmm) REVERT: D 125 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7781 (mt-10) REVERT: D 136 ILE cc_start: 0.8611 (mt) cc_final: 0.8345 (tt) REVERT: D 161 HIS cc_start: 0.8747 (p-80) cc_final: 0.8430 (p90) REVERT: D 167 GLU cc_start: 0.8430 (tp30) cc_final: 0.8134 (tp30) REVERT: D 205 GLU cc_start: 0.6568 (mp0) cc_final: 0.6142 (mp0) REVERT: D 249 THR cc_start: 0.7286 (p) cc_final: 0.7017 (p) REVERT: D 291 LYS cc_start: 0.8775 (tttt) cc_final: 0.8183 (ttpp) REVERT: D 296 ASN cc_start: 0.8687 (m-40) cc_final: 0.8083 (m-40) REVERT: D 313 MET cc_start: 0.7695 (tpp) cc_final: 0.7326 (tpt) REVERT: D 328 LYS cc_start: 0.7541 (tttt) cc_final: 0.7024 (tttt) REVERT: D 360 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8196 (tm-30) REVERT: D 361 GLU cc_start: 0.7992 (tt0) cc_final: 0.7511 (tt0) outliers start: 10 outliers final: 3 residues processed: 1164 average time/residue: 0.2241 time to fit residues: 410.5196 Evaluate side-chains 838 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 833 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 614 LEU Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain D residue 16 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.3980 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 6.9990 chunk 424 optimal weight: 30.0000 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 49 GLN A 73 HIS A 88 HIS ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN A 353 GLN F 79 GLN F 160 ASN F 171 ASN ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 391 ASN ** F 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 691 HIS B 12 ASN B 49 GLN B 88 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN G 171 ASN G 222 GLN ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 276 GLN G 482 ASN G 486 GLN ** G 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 711 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN C 88 HIS C 111 ASN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 HIS H 104 ASN H 126 ASN ** H 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 ASN H 419 GLN H 451 GLN H 482 ASN H 711 ASN E 12 ASN E 49 GLN E 88 HIS E 121 GLN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 ASN ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN D 49 GLN D 88 HIS D 121 GLN D 275 HIS D 314 GLN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.178580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.150505 restraints weight = 80014.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.150186 restraints weight = 86111.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.151721 restraints weight = 64514.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.152098 restraints weight = 38064.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.152624 restraints weight = 35647.769| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3735 r_free = 0.3735 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3735 r_free = 0.3735 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 34619 Z= 0.240 Angle : 0.759 10.671 46858 Z= 0.389 Chirality : 0.047 0.243 5197 Planarity : 0.006 0.050 6060 Dihedral : 6.730 88.592 4776 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.08 % Allowed : 11.12 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.12), residues: 4052 helix: -1.68 (0.11), residues: 1689 sheet: -2.73 (0.20), residues: 516 loop : -1.65 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 29 TYR 0.032 0.002 TYR E 294 PHE 0.037 0.003 PHE F 489 TRP 0.033 0.003 TRP A 340 HIS 0.012 0.002 HIS H 358 Details of bonding type rmsd covalent geometry : bond 0.00537 (34619) covalent geometry : angle 0.75948 (46858) hydrogen bonds : bond 0.04226 ( 1508) hydrogen bonds : angle 5.72991 ( 4146) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 963 time to evaluate : 1.097 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: A 82 MET cc_start: 0.9148 (tpt) cc_final: 0.8842 (tpp) REVERT: A 143 TYR cc_start: 0.8957 (m-80) cc_final: 0.8400 (m-80) REVERT: A 191 LYS cc_start: 0.7873 (ttmt) cc_final: 0.7625 (ttpp) REVERT: A 195 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7428 (tm-30) REVERT: A 296 ASN cc_start: 0.8689 (m-40) cc_final: 0.8331 (m-40) REVERT: F 17 ARG cc_start: 0.5584 (tpt170) cc_final: 0.5377 (tpt170) REVERT: F 79 GLN cc_start: 0.6100 (OUTLIER) cc_final: 0.4755 (tm-30) REVERT: F 99 PRO cc_start: 0.6649 (Cg_endo) cc_final: 0.6382 (Cg_exo) REVERT: F 162 TYR cc_start: 0.7214 (t80) cc_final: 0.6983 (t80) REVERT: F 165 MET cc_start: 0.7529 (tpt) cc_final: 0.6761 (tpt) REVERT: F 433 GLU cc_start: 0.7369 (tt0) cc_final: 0.7014 (tm-30) REVERT: F 439 MET cc_start: 0.7489 (ttp) cc_final: 0.7136 (tmm) REVERT: F 483 GLU cc_start: 0.7435 (tp30) cc_final: 0.7086 (tp30) REVERT: F 484 LYS cc_start: 0.8599 (tptt) cc_final: 0.8391 (tppt) REVERT: F 506 ILE cc_start: 0.6559 (mm) cc_final: 0.6349 (mm) REVERT: F 526 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8190 (mmtt) REVERT: F 537 GLU cc_start: 0.7797 (tp30) cc_final: 0.7376 (tp30) REVERT: F 594 LEU cc_start: 0.8515 (mt) cc_final: 0.8124 (mt) REVERT: B 14 SER cc_start: 0.8309 (t) cc_final: 0.7622 (m) REVERT: B 169 TYR cc_start: 0.8835 (m-80) cc_final: 0.8633 (m-80) REVERT: B 203 THR cc_start: 0.8687 (p) cc_final: 0.8459 (t) REVERT: B 205 GLU cc_start: 0.7447 (mp0) cc_final: 0.7042 (mp0) REVERT: B 288 ASP cc_start: 0.7191 (p0) cc_final: 0.6935 (t0) REVERT: G 33 LEU cc_start: 0.6412 (mt) cc_final: 0.4546 (pt) REVERT: G 345 GLU cc_start: 0.7810 (pp20) cc_final: 0.6684 (tt0) REVERT: G 349 MET cc_start: 0.8679 (mmt) cc_final: 0.8249 (mmp) REVERT: G 353 THR cc_start: 0.8340 (p) cc_final: 0.8117 (p) REVERT: G 357 MET cc_start: 0.5423 (mmm) cc_final: 0.4690 (mmm) REVERT: G 388 MET cc_start: 0.6056 (mpp) cc_final: 0.5760 (mpp) REVERT: G 438 TRP cc_start: 0.8296 (t60) cc_final: 0.7965 (t60) REVERT: G 539 MET cc_start: 0.8197 (mmm) cc_final: 0.7948 (mmp) REVERT: G 666 HIS cc_start: 0.6689 (t70) cc_final: 0.6245 (t-90) REVERT: G 668 HIS cc_start: 0.6265 (m-70) cc_final: 0.5745 (m-70) REVERT: G 778 ASP cc_start: 0.7347 (m-30) cc_final: 0.7142 (m-30) REVERT: C 16 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8824 (mp) REVERT: C 87 HIS cc_start: 0.7340 (t70) cc_final: 0.7081 (t-90) REVERT: C 313 MET cc_start: 0.8174 (tpp) cc_final: 0.7926 (ttt) REVERT: C 325 MET cc_start: 0.8322 (tpp) cc_final: 0.8027 (tpp) REVERT: H 112 TRP cc_start: 0.3916 (m-90) cc_final: 0.3621 (m-90) REVERT: H 165 MET cc_start: 0.5948 (tpt) cc_final: 0.5674 (tpp) REVERT: H 359 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7260 (m-10) REVERT: H 422 TYR cc_start: 0.7990 (m-80) cc_final: 0.7297 (m-10) REVERT: H 486 GLN cc_start: 0.8225 (tp-100) cc_final: 0.7803 (tp-100) REVERT: H 657 LYS cc_start: 0.7943 (tmtm) cc_final: 0.7458 (tptp) REVERT: H 659 MET cc_start: 0.7795 (tpp) cc_final: 0.6584 (tmm) REVERT: E 111 ASN cc_start: 0.8452 (m-40) cc_final: 0.8175 (m-40) REVERT: E 117 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7150 (mt-10) REVERT: E 143 TYR cc_start: 0.8804 (m-80) cc_final: 0.8490 (m-80) REVERT: E 155 SER cc_start: 0.8925 (t) cc_final: 0.8619 (m) REVERT: E 211 ASP cc_start: 0.8400 (t0) cc_final: 0.8106 (m-30) REVERT: E 244 ASP cc_start: 0.8113 (p0) cc_final: 0.7909 (p0) REVERT: E 252 ASN cc_start: 0.7574 (t0) cc_final: 0.6545 (t160) REVERT: E 259 GLU cc_start: 0.8760 (tp30) cc_final: 0.7894 (mm-30) REVERT: E 284 LYS cc_start: 0.8420 (tppp) cc_final: 0.7930 (tppt) REVERT: E 296 ASN cc_start: 0.8608 (m-40) cc_final: 0.8322 (m-40) REVERT: D 249 THR cc_start: 0.8047 (p) cc_final: 0.7816 (p) REVERT: D 291 LYS cc_start: 0.8423 (tttt) cc_final: 0.8133 (ttpp) REVERT: D 296 ASN cc_start: 