Starting phenix.real_space_refine on Tue Aug 26 16:25:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3j_44142/08_2025/9b3j_44142.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3j_44142/08_2025/9b3j_44142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b3j_44142/08_2025/9b3j_44142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3j_44142/08_2025/9b3j_44142.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3j_44142/08_2025/9b3j_44142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3j_44142/08_2025/9b3j_44142.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 1.020 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 16 5.49 5 Mg 4 5.21 5 S 166 5.16 5 C 24954 2.51 5 N 6617 2.21 5 O 7338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39095 Number of models: 1 Model: "" Number of chains: 33 Chain: "1" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "2" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "3" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "4" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "5" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "6" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "7" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "8" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "A" Number of atoms: 3815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3815 Classifications: {'peptide': 500} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 478} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3842 Classifications: {'peptide': 503} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} Chain: "C" Number of atoms: 3828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3828 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 479} Chain: "D" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3525 Classifications: {'peptide': 465} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 439} Chain: "E" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3454 Classifications: {'peptide': 455} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 432} Chain breaks: 1 Chain: "F" Number of atoms: 3554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3554 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 443} Chain: "G" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1792 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 226} Chain breaks: 3 Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 984 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "I" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 304 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "K" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1686 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 6, 'TRANS': 201} Chain: "L" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 594 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 4, 'TRANS': 70} Chain: "M" Number of atoms: 1309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1309 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 14, 'TRANS': 146} Chain: "N" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1695 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "O" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1463 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "P" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 220 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'TRANS': 43} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'UNK:plan-1': 44} Unresolved non-hydrogen planarities: 44 Chain: "Q" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "R" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 856 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 96} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "S" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 596 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain: "T" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 607 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 82 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "S" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 75 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Time building chain proxies: 9.37, per 1000 atoms: 0.24 Number of scatterers: 39095 At special positions: 0 Unit cell: (128.16, 159.132, 256.32, 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 166 16.00 P 16 15.00 Mg 4 11.99 O 7338 8.00 N 6617 7.00 C 24954 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: 3.12 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 9974 Ramachandran restraints generated. 4987 Oldfield, 0 Emsley, 4987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9304 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 29 sheets defined 58.8% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain '1' and resid 2 through 15 removed outlier: 3.602A pdb=" N LYS 1 7 " --> pdb=" O ASP 1 3 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE 1 8 " --> pdb=" O SER 1 4 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE 1 9 " --> pdb=" O ALA 1 5 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 39 Processing helix chain '1' and resid 42 through 74 removed outlier: 3.577A pdb=" N SER 1 48 " --> pdb=" O GLN 1 44 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 15 Processing helix chain '2' and resid 17 through 39 removed outlier: 3.763A pdb=" N SER 2 21 " --> pdb=" O GLY 2 17 " (cutoff:3.500A) Processing helix chain '2' and resid 42 through 71 Processing helix chain '3' and resid 2 through 16 Processing helix chain '3' and resid 18 through 39 Processing helix chain '3' and resid 40 through 43 removed outlier: 4.019A pdb=" N LYS 3 43 " --> pdb=" O PRO 3 40 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 40 through 43' Processing helix chain '3' and resid 44 through 74 Processing helix chain '4' and resid 2 through 15 Processing helix chain '4' and resid 17 through 39 removed outlier: 3.830A pdb=" N SER 4 21 " --> pdb=" O GLY 4 17 " (cutoff:3.500A) Processing helix chain '4' and resid 42 through 