0.8441 (m-40) cc_final: 0.8130 (m-40) REVERT: D 317 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8391 (mt) REVERT: D 330 ILE cc_start: 0.9123 (mp) cc_final: 0.8873 (mm) REVERT: D 360 GLN cc_start: 0.7554 (tm-30) cc_final: 0.7309 (tm-30) REVERT: D 361 GLU cc_start: 0.7573 (tt0) cc_final: 0.7001 (tt0) outliers start: 68 outliers final: 28 residues processed: 1001 average time/residue: 0.2079 time to fit residues: 336.1486 Evaluate side-chains 836 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 804 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 262 ASP Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 359 PHE Chi-restraints excluded: chain H residue 538 CYS Chi-restraints excluded: chain H residue 674 ILE Chi-restraints excluded: chain H residue 761 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 317 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 16 optimal weight: 2.9990 chunk 346 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 371 optimal weight: 5.9990 chunk 318 optimal weight: 5.9990 chunk 228 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 387 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 486 GLN B 12 ASN B 49 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN G 75 GLN ** G 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 486 GLN C 12 ASN H 97 HIS H 126 ASN ** H 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 ASN ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 ASN ** H 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 419 GLN H 562 ASN E 121 GLN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 HIS D 88 HIS ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.190115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.163676 restraints weight = 69561.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.163120 restraints weight = 89635.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.164767 restraints weight = 64452.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.164966 restraints weight = 39203.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.165275 restraints weight = 36483.813| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 34619 Z= 0.142 Angle : 0.664 9.471 46858 Z= 0.335 Chirality : 0.043 0.205 5197 Planarity : 0.005 0.066 6060 Dihedral : 6.057 87.971 4770 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.51 % Allowed : 15.17 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.13), residues: 4052 helix: -0.89 (0.12), residues: 1695 sheet: -2.30 (0.22), residues: 486 loop : -1.42 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 403 TYR 0.027 0.002 TYR F 164 PHE 0.028 0.002 PHE F 155 TRP 0.029 0.002 TRP A 340 HIS 0.013 0.002 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00325 (34619) covalent geometry : angle 0.66370 (46858) hydrogen bonds : bond 0.03546 ( 1508) hydrogen bonds : angle 5.05592 ( 4146) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 843 time to evaluate : 1.030 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: A 24 ASP cc_start: 0.8482 (m-30) cc_final: 0.7999 (m-30) REVERT: A 82 MET cc_start: 0.9174 (tpt) cc_final: 0.8736 (tpp) REVERT: A 111 ASN cc_start: 0.8198 (m-40) cc_final: 0.7542 (t0) REVERT: A 143 TYR cc_start: 0.8785 (m-80) cc_final: 0.8423 (m-80) REVERT: A 191 LYS cc_start: 0.7993 (ttmt) cc_final: 0.7708 (ttpp) REVERT: A 195 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7335 (tm-30) REVERT: A 244 ASP cc_start: 0.8191 (p0) cc_final: 0.7390 (p0) REVERT: A 296 ASN cc_start: 0.8476 (m-40) cc_final: 0.8184 (m-40) REVERT: F 17 ARG cc_start: 0.5711 (tpt170) cc_final: 0.4737 (tpt170) REVERT: F 99 PRO cc_start: 0.6239 (Cg_endo) cc_final: 0.5981 (Cg_exo) REVERT: F 117 TYR cc_start: 0.5968 (m-10) cc_final: 0.5631 (m-80) REVERT: F 165 MET cc_start: 0.7633 (tpt) cc_final: 0.7245 (tpt) REVERT: F 239 ASP cc_start: 0.7594 (m-30) cc_final: 0.7239 (t70) REVERT: F 420 VAL cc_start: 0.9513 (p) cc_final: 0.9281 (t) REVERT: F 433 GLU cc_start: 0.7401 (tt0) cc_final: 0.6971 (tm-30) REVERT: F 439 MET cc_start: 0.7522 (ttp) cc_final: 0.7114 (tmm) REVERT: F 470 PHE cc_start: 0.7410 (t80) cc_final: 0.7167 (p90) REVERT: F 484 LYS cc_start: 0.8561 (tptt) cc_final: 0.8329 (tppt) REVERT: F 525 GLU cc_start: 0.7623 (tt0) cc_final: 0.6934 (tt0) REVERT: F 526 LYS cc_start: 0.8447 (mmtt) cc_final: 0.7903 (mmtt) REVERT: F 537 GLU cc_start: 0.7615 (tp30) cc_final: 0.7154 (tp30) REVERT: B 14 SER cc_start: 0.8149 (t) cc_final: 0.7579 (m) REVERT: B 64 ILE cc_start: 0.8571 (tp) cc_final: 0.8349 (pt) REVERT: B 162 ASN cc_start: 0.8397 (m-40) cc_final: 0.8167 (t0) REVERT: B 202 THR cc_start: 0.8494 (m) cc_final: 0.7936 (p) REVERT: B 205 GLU cc_start: 0.7299 (mp0) cc_final: 0.5824 (mp0) REVERT: B 217 CYS cc_start: 0.8125 (m) cc_final: 0.7805 (m) REVERT: B 244 ASP cc_start: 0.8283 (p0) cc_final: 0.8041 (p0) REVERT: G 33 LEU cc_start: 0.5913 (mt) cc_final: 0.4313 (pt) REVERT: G 280 GLU cc_start: 0.4905 (mt-10) cc_final: 0.4608 (tt0) REVERT: G 313 ILE cc_start: 0.6782 (mm) cc_final: 0.6504 (mm) REVERT: G 345 GLU cc_start: 0.7860 (pp20) cc_final: 0.6961 (tt0) REVERT: G 353 THR cc_start: 0.8404 (p) cc_final: 0.8184 (p) REVERT: G 357 MET cc_start: 0.5735 (mmm) cc_final: 0.4823 (mmm) REVERT: G 422 TYR cc_start: 0.7571 (m-80) cc_final: 0.7012 (m-10) REVERT: G 429 LYS cc_start: 0.7972 (ptpp) cc_final: 0.7595 (mtmt) REVERT: G 436 PHE cc_start: 0.7495 (t80) cc_final: 0.7184 (t80) REVERT: G 539 MET cc_start: 0.8348 (mmm) cc_final: 0.7971 (mmp) REVERT: G 700 GLU cc_start: 0.5312 (tm-30) cc_final: 0.5036 (tm-30) REVERT: C 132 MET cc_start: 0.8312 (ppp) cc_final: 0.7819 (ppp) REVERT: C 143 TYR cc_start: 0.8441 (m-80) cc_final: 0.7882 (m-80) REVERT: C 291 LYS cc_start: 0.7713 (tttt) cc_final: 0.7469 (ttmt) REVERT: C 325 MET cc_start: 0.8503 (tpp) cc_final: 0.8059 (tpp) REVERT: H 165 MET cc_start: 0.6249 (tpt) cc_final: 0.5845 (tpp) REVERT: H 359 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.7006 (m-10) REVERT: H 387 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8771 (mm) REVERT: H 436 PHE cc_start: 0.8398 (t80) cc_final: 0.8087 (t80) REVERT: H 486 GLN cc_start: 0.8080 (tp-100) cc_final: 0.7446 (tp-100) REVERT: H 553 TYR cc_start: 0.8024 (m-80) cc_final: 0.7806 (m-80) REVERT: H 565 LYS cc_start: 0.8429 (mmmt) cc_final: 0.7831 (mmmt) REVERT: H 657 LYS cc_start: 0.7823 (tmtm) cc_final: 0.7349 (tptp) REVERT: H 659 MET cc_start: 0.7669 (tpp) cc_final: 0.7317 (tpt) REVERT: E 127 PHE cc_start: 0.8290 (m-80) cc_final: 0.8066 (m-80) REVERT: E 250 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7511 (pt) REVERT: E 253 GLU cc_start: 0.7373 (mp0) cc_final: 0.7132 (mp0) REVERT: E 284 LYS cc_start: 0.8500 (tppp) cc_final: 0.8140 (tppt) REVERT: E 296 ASN cc_start: 0.8496 (m-40) cc_final: 0.8290 (m-40) REVERT: D 99 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7245 (mm-30) REVERT: D 167 GLU cc_start: 0.7563 (tp30) cc_final: 0.7341 (tp30) REVERT: D 253 GLU cc_start: 0.7997 (mp0) cc_final: 0.7709 (mp0) REVERT: D 291 LYS cc_start: 0.8376 (tttt) cc_final: 0.8061 (ttpp) REVERT: D 296 ASN cc_start: 0.8363 (m-40) cc_final: 0.8010 (m-40) REVERT: D 328 LYS cc_start: 0.7946 (tttt) cc_final: 0.7600 (tttm) REVERT: D 330 ILE cc_start: 0.9142 (mp) cc_final: 0.8890 (mm) outliers start: 83 outliers final: 41 residues processed: 888 average time/residue: 0.1983 time to fit residues: 287.6201 Evaluate side-chains 825 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 781 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 486 GLN Chi-restraints excluded: chain F residue 538 CYS Chi-restraints excluded: chain F residue 545 ASP Chi-restraints excluded: chain F residue 674 ILE Chi-restraints excluded: chain F residue 770 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 521 ILE Chi-restraints excluded: chain G residue 646 THR Chi-restraints excluded: chain G residue 674 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain H residue 6 MET Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 262 ASP Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 359 PHE Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 538 CYS Chi-restraints excluded: chain H residue 557 LEU Chi-restraints excluded: chain H residue 674 ILE Chi-restraints excluded: chain H residue 702 ILE Chi-restraints excluded: chain H residue 761 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 308 optimal weight: 3.9990 chunk 419 optimal weight: 20.0000 chunk 366 optimal weight: 5.9990 chunk 191 optimal weight: 20.0000 chunk 154 optimal weight: 50.0000 chunk 102 optimal weight: 6.9990 chunk 373 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 300 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 425 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS F 104 ASN F 126 ASN ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 490 ASN F 651 HIS F 666 HIS B 12 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 219 GLN ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 691 HIS H 135 ASN ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 482 ASN ** H 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.167671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.140039 restraints weight = 78661.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.139817 restraints weight = 81914.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.141102 restraints weight = 66475.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.141616 restraints weight = 39163.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.142157 restraints weight = 35891.761| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 34619 Z= 0.241 Angle : 0.745 9.369 46858 Z= 0.378 Chirality : 0.047 0.264 5197 Planarity : 0.005 0.098 6060 Dihedral : 6.122 88.243 4764 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.31 % Allowed : 16.45 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.13), residues: 4052 helix: -0.61 (0.12), residues: 1684 sheet: -2.19 (0.23), residues: 457 loop : -1.50 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 703 TYR 0.031 0.002 TYR F 194 PHE 0.026 0.002 PHE H 494 TRP 0.027 0.003 TRP E 340 HIS 0.018 0.002 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00556 (34619) covalent geometry : angle 0.74539 (46858) hydrogen bonds : bond 0.03907 ( 1508) hydrogen bonds : angle 5.12982 ( 4146) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 830 time to evaluate : 0.962 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: A 24 ASP cc_start: 0.8624 (m-30) cc_final: 0.8198 (m-30) REVERT: A 61 LYS cc_start: 0.8392 (mtmm) cc_final: 0.8083 (mttp) REVERT: A 64 ILE cc_start: 0.8859 (tp) cc_final: 0.8515 (pt) REVERT: A 143 TYR cc_start: 0.8773 (m-80) cc_final: 0.8311 (m-80) REVERT: A 191 LYS cc_start: 0.8026 (ttmt) cc_final: 0.7660 (ttpp) REVERT: A 259 GLU cc_start: 0.8715 (tp30) cc_final: 0.7914 (mm-30) REVERT: F 17 ARG cc_start: 0.6090 (tpt170) cc_final: 0.5799 (tpt170) REVERT: F 99 PRO cc_start: 0.6509 (Cg_endo) cc_final: 0.6207 (Cg_exo) REVERT: F 163 GLN cc_start: 0.8221 (mt0) cc_final: 0.7893 (mp10) REVERT: F 165 MET cc_start: 0.7900 (tpt) cc_final: 0.7335 (tpt) REVERT: F 330 MET cc_start: 0.7000 (ttm) cc_final: 0.6744 (ttm) REVERT: F 433 GLU cc_start: 0.7511 (tt0) cc_final: 0.7077 (tm-30) REVERT: F 439 MET cc_start: 0.7723 (ttp) cc_final: 0.7238 (tmm) REVERT: F 478 ILE cc_start: 0.8690 (mm) cc_final: 0.8255 (mt) REVERT: F 484 LYS cc_start: 0.8706 (tptt) cc_final: 0.8243 (tppt) REVERT: F 486 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7054 (mm-40) REVERT: F 537 GLU cc_start: 0.7926 (tp30) cc_final: 0.7473 (tp30) REVERT: F 687 PRO cc_start: 0.8018 (Cg_exo) cc_final: 0.7650 (Cg_endo) REVERT: B 14 SER cc_start: 0.8119 (t) cc_final: 0.7743 (m) REVERT: B 82 MET cc_start: 0.8240 (mmm) cc_final: 0.7990 (tmm) REVERT: B 202 THR cc_start: 0.8822 (m) cc_final: 0.8196 (p) REVERT: B 205 GLU cc_start: 0.7392 (mp0) cc_final: 0.6088 (mp0) REVERT: B 217 CYS cc_start: 0.8211 (m) cc_final: 0.7843 (m) REVERT: G 92 MET cc_start: 0.6624 (OUTLIER) cc_final: 0.6274 (mmm) REVERT: G 280 GLU cc_start: 0.5133 (mt-10) cc_final: 0.4887 (tt0) REVERT: G 357 MET cc_start: 0.5939 (mmm) cc_final: 0.5041 (mmm) REVERT: G 429 LYS cc_start: 0.7994 (ptpp) cc_final: 0.7569 (mtmm) REVERT: G 436 PHE cc_start: 0.7635 (t80) cc_final: 0.7365 (t80) REVERT: G 528 MET cc_start: 0.8556 (mmm) cc_final: 0.8252 (tpp) REVERT: G 546 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6928 (mtp) REVERT: G 596 LYS cc_start: 0.8340 (ptpt) cc_final: 0.8120 (ptmt) REVERT: C 128 ASN cc_start: 0.8594 (p0) cc_final: 0.8351 (p0) REVERT: C 132 MET cc_start: 0.8231 (ppp) cc_final: 0.7845 (ppp) REVERT: C 143 TYR cc_start: 0.8547 (m-80) cc_final: 0.7957 (m-80) REVERT: C 244 ASP cc_start: 0.8392 (p0) cc_final: 0.7942 (p0) REVERT: C 325 MET cc_start: 0.8541 (tpp) cc_final: 0.8317 (tpt) REVERT: H 172 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7651 (tp40) REVERT: H 422 TYR cc_start: 0.8100 (m-80) cc_final: 0.7666 (m-80) REVERT: H 434 LYS cc_start: 0.8077 (mmtm) cc_final: 0.7798 (mmtm) REVERT: H 436 PHE cc_start: 0.8420 (t80) cc_final: 0.8098 (t80) REVERT: H 451 GLN cc_start: 0.6963 (mp10) cc_final: 0.6681 (mp10) REVERT: H 473 PHE cc_start: 0.8223 (t80) cc_final: 0.7995 (t80) REVERT: H 486 GLN cc_start: 0.8223 (tp-100) cc_final: 0.7931 (tp-100) REVERT: H 553 TYR cc_start: 0.8493 (m-80) cc_final: 0.8066 (m-80) REVERT: H 565 LYS cc_start: 0.8493 (mmmt) cc_final: 0.7972 (mmmt) REVERT: H 657 LYS cc_start: 0.8159 (tmtm) cc_final: 0.7744 (tptp) REVERT: H 659 MET cc_start: 0.7822 (tpp) cc_final: 0.6764 (tpt) REVERT: E 16 LEU cc_start: 0.9148 (mt) cc_final: 0.8938 (mp) REVERT: E 81 ASP cc_start: 0.7641 (m-30) cc_final: 0.7428 (m-30) REVERT: E 143 TYR cc_start: 0.8472 (m-80) cc_final: 0.7860 (m-80) REVERT: E 250 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.8038 (pt) REVERT: E 253 GLU cc_start: 0.7529 (mp0) cc_final: 0.7140 (mp0) REVERT: E 284 LYS cc_start: 0.8720 (tppp) cc_final: 0.8236 (tppt) REVERT: E 296 ASN cc_start: 0.8271 (m-40) cc_final: 0.8040 (m-40) REVERT: E 314 GLN cc_start: 0.6975 (tt0) cc_final: 0.6655 (tt0) REVERT: E 325 MET cc_start: 0.8031 (tpp) cc_final: 0.7728 (tpp) REVERT: D 167 GLU cc_start: 0.7626 (tp30) cc_final: 0.7237 (tp30) REVERT: D 252 ASN cc_start: 0.8255 (p0) cc_final: 0.7953 (p0) REVERT: D 253 GLU cc_start: 0.8168 (mp0) cc_final: 0.7939 (mp0) REVERT: D 291 LYS cc_start: 0.8352 (tttt) cc_final: 0.8028 (ttpp) REVERT: D 296 ASN cc_start: 0.8259 (m-40) cc_final: 0.7935 (m-40) REVERT: D 361 GLU cc_start: 0.8019 (tp30) cc_final: 0.7794 (tp30) outliers start: 111 outliers final: 66 residues processed: 886 average time/residue: 0.1927 time to fit residues: 281.5491 Evaluate side-chains 835 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 766 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 538 CYS Chi-restraints excluded: chain F residue 770 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain G residue 92 MET Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 446 THR Chi-restraints excluded: chain G residue 521 ILE Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 674 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 262 ASP Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 538 CYS Chi-restraints excluded: chain H residue 557 LEU Chi-restraints excluded: chain H residue 601 LEU Chi-restraints excluded: chain H residue 674 ILE Chi-restraints excluded: chain H residue 699 LEU Chi-restraints excluded: chain H residue 702 ILE Chi-restraints excluded: chain H residue 761 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 307 optimal weight: 0.9990 chunk 381 optimal weight: 3.9990 chunk 250 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 324 optimal weight: 10.0000 chunk 330 optimal weight: 0.0070 chunk 314 optimal weight: 7.9990 chunk 417 optimal weight: 30.0000 chunk 110 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 576 HIS F 595 GLN B 12 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 GLN ** H 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 HIS H 358 HIS ** H 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 518 GLN H 562 ASN H 576 HIS ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.174429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.157816 restraints weight = 69342.