71 removed outlier: 4.619A pdb=" N ALA 4 59 " --> pdb=" O ALA 4 55 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 15 Processing helix chain '5' and resid 16 through 39 removed outlier: 4.222A pdb=" N GLY 5 20 " --> pdb=" O VAL 5 16 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER 5 21 " --> pdb=" O GLY 5 17 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 57 removed outlier: 3.715A pdb=" N SER 5 48 " --> pdb=" O GLN 5 44 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU 5 52 " --> pdb=" O SER 5 48 " (cutoff:3.500A) Processing helix chain '5' and resid 58 through 71 Processing helix chain '6' and resid 2 through 15 Processing helix chain '6' and resid 17 through 37 removed outlier: 3.801A pdb=" N SER 6 21 " --> pdb=" O GLY 6 17 " (cutoff:3.500A) Processing helix chain '6' and resid 39 through 43 Processing helix chain '6' and resid 44 through 65 removed outlier: 4.544A pdb=" N ALA 6 59 " --> pdb=" O ALA 6 55 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY 6 61 " --> pdb=" O SER 6 57 " (cutoff:3.500A) Processing helix chain '6' and resid 65 through 73 removed outlier: 3.760A pdb=" N LEU 6 71 " --> pdb=" O MET 6 67 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 15 Processing helix chain '7' and resid 17 through 39 removed outlier: 3.934A pdb=" N SER 7 21 " --> pdb=" O GLY 7 17 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG 7 38 " --> pdb=" O ILE 7 34 " (cutoff:3.500A) Processing helix chain '7' and resid 42 through 68 removed outlier: 3.702A pdb=" N ALA 7 55 " --> pdb=" O ILE 7 51 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA 7 59 " --> pdb=" O ALA 7 55 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 15 Processing helix chain '8' and resid 17 through 39 removed outlier: 4.277A pdb=" N SER 8 21 " --> pdb=" O GLY 8 17 " (cutoff:3.500A) Processing helix chain '8' and resid 42 through 74 removed outlier: 3.504A pdb=" N LEU 8 56 " --> pdb=" O LEU 8 52 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER 8 57 " --> pdb=" O GLY 8 53 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU 8 58 " --> pdb=" O PHE 8 54 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE 8 63 " --> pdb=" O ALA 8 59 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU 8 72 " --> pdb=" O ALA 8 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 19 Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.978A pdb=" N HIS A 81 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 82 " --> pdb=" O ASP A 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 78 through 82' Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.726A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.899A pdb=" N GLN A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 209 through 223 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 239 through 260 Proline residue: A 247 - end of helix removed outlier: 3.927A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.512A pdb=" N GLN A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 374 through 379 removed outlier: 4.003A pdb=" N ALA A 377 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN A 379 " --> pdb=" O SER A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 402 removed outlier: 4.025A pdb=" N SER A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 428 Processing helix chain 'A' and resid 437 through 450 Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 460 through 476 Processing helix chain 'A' and resid 476 through 487 removed outlier: 3.647A pdb=" N LEU A 480 " --> pdb=" O HIS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 509 Processing helix chain 'B' and resid 8 through 17 Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.743A pdb=" N HIS B 81 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.604A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.910A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 239 through 260 Proline residue: B 247 - end of helix removed outlier: 3.849A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.687A pdb=" N GLN B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.684A pdb=" N HIS B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.627A pdb=" N GLY B 317 " --> pdb=" O GLU B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 346 Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.673A pdb=" N ALA B 377 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 402 removed outlier: 3.952A pdb=" N SER B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 429 removed outlier: 3.723A pdb=" N LYS B 429 " --> pdb=" O THR B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 457 through 459 No H-bonds generated for 'chain 'B' and resid 457 through 459' Processing helix chain 'B' and resid 460 through 475 removed outlier: 3.890A pdb=" N SER B 469 " --> pdb=" O GLU B 465 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 487 removed outlier: 3.862A pdb=" N LEU B 480 " --> pdb=" O HIS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 508 Processing helix chain 'C' and resid 9 through 20 removed outlier: 4.019A pdb=" N ALA C 20 " --> pdb=" O ILE C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.983A pdb=" N HIS C 81 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.685A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 156 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.861A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 209 through 223 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 239 through 260 Proline residue: C 247 - end of helix removed outlier: 3.747A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.704A pdb=" N GLN C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 297 through 307 Processing helix chain 'C' and resid 336 through 346 Processing helix chain 'C' and resid 353 through 359 Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.687A pdb=" N ALA C 377 " --> pdb=" O VAL C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 401 removed outlier: 4.106A pdb=" N SER C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 