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.151329 restraints weight = 108814.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.149120 restraints weight = 74337.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.148936 restraints weight = 82701.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.149390 restraints weight = 65268.283| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 34619 Z= 0.127 Angle : 0.650 11.586 46858 Z= 0.325 Chirality : 0.043 0.242 5197 Planarity : 0.004 0.057 6060 Dihedral : 5.750 89.054 4764 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.48 % Allowed : 18.42 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.13), residues: 4052 helix: -0.30 (0.12), residues: 1699 sheet: -1.89 (0.24), residues: 442 loop : -1.29 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 237 TYR 0.026 0.002 TYR G 455 PHE 0.023 0.002 PHE G 95 TRP 0.025 0.002 TRP A 340 HIS 0.016 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00286 (34619) covalent geometry : angle 0.65016 (46858) hydrogen bonds : bond 0.03263 ( 1508) hydrogen bonds : angle 4.72543 ( 4146) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 823 time to evaluate : 1.237 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: A 24 ASP cc_start: 0.8315 (m-30) cc_final: 0.7823 (m-30) REVERT: A 61 LYS cc_start: 0.8307 (mtmm) cc_final: 0.8026 (mttp) REVERT: A 64 ILE cc_start: 0.8744 (tp) cc_final: 0.8425 (pt) REVERT: A 118 LYS cc_start: 0.8438 (tppt) cc_final: 0.8010 (tptt) REVERT: A 143 TYR cc_start: 0.8735 (m-80) cc_final: 0.8344 (m-80) REVERT: A 191 LYS cc_start: 0.7979 (ttmt) cc_final: 0.7713 (ttpp) REVERT: A 259 GLU cc_start: 0.8473 (tp30) cc_final: 0.8018 (mm-30) REVERT: A 337 TYR cc_start: 0.8158 (m-80) cc_final: 0.7891 (m-80) REVERT: F 99 PRO cc_start: 0.6318 (Cg_endo) cc_final: 0.6041 (Cg_exo) REVERT: F 165 MET cc_start: 0.8063 (tpt) cc_final: 0.7830 (tpt) REVERT: F 239 ASP cc_start: 0.7573 (m-30) cc_final: 0.7280 (t70) REVERT: F 330 MET cc_start: 0.6863 (ttm) cc_final: 0.6659 (ttm) REVERT: F 433 GLU cc_start: 0.7404 (tt0) cc_final: 0.6918 (tm-30) REVERT: F 439 MET cc_start: 0.7410 (ttp) cc_final: 0.7060 (tmm) REVERT: F 525 GLU cc_start: 0.7431 (tt0) cc_final: 0.7085 (tt0) REVERT: F 537 GLU cc_start: 0.7605 (tp30) cc_final: 0.7266 (tp30) REVERT: B 202 THR cc_start: 0.8465 (m) cc_final: 0.8071 (p) REVERT: B 205 GLU cc_start: 0.7019 (mp0) cc_final: 0.5913 (mp0) REVERT: B 217 CYS cc_start: 0.7864 (m) cc_final: 0.7414 (m) REVERT: B 253 GLU cc_start: 0.8506 (mp0) cc_final: 0.8003 (mt-10) REVERT: G 160 ASN cc_start: 0.7602 (p0) cc_final: 0.7224 (p0) REVERT: G 280 GLU cc_start: 0.4976 (mt-10) cc_final: 0.4594 (tt0) REVERT: G 357 MET cc_start: 0.5917 (mmm) cc_final: 0.5167 (mmm) REVERT: G 429 LYS cc_start: 0.8174 (ptpp) cc_final: 0.7782 (mtmm) REVERT: G 436 PHE cc_start: 0.7574 (t80) cc_final: 0.7120 (t80) REVERT: C 128 ASN cc_start: 0.8532 (p0) cc_final: 0.8276 (p0) REVERT: C 132 MET cc_start: 0.8207 (ppp) cc_final: 0.7940 (ptm) REVERT: C 191 LYS cc_start: 0.8374 (ttmm) cc_final: 0.8094 (ttpt) REVERT: C 244 ASP cc_start: 0.7821 (p0) cc_final: 0.7378 (p0) REVERT: C 291 LYS cc_start: 0.7838 (ttmt) cc_final: 0.7509 (ttpt) REVERT: H 165 MET cc_start: 0.6356 (tpt) cc_final: 0.5929 (tpt) REVERT: H 170 GLU cc_start: 0.5805 (pt0) cc_final: 0.5589 (pm20) REVERT: H 171 ASN cc_start: 0.7561 (t0) cc_final: 0.7320 (t0) REVERT: H 172 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7117 (mm-40) REVERT: H 367 LYS cc_start: 0.7690 (mtpt) cc_final: 0.7472 (mtpp) REVERT: H 434 LYS cc_start: 0.7843 (mmtm) cc_final: 0.7628 (mmtm) REVERT: H 435 MET cc_start: 0.8479 (tmm) cc_final: 0.8207 (tmm) REVERT: H 436 PHE cc_start: 0.8336 (t80) cc_final: 0.7994 (t80) REVERT: H 451 GLN cc_start: 0.6879 (mp10) cc_final: 0.6643 (mp10) REVERT: H 486 GLN cc_start: 0.7873 (tp-100) cc_final: 0.7380 (tp-100) REVERT: H 657 LYS cc_start: 0.7891 (tmtm) cc_final: 0.7481 (tptp) REVERT: H 659 MET cc_start: 0.7747 (tpp) cc_final: 0.6919 (tpt) REVERT: E 16 LEU cc_start: 0.9168 (mt) cc_final: 0.8936 (mp) REVERT: E 143 TYR cc_start: 0.8471 (m-80) cc_final: 0.7968 (m-80) REVERT: E 250 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7893 (pt) REVERT: E 253 GLU cc_start: 0.7361 (mp0) cc_final: 0.7018 (pm20) REVERT: E 284 LYS cc_start: 0.8626 (tppp) cc_final: 0.8404 (tppt) REVERT: E 314 GLN cc_start: 0.6464 (tt0) cc_final: 0.6255 (tt0) REVERT: E 369 ILE cc_start: 0.9018 (tp) cc_final: 0.8711 (tp) REVERT: D 167 GLU cc_start: 0.7394 (tp30) cc_final: 0.7007 (tp30) REVERT: D 202 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8578 (t) REVERT: D 253 GLU cc_start: 0.7959 (mp0) cc_final: 0.7704 (mp0) REVERT: D 283 MET cc_start: 0.8268 (mmm) cc_final: 0.8065 (mmt) outliers start: 82 outliers final: 57 residues processed: 868 average time/residue: 0.1947 time to fit residues: 279.4165 Evaluate side-chains 817 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 758 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 153 HIS Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 521 ILE Chi-restraints excluded: chain F residue 538 CYS Chi-restraints excluded: chain F residue 545 ASP Chi-restraints excluded: chain F residue 674 ILE Chi-restraints excluded: chain F residue 702 ILE Chi-restraints excluded: chain F residue 770 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 521 ILE Chi-restraints excluded: chain G residue 658 LEU Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 674 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 262 ASP Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 538 CYS Chi-restraints excluded: chain H residue 557 LEU Chi-restraints excluded: chain H residue 617 LEU Chi-restraints excluded: chain H residue 674 ILE Chi-restraints excluded: chain H residue 699 LEU Chi-restraints excluded: chain H residue 702 ILE Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 248 optimal weight: 0.0170 chunk 16 optimal weight: 4.9990 chunk 234 optimal weight: 6.9990 chunk 341 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 294 optimal weight: 0.0370 chunk 219 optimal weight: 7.9990 chunk 306 optimal weight: 10.0000 chunk 195 optimal weight: 7.9990 chunk 330 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 overall best weight: 2.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 475 GLN ** F 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 444 ASN G 486 GLN ** G 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 HIS ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 518 GLN ** H 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.168915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.151877 restraints weight = 93283.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.149517 restraints weight = 139518.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.145672 restraints weight = 70221.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145837 restraints weight = 90117.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.146358 restraints weight = 53260.527| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 34619 Z= 0.155 Angle : 0.670 14.352 46858 Z= 0.332 Chirality : 0.044 0.206 5197 Planarity : 0.004 0.050 6060 Dihedral : 5.710 88.838 4764 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.71 % Allowed : 19.36 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.13), residues: 4052 helix: -0.12 (0.13), residues: 1695 sheet: -1.79 (0.25), residues: 448 loop : -1.26 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 237 TYR 0.023 0.002 TYR G 455 PHE 0.026 0.002 PHE G 488 TRP 0.024 0.002 TRP A 340 HIS 0.018 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00360 (34619) covalent geometry : angle 0.67005 (46858) hydrogen bonds : bond 0.03296 ( 1508) hydrogen bonds : angle 4.66202 ( 4146) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 789 time to evaluate : 1.184 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: A 24 ASP cc_start: 0.8360 (m-30) cc_final: 0.7872 (m-30) REVERT: A 61 LYS cc_start: 0.8342 (mtmm) cc_final: 0.8006 (mttp) REVERT: A 64 ILE cc_start: 0.8746 (tp) cc_final: 0.8408 (pt) REVERT: A 118 LYS cc_start: 0.8435 (tppt) cc_final: 0.8227 (tptt) REVERT: A 143 TYR cc_start: 0.8742 (m-80) cc_final: 0.8337 (m-80) REVERT: A 191 LYS cc_start: 0.8072 (ttmt) cc_final: 0.7729 (ttpp) REVERT: A 259 GLU cc_start: 0.8566 (tp30) cc_final: 0.7869 (mm-30) REVERT: F 44 GLU cc_start: 0.6529 (mm-30) cc_final: 0.6240 (mm-30) REVERT: F 99 PRO cc_start: 0.6382 (Cg_endo) cc_final: 0.6037 (Cg_exo) REVERT: F 165 MET cc_start: 0.8156 (tpt) cc_final: 0.7398 (tpt) REVERT: F 239 ASP cc_start: 0.7716 (m-30) cc_final: 0.7422 (t70) REVERT: F 410 TYR cc_start: 0.7550 (m-10) cc_final: 0.7306 (m-80) REVERT: F 439 MET cc_start: 0.7478 (ttp) cc_final: 0.7094 (tmm) REVERT: F 484 LYS cc_start: 0.8496 (tttt) cc_final: 0.8146 (tttm) REVERT: F 525 GLU cc_start: 0.7478 (tt0) cc_final: 0.7178 (tt0) REVERT: F 537 GLU cc_start: 0.7772 (tp30) cc_final: 0.7475 (tp30) REVERT: B 14 SER cc_start: 0.7708 (t) cc_final: 0.7490 (m) REVERT: B 202 THR cc_start: 0.8678 (m) cc_final: 0.8215 (p) REVERT: B 205 GLU cc_start: 0.7133 (mp0) cc_final: 0.5947 (mp0) REVERT: B 217 CYS cc_start: 0.7950 (m) cc_final: 0.7449 (m) REVERT: B 253 GLU cc_start: 0.8590 (mp0) cc_final: 0.7944 (mt-10) REVERT: B 259 GLU cc_start: 0.8503 (tp30) cc_final: 0.8075 (tp30) REVERT: G 92 MET cc_start: 0.6762 (OUTLIER) cc_final: 0.6542 (mmm) REVERT: G 280 GLU cc_start: 0.5014 (mt-10) cc_final: 0.4756 (tt0) REVERT: G 357 MET cc_start: 0.5947 (mmm) cc_final: 0.5093 (mmm) REVERT: G 429 LYS cc_start: 0.8108 (ptpp) cc_final: 0.7678 (mtmt) REVERT: G 436 PHE cc_start: 0.7542 (t80) cc_final: 0.7311 (t80) REVERT: C 128 ASN cc_start: 0.8568 (p0) cc_final: 0.8336 (p0) REVERT: C 132 MET cc_start: 0.8253 (ppp) cc_final: 0.8022 (ptm) REVERT: C 143 TYR cc_start: 0.8447 (m-80) cc_final: 0.7999 (m-80) REVERT: C 244 ASP cc_start: 0.8167 (p0) cc_final: 0.7612 (p0) REVERT: H 6 MET cc_start: 0.3139 (tpt) cc_final: 0.2573 (tpt) REVERT: H 113 MET cc_start: 0.5719 (ttp) cc_final: 0.5246 (ttm) REVERT: H 165 MET cc_start: 0.6429 (tpt) cc_final: 0.6114 (tpt) REVERT: H 171 ASN cc_start: 0.7601 (t0) cc_final: 0.7289 (t0) REVERT: H 172 GLN cc_start: 0.7723 (mm-40) cc_final: 0.7201 (tp40) REVERT: H 367 LYS cc_start: 0.7744 (mtpt) cc_final: 0.7516 (mtpp) REVERT: H 435 MET cc_start: 0.8403 (tmm) cc_final: 0.8130 (tmm) REVERT: H 436 PHE cc_start: 0.8332 (t80) cc_final: 0.8090 (t80) REVERT: H 486 GLN cc_start: 0.7910 (tp40) cc_final: 0.7332 (tp-100) REVERT: H 657 LYS cc_start: 0.7995 (tmtm) cc_final: 0.7580 (tptp) REVERT: H 696 ASN cc_start: 0.6806 (p0) cc_final: 0.6440 (p0) REVERT: E 16 LEU cc_start: 0.9194 (mt) cc_final: 0.8928 (mp) REVERT: E 143 TYR cc_start: 0.8449 (m-80) cc_final: 0.7859 (m-80) REVERT: E 248 ILE cc_start: 0.8661 (pt) cc_final: 0.8314 (pt) REVERT: E 250 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7930 (pt) REVERT: E 253 GLU cc_start: 0.7353 (mp0) cc_final: 0.7101 (pm20) REVERT: E 284 LYS cc_start: 0.8744 (tppp) cc_final: 0.8473 (tppt) REVERT: D 68 LYS cc_start: 0.8562 (mmmt) cc_final: 0.8279 (mmtm) REVERT: D 167 GLU cc_start: 0.7487 (tp30) cc_final: 0.7071 (tp30) REVERT: D 202 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8627 (t) REVERT: D 360 GLN cc_start: 0.7844 (pp30) cc_final: 0.7640 (pp30) outliers start: 90 outliers final: 65 residues processed: 834 average time/residue: 0.1930 time to fit residues: 267.1211 Evaluate side-chains 824 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 756 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 153 HIS Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 521 ILE Chi-restraints excluded: chain F residue 545 ASP Chi-restraints excluded: chain F residue 674 ILE Chi-restraints excluded: chain F residue 770 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain G residue 92 MET Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 444 ASN Chi-restraints excluded: chain G residue 445 THR Chi-restraints excluded: chain G residue 486 GLN Chi-restraints excluded: chain G residue 521 ILE Chi-restraints excluded: chain G residue 620 LEU Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 674 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 262 ASP Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 457 ILE Chi-restraints excluded: chain H residue 538 CYS Chi-restraints excluded: chain H residue 557 LEU Chi-restraints excluded: chain H residue 601 LEU Chi-restraints excluded: chain H residue 674 ILE Chi-restraints excluded: chain H residue 699 LEU Chi-restraints excluded: chain H residue 702 ILE Chi-restraints excluded: chain H residue 714 LEU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 396 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 276 optimal weight: 20.0000 chunk 334 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 366 optimal weight: 0.7980 chunk 135 optimal weight: 6.9990 chunk 200 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS F 65 HIS ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 486 GLN ** F 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 240 ASN ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 451 GLN G 486 GLN ** G 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 518 GLN ** H 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 755 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.172239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.155587 restraints weight = 91038.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.153042 restraints weight = 145804.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.149375 restraints weight = 73415.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.149762 restraints weight = 66951.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.150247 restraints weight = 41222.165| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.6171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 34619 Z= 0.164 Angle : 0.683 14.031 46858 Z= 0.338 Chirality : 0.044 0.176 5197 Planarity : 0.004 0.047 6060 Dihedral : 5.701 89.329 4764 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.05 % Allowed : 19.53 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.13), residues: 4052 helix: -0.07 (0.13), residues: 1692 sheet: -1.61 (0.25), residues: 442 loop : -1.26 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 290 TYR 0.024 0.002 TYR G 194 PHE 0.036 0.002 PHE G 470 TRP 0.020 0.002 TRP E 340 HIS 0.022 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00382 (34619) covalent geometry : angle 0.68290 (46858) hydrogen bonds : bond 0.03286 ( 1508) hydrogen bonds : angle 4.65342 ( 4146) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 790 time to evaluate : 1.025 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: A 24 ASP cc_start: 0.8266 (m-30) cc_final: 0.7857 (m-30) REVERT: A 64 ILE cc_start: 0.8791 (tp) cc_final: 0.8435 (pt) REVERT: A 143 TYR cc_start: 0.8734 (m-80) cc_final: 0.8353 (m-80) REVERT: A 191 LYS cc_start: 0.8110 (ttmt) cc_final: 0.7725 (ttpp) REVERT: A 259 GLU cc_start: 0.8601 (tp30) cc_final: 0.7848 (mm-30) REVERT: F 99 PRO cc_start: 0.6559 (Cg_endo) cc_final: 0.6151 (Cg_exo) REVERT: F 165 MET cc_start: 0.8246 (tpt) cc_final: 0.7963 (tpt) REVERT: F 239 ASP cc_start: 0.7716 (m-30) cc_final: 0.7360 (t70) REVERT: F 410 TYR cc_start: 0.7749 (m-10) cc_final: 0.7481 (m-80) REVERT: F 439 MET cc_start: 0.7341 (ttp) cc_final: 0.7035 (tmm) REVERT: F 484 LYS cc_start: 0.8433 (tttt) cc_final: 0.8081 (tttm) REVERT: F 700 GLU cc_start: 0.7240 (pp20) cc_final: 0.6196 (pp20) REVERT: B 202 THR cc_start: 0.8739 (m) cc_final: 0.8305 (p) REVERT: B 205 GLU cc_start: 0.7190 (mp0) cc_final: 0.6183 (mp0) REVERT: B 217 CYS cc_start: 0.7924 (m) cc_final: 0.7384 (m) REVERT: G 160 ASN cc_start: 0.7577 (p0) cc_final: 0.7179 (p0) REVERT: G 280 GLU cc_start: 0.5177 (mt-10) cc_final: 0.4778 (tt0) REVERT: G 357 MET cc_start: 0.5828 (mmm) cc_final: 0.5056 (mmm) REVERT: G 429 LYS cc_start: 0.8139 (ptpp) cc_final: 0.7750 (mtmm) REVERT: G 436 PHE cc_start: 0.7676 (t80) cc_final: 0.7384 (t80) REVERT: G 531 MET cc_start: 0.6968 (tmm) cc_final: 0.6759 (tmm) REVERT: C 128 ASN cc_start: 0.8567 (p0) cc_final: 0.8332 (p0) REVERT: C 132 MET cc_start: 0.8242 (ppp) cc_final: 0.7998 (ptm) REVERT: C 244 ASP cc_start: 0.8153 (p0) cc_final: 0.7626 (p0) REVERT: H 6 MET cc_start: 0.3290 (tpt) cc_final: 0.3023 (tpt) REVERT: H 336 PHE cc_start: 0.3467 (OUTLIER) cc_final: 0.1985 (m-10) REVERT: H 367 LYS cc_start: 0.7765 (mtpt) cc_final: 0.7212 (mtpp) REVERT: H 435 MET cc_start: 0.8284 (tmm) cc_final: 0.7989 (tmm) REVERT: H 436 PHE cc_start: 0.8351 (t80) cc_final: 0.8097 (t80) REVERT: H 486 GLN cc_start: 0.7838 (tp40) cc_final: 0.7410 (tp-100) REVERT: H 657 LYS cc_start: 0.8001 (tmtm) cc_final: 0.7627 (tptp) REVERT: H 659 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7085 (tmm) REVERT: H 696 ASN cc_start: 0.6808 (p0) cc_final: 0.6373 (p0) REVERT: H 755 GLN cc_start: 0.4153 (tp-100) cc_final: 0.3660 (tm-30) REVERT: E 16 LEU cc_start: 0.9175 (mt) cc_final: 0.8939 (mp) REVERT: E 143 TYR cc_start: 0.8471 (m-80) cc_final: 0.7858 (m-80) REVERT: E 250 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.8043 (pt) REVERT: E 252 ASN cc_start: 0.7647 (t0) cc_final: 0.7323 (t0) REVERT: E 253 GLU cc_start: 0.7476 (mp0) cc_final: 0.7064 (pm20) REVERT: E 284 LYS cc_start: 0.8746 (tppp) cc_final: 0.8430 (tppt) REVERT: D 68 LYS cc_start: 0.8540 (mmmt) cc_final: 0.8281 (mmtm) REVERT: D 167 GLU cc_start: 0.7523 (tp30) cc_final: 0.7104 (tp30) REVERT: D 202 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8465 (t) outliers start: 102 outliers final: 72 residues processed: 844 average time/residue: 0.1937 time to fit residues: 271.2021 Evaluate side-chains 837 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 761 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 153 HIS Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 521 ILE Chi-restraints excluded: chain F residue 545 ASP Chi-restraints excluded: chain F residue 702 ILE Chi-restraints excluded: chain F residue 770 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 378 THR Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 486 GLN Chi-restraints excluded: chain G residue 521 ILE Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 620 LEU Chi-restraints excluded: chain G residue 674 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 262 ASP Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 300 MET Chi-restraints excluded: chain H residue 336 PHE Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 457 ILE Chi-restraints excluded: chain H residue 538 CYS Chi-restraints excluded: chain H residue 557 LEU Chi-restraints excluded: chain H residue 659 MET Chi-restraints excluded: chain H residue 674 ILE Chi-restraints excluded: chain H residue 699 LEU Chi-restraints excluded: chain H residue 702 ILE Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 159 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 313 optimal weight: 5.9990 chunk 232 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 432 optimal weight: 20.0000 chunk 367 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 chunk 148 optimal weight: 30.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS F 160 ASN ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 475 GLN B 111 ASN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 518 GLN ** H 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.170174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.152993 restraints weight = 67509.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.151839 restraints weight = 100519.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.151836 restraints weight = 83009.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.151143 restraints weight = 62037.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.151725 restraints weight = 48022.447| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.6375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 34619 Z= 0.159 Angle : 0.689 13.879 46858 Z= 0.339 Chirality : 0.044 0.170 5197 Planarity : 0.004 0.047 6060 Dihedral : 5.629 80.087 4764 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.11 % Allowed : 19.79 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.13), residues: 4052 helix: -0.01 (0.13), residues: 1692 sheet: -1.56 (0.25), residues: 442 loop : -1.25 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 290 TYR 0.023 0.002 TYR G 266 PHE 0.032 0.002 PHE G 470 TRP 0.019 0.002 TRP E 340 HIS 0.010 0.001 HIS H 358 Details of bonding type rmsd covalent geometry : bond 0.00373 (34619) covalent geometry : angle 0.68945 (46858) hydrogen bonds : bond 0.03246 ( 1508) hydrogen bonds : angle 4.64160 ( 4146) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 794 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9051 (mp) REVERT: A 24 ASP cc_start: 0.8216 (m-30) cc_final: 0.7779 (m-30) REVERT: A 61 LYS cc_start: 0.8262 (mtmm) cc_final: 0.8049 (mttp) REVERT: A 64 ILE cc_start: 0.8755 (tp) cc_final: 0.8339 (pt) REVERT: A 143 TYR cc_start: 0.8705 (m-80) cc_final: 0.8329 (m-80) REVERT: A 191 LYS cc_start: 0.8067 (ttmt) cc_final: 0.7638 (ttpp) REVERT: A 270 GLU cc_start: 0.6689 (mm-30) cc_final: 0.6146 (mm-30) REVERT: F 410 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.7553 (m-80) REVERT: F 486 GLN cc_start: 0.7861 (tp-100) cc_final: 0.7406 (tp-100) REVERT: B 217 CYS cc_start: 0.7841 (m) cc_final: 0.7330 (m) REVERT: B 253 GLU cc_start: 0.8672 (mp0) cc_final: 0.8075 (mt-10) REVERT: G 160 ASN cc_start: 0.7118 (p0) cc_final: 0.6811 (p0) REVERT: G 280 GLU cc_start: 0.4823 (mt-10) cc_final: 0.4559 (tt0) REVERT: G 357 MET cc_start: 0.5567 (mmm) cc_final: 0.4838 (mmm) REVERT: G 429 LYS cc_start: 0.8187 (ptpp) cc_final: 0.7845 (mtmm) REVERT: C 128 ASN cc_start: 0.8576 (p0) cc_final: 0.8370 (p0) REVERT: C 167 GLU cc_start: 0.7825 (tp30) cc_final: 0.7591 (tp30) REVERT: C 244 ASP cc_start: 0.7970 (p0) cc_final: 0.7478 (p0) REVERT: H 138 VAL cc_start: 0.3322 (OUTLIER) cc_final: 0.2898 (p) REVERT: H 434 LYS cc_start: 0.7589 (mmtm) cc_final: 0.7274 (mmtm) REVERT: H 435 MET cc_start: 0.8210 (tmm) cc_final: 0.7864 (tmm) REVERT: H 436 PHE cc_start: 0.8230 (t80) cc_final: 0.8005 (t80) REVERT: H 657 LYS cc_start: 0.7861 (tmtm) cc_final: 0.7385 (tttt) REVERT: H 659 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7110 (tmm) REVERT: H 696 ASN cc_start: 0.6680 (p0) cc_final: 0.6281 (p0) REVERT: E 16 LEU cc_start: 0.9147 (mt) cc_final: 0.8936 (mp) REVERT: E 143 TYR cc_start: 0.8466 (m-80) cc_final: 0.7877 (m-80) REVERT: E 250 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7705 (pt) REVERT: E 284 LYS cc_start: 0.8664 (tppp) cc_final: 0.8360 (tppt) REVERT: E 291 LYS cc_start: 0.7840 (mttp) cc_final: 0.7373 (mtmm) REVERT: D 68 LYS cc_start: 0.8483 (mmmt) cc_final: 0.8094 (mmtm) REVERT: D 167 GLU cc_start: 0.7419 (tp30) cc_final: 0.7054 (tp30) REVERT: D 334 GLU cc_start: 0.6815 (mp0) cc_final: 0.6594 (mp0) outliers start: 104 outliers final: 75 residues processed: 845 average time/residue: 0.1871 time to fit residues: 262.0447 Evaluate side-chains 844 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 764 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 153 HIS Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 410 TYR Chi-restraints excluded: chain F residue 521 ILE Chi-restraints excluded: chain F residue 545 ASP Chi-restraints excluded: chain F residue 684 ILE Chi-restraints excluded: chain F residue 691 HIS Chi-restraints excluded: chain F residue 770 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 353 THR Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 489 PHE Chi-restraints excluded: chain G residue 620 LEU Chi-restraints excluded: chain G residue 669 PHE Chi-restraints excluded: chain G residue 674 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 262 ASP Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 446 THR Chi-restraints excluded: chain H residue 538 CYS Chi-restraints excluded: chain H residue 557 LEU Chi-restraints excluded: chain H residue 601 LEU Chi-restraints excluded: chain H residue 659 MET Chi-restraints excluded: chain H residue 674 ILE Chi-restraints excluded: chain H residue 702 ILE Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 368 optimal weight: 8.9990 chunk 402 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 426 optimal weight: 30.0000 chunk 51 optimal weight: 5.9990 chunk 419 optimal weight: 30.0000 chunk 323 optimal weight: 0.0870 chunk 93 optimal weight: 5.9990 chunk 297 optimal weight: 0.6980 chunk 427 optimal weight: 20.0000 chunk 201 optimal weight: 0.5980 overall best weight: 2.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 444 ASN ** G 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.170467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.152564 restraints weight = 72574.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.148384 restraints weight = 110968.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.145681 restraints weight = 69246.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.146114 restraints weight = 65083.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.146647 restraints weight = 45224.082| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.6554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 34619 Z= 0.157 Angle : 0.700 15.965 46858 Z= 0.344 Chirality : 0.044 0.266 5197 Planarity : 0.004 0.048 6060 Dihedral : 5.643 79.536 4764 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.88 % Allowed : 20.50 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.13), residues: 4052 helix: 0.02 (0.13), residues: 1689 sheet: -1.51 (0.24), residues: 454 loop : -1.16 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 17 TYR 0.022 0.002 TYR F 194 PHE 0.035 0.002 PHE G 488 TRP 0.020 0.002 TRP F 112 HIS 0.019 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00368 (34619) covalent geometry : angle 0.69952 (46858) hydrogen bonds : bond 0.03237 ( 1508) hydrogen bonds : angle 4.61875 ( 4146) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 804 time to evaluate : 1.122 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: A 16 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8962 (mp) REVERT: A 24 ASP cc_start: 0.8186 (m-30) cc_final: 0.7803 (m-30) REVERT: A 61 LYS cc_start: 0.8303 (mtmm) cc_final: 0.8050 (mttp) REVERT: A 143 TYR cc_start: 0.8688 (m-80) cc_final: 0.8333 (m-80) REVERT: A 191 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7810 (ttpp) REVERT: F 99 PRO cc_start: 0.6796 (Cg_endo) cc_final: 0.6257 (Cg_exo) REVERT: F 410 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.7631 (m-10) REVERT: F 486 GLN cc_start: 0.7913 (tp-100) cc_final: 0.7362 (tp-100) REVERT: F 521 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.7946 (mm) REVERT: B 217 CYS cc_start: 0.7923 (m) cc_final: 0.7409 (m) REVERT: G 160 ASN cc_start: 0.7454 (p0) cc_final: 0.7041 (p0) REVERT: G 280 GLU cc_start: 0.4951 (mt-10) cc_final: 0.4686 (tt0) REVERT: G 357 MET cc_start: 0.6109 (mmm) cc_final: 0.5160 (mmm) REVERT: G 429 LYS cc_start: 0.8148 (ptpp) cc_final: 0.7759 (mtmm) REVERT: G 539 MET cc_start: 0.8580 (mmm) cc_final: 0.8313 (mmp) REVERT: G 572 ARG cc_start: 0.6047 (mmp80) cc_final: 0.5833 (mmp80) REVERT: C 128 ASN cc_start: 0.8596 (p0) cc_final: 0.8353 (p0) REVERT: C 132 MET cc_start: 0.8223 (ptm) cc_final: 0.7836 (ppp) REVERT: C 244 ASP cc_start: 0.8169 (p0) cc_final: 0.7674 (p0) REVERT: H 113 MET cc_start: 0.5253 (ttp) cc_final: 0.4969 (ttm) REVERT: H 138 VAL cc_start: 0.3304 (OUTLIER) cc_final: 0.2881 (p) REVERT: H 435 MET cc_start: 0.8236 (tmm) cc_final: 0.7912 (tmm) REVERT: H 436 PHE cc_start: 0.8225 (t80) cc_final: 0.7924 (t80) REVERT: H 486 GLN cc_start: 0.7455 (tp-100) cc_final: 0.7190 (tp40) REVERT: H 657 LYS cc_start: 0.7814 (tmtm) cc_final: 0.7548 (tttt) REVERT: H 659 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.6962 (tmm) REVERT: H 662 LEU cc_start: 0.7785 (tp) cc_final: 0.7547 (tp) REVERT: H 696 ASN cc_start: 0.6880 (p0) cc_final: 0.6503 (p0) REVERT: E 16 LEU cc_start: 0.9166 (mt) cc_final: 0.8952 (mp) REVERT: E 143 TYR cc_start: 0.8472 (m-80) cc_final: 0.7875 (m-80) REVERT: E 252 ASN cc_start: 0.7663 (t0) cc_final: 0.7444 (t0) REVERT: E 284 LYS cc_start: 0.8668 (tppp) cc_final: 0.8375 (tppt) REVERT: D 68 LYS cc_start: 0.8539 (mmmt) cc_final: 0.8249 (mmtm) REVERT: D 167 GLU cc_start: 0.7378 (tp30) cc_final: 0.7075 (tp30) REVERT: D 283 MET cc_start: 0.8162 (mmm) cc_final: 0.7914 (mmp) outliers start: 96 outliers final: 78 residues processed: 847 average time/residue: 0.1940 time to fit residues: 272.3365 Evaluate side-chains 850 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 767 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 153 HIS Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 410 TYR Chi-restraints excluded: chain F residue 491 HIS Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 521 ILE Chi-restraints excluded: chain F residue 545 ASP Chi-restraints excluded: chain F residue 601 LEU Chi-restraints excluded: chain F residue 684 ILE Chi-restraints excluded: chain F residue 691 HIS Chi-restraints excluded: chain F residue 770 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 378 THR Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 444 ASN Chi-restraints excluded: chain G residue 669 PHE Chi-restraints excluded: chain G residue 674 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 262 ASP Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 446 THR Chi-restraints excluded: chain H residue 538 CYS Chi-restraints excluded: chain H residue 557 LEU Chi-restraints excluded: chain H residue 601 LEU Chi-restraints excluded: chain H residue 659 MET Chi-restraints excluded: chain H residue 674 ILE Chi-restraints excluded: chain H residue 702 ILE Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 4 optimal weight: 9.9990 chunk 363 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 356 optimal weight: 2.9990 chunk 289 optimal weight: 50.0000 chunk 349 optimal weight: 0.8980 chunk 75 optimal weight: 0.0010 chunk 319 optimal weight: 0.0770 chunk 287 optimal weight: 0.9990 chunk 229 optimal weight: 0.8980 overall best weight: 0.5746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS F 79 GLN ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 401 HIS ** F 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 444 ASN ** H 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 755 GLN D 12 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.176131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.160128 restraints weight = 85127.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.156410 restraints weight = 113350.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.151187 restraints weight = 72269.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.151987 restraints weight = 76831.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.152214 restraints weight = 55551.463| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3632 r_free = 0.3632 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3632 r_free = 0.3632 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.6639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 34619 Z= 0.125 Angle : 0.712 17.915 46858 Z= 0.348 Chirality : 0.043 0.202 5197 Planarity : 0.004 0.063 6060 Dihedral : 5.542 78.050 4764 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.00 % Allowed : 22.10 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 4052 helix: 0.09 (0.13), residues: 1695 sheet: -1.34 (0.25), residues: 449 loop : -1.10 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 281 TYR 0.022 0.001 TYR G 194 PHE 0.027 0.001 PHE G 470 TRP 0.025 0.002 TRP A 340 HIS 0.033 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00287 (34619) covalent geometry : angle 0.71224 (46858) hydrogen bonds : bond 0.03059 ( 1508) hydrogen bonds : angle 4.50877 ( 4146) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 795 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8101 (m-30) cc_final: 0.7709 (m-30) REVERT: A 143 TYR cc_start: 0.8595 (m-80) cc_final: 0.8242 (m-80) REVERT: A 191 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7780 (ttpp) REVERT: A 284 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.7907 (mmtm) REVERT: F 6 MET cc_start: 0.3768 (mmm) cc_final: 0.3124 (pmm) REVERT: F 34 LYS cc_start: 0.6151 (mptt) cc_final: 0.5891 (mptt) REVERT: F 99 PRO cc_start: 0.6763 (Cg_endo) cc_final: 0.6234 (Cg_exo) REVERT: F 280 GLU cc_start: 0.6423 (pm20) cc_final: 0.5923 (pm20) REVERT: F 302 LEU cc_start: 0.7585 (mp) cc_final: 0.6928 (mt) REVERT: F 410 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.7580 (m-10) REVERT: F 486 GLN cc_start: 0.7847 (tp-100) cc_final: 0.7310 (tp-100) REVERT: F 774 GLU cc_start: 0.6036 (tm-30) cc_final: 0.5598 (tm-30) REVERT: B 217 CYS cc_start: 0.7818 (m) cc_final: 0.7304 (m) REVERT: G 160 ASN cc_start: 0.7460 (p0) cc_final: 0.7085 (p0) REVERT: G 280 GLU cc_start: 0.4873 (mt-10) cc_final: 0.4663 (tt0) REVERT: G 357 MET cc_start: 0.6005 (mmm) cc_final: 0.5001 (mmm) REVERT: G 394 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7231 (t70) REVERT: G 429 LYS cc_start: 0.8093 (ptpp) cc_final: 0.7822 (mtmm) REVERT: C 128 ASN cc_start: 0.8550 (p0) cc_final: 0.8313 (p0) REVERT: C 133 TYR cc_start: 0.8409 (t80) cc_final: 0.8069 (t80) REVERT: C 244 ASP cc_start: 0.7940 (p0) cc_final: 0.7437 (p0) REVERT: H 113 MET cc_start: 0.5136 (ttp) cc_final: 0.4819 (ttm) REVERT: H 138 VAL cc_start: 0.3249 (OUTLIER) cc_final: 0.2827 (p) REVERT: H 434 LYS cc_start: 0.7628 (mmtm) cc_final: 0.7366 (mmtm) REVERT: H 436 PHE cc_start: 0.8216 (t80) cc_final: 0.7916 (t80) REVERT: H 486 GLN cc_start: 0.7382 (tp-100) cc_final: 0.7085 (tp-100) REVERT: H 562 ASN cc_start: 0.6871 (t0) cc_final: 0.6658 (m-40) REVERT: H 659 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.6823 (tmm) REVERT: H 696 ASN cc_start: 0.6786 (p0) cc_final: 0.6555 (p0) REVERT: E 16 LEU cc_start: 0.9095 (mt) cc_final: 0.8871 (mp) REVERT: E 143 TYR cc_start: 0.8476 (m-80) cc_final: 0.7903 (m-80) REVERT: D 68 LYS cc_start: 0.8450 (mmmt) cc_final: 0.8225 (mmtm) REVERT: D 167 GLU cc_start: 0.7295 (tp30) cc_final: 0.7003 (tp30) outliers start: 65 outliers final: 50 residues processed: 827 average time/residue: 0.1906 time to fit residues: 262.7618 Evaluate side-chains 832 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 777 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 153 HIS Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 410 TYR Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 545 ASP Chi-restraints excluded: chain F residue 674 ILE Chi-restraints excluded: chain F residue 684 ILE Chi-restraints excluded: chain F residue 770 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain G residue 80 ASN Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 394 ASP Chi-restraints excluded: chain G residue 674 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 257 LYS Chi-restraints excluded: chain H residue 262 ASP Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 538 CYS Chi-restraints excluded: chain H residue 557 LEU Chi-restraints excluded: chain H residue 659 MET Chi-restraints excluded: chain H residue 674 ILE Chi-restraints excluded: chain H residue 702 ILE Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 184 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 310 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 211 optimal weight: 0.0470 chunk 184 optimal weight: 5.9990 chunk 217 optimal weight: 10.0000 chunk 408 optimal weight: 20.0000 chunk 359 optimal weight: 0.9980 chunk 332 optimal weight: 20.0000 chunk 120 optimal weight: 0.9980 chunk 261 optimal weight: 0.0170 chunk 79 optimal weight: 10.0000 overall best weight: 1.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.172338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.155897 restraints weight = 82105.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.152042 restraints weight = 126589.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.148139 restraints weight = 75524.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.148695 restraints weight = 71985.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.149136 restraints weight = 48228.102| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.6729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34619 Z= 0.136 Angle : 0.714 20.166 46858 Z= 0.348 Chirality : 0.044 0.205 5197 Planarity : 0.004 0.087 6060 Dihedral : 5.503 77.344 4764 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.22 % Allowed : 21.96 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.13), residues: 4052 helix: 0.17 (0.13), residues: 1698 sheet: -1.26 (0.25), residues: 454 loop : -1.08 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 442 TYR 0.028 0.001 TYR G 266 PHE 0.022 0.001 PHE F 765 TRP 0.027 0.002 TRP F 438 HIS 0.011 0.001 HIS F 492 Details of bonding type rmsd covalent geometry : bond 0.00320 (34619) covalent geometry : angle 0.71362 (46858) hydrogen bonds : bond 0.03089 ( 1508) hydrogen bonds : angle 4.50994 ( 4146) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7260.73 seconds wall clock time: 125 minutes 34.71 seconds (7534.71 seconds total)