429 removed outlier: 3.639A pdb=" N LYS C 429 " --> pdb=" O THR C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 450 Processing helix chain 'C' and resid 457 through 459 No H-bonds generated for 'chain 'C' and resid 457 through 459' Processing helix chain 'C' and resid 460 through 473 removed outlier: 4.319A pdb=" N SER C 469 " --> pdb=" O GLU C 465 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLN C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 487 removed outlier: 3.534A pdb=" N LEU C 480 " --> pdb=" O HIS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 507 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 192 through 206 Processing helix chain 'D' and resid 228 through 233 Processing helix chain 'D' and resid 234 through 248 Processing helix chain 'D' and resid 260 through 271 removed outlier: 3.968A pdb=" N PHE D 264 " --> pdb=" O ASN D 260 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER D 269 " --> pdb=" O THR D 265 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 284 removed outlier: 3.520A pdb=" N TYR D 284 " --> pdb=" O ALA D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 297 Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 322 through 330 removed outlier: 4.392A pdb=" N ALA D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 345 Processing helix chain 'D' and resid 367 through 395 removed outlier: 4.354A pdb=" N ASP D 389 " --> pdb=" O LYS D 385 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE D 390 " --> pdb=" O SER D 386 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE D 393 " --> pdb=" O ASP D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 418 removed outlier: 3.751A pdb=" N SER D 418 " --> pdb=" O GLN D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 429 Processing helix chain 'D' and resid 436 through 449 Processing helix chain 'D' and resid 456 through 461 Processing helix chain 'D' and resid 465 through 476 Processing helix chain 'E' and resid 90 through 94 removed outlier: 3.547A pdb=" N THR E 93 " --> pdb=" O GLY E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 146 Processing helix chain 'E' and resid 164 through 180 Processing helix chain 'E' and resid 192 through 206 Processing helix chain 'E' and resid 228 through 233 Processing helix chain 'E' and resid 234 through 249 Processing helix chain 'E' and resid 260 through 276 Processing helix chain 'E' and resid 292 through 298 Processing helix chain 'E' and resid 339 through 345 removed outlier: 3.604A pdb=" N ALA E 343 " --> pdb=" O SER E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 394 Processing helix chain 'E' and resid 401 through 418 removed outlier: 3.821A pdb=" N SER E 418 " --> pdb=" O GLN E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 449 Processing helix chain 'E' and resid 456 through 461 removed outlier: 3.593A pdb=" N TYR E 461 " --> pdb=" O VAL E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 480 Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 140 through 146 Processing helix chain 'F' and resid 164 through 179 Processing helix chain 'F' and resid 192 through 206 Processing helix chain 'F' and resid 228 through 249 removed outlier: 4.686A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 275 removed outlier: 3.708A pdb=" N PHE F 264 " --> pdb=" O ASN F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 284 Processing helix chain 'F' and resid 287 through 297 Processing helix chain 'F' and resid 315 through 319 removed outlier: 3.513A pdb=" N ASP F 318 " --> pdb=" O VAL F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 329 Processing helix chain 'F' and resid 339 through 345 Processing helix chain 'F' and resid 367 through 394 removed outlier: 4.112A pdb=" N ASP F 389 " --> pdb=" O LYS F 385 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE F 390 " --> pdb=" O SER F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 417 Processing helix chain 'F' and resid 424 through 429 Processing helix chain 'F' and resid 436 through 449 Processing helix chain 'F' and resid 456 through 461 Processing helix chain 'F' and resid 466 through 480 Processing helix chain 'G' and resid 3 through 56 removed outlier: 3.965A pdb=" N VAL G 40 " --> pdb=" O ARG G 36 " (cutoff:3.500A) Proline residue: G 43 - end of helix removed outlier: 4.144A pdb=" N PHE G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TYR G 52 " --> pdb=" O ALA G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 112 removed outlier: 4.318A pdb=" N ARG G 109 " --> pdb=" O GLY G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 146 removed outlier: 3.557A pdb=" N ALA G 137 " --> pdb=" O VAL G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 182 Processing helix chain 'G' and resid 184 through 189 removed outlier: 3.812A pdb=" N ALA G 187 " --> pdb=" O ASP G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 267 Processing helix chain 'H' and resid 104 through 123 removed outlier: 4.405A pdb=" N GLY H 123 " --> pdb=" O VAL H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 148 Processing helix chain 'I' and resid 12 through 16 Processing helix chain 'I' and resid 19 through 30 removed outlier: 3.561A pdb=" N SER I 23 " --> pdb=" O ASP I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 44 removed outlier: 3.799A pdb=" N GLU I 42 " --> pdb=" O GLU I 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 24 Processing helix chain 'K' and resid 32 through 48 Processing helix chain 'K' and resid 56 through 183 removed outlier: 5.800A pdb=" N LYS K 76 " --> pdb=" O LYS K 72 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N GLN K 77 " --> pdb=" O LYS K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 207 Processing helix chain 'L' and resid 5 through 25 Processing helix chain 'L' and resid 33 through 51 Processing helix chain 'M' and resid 26 through 44 removed outlier: 3.727A pdb=" N GLN M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP M 36 " --> pdb=" O LYS M 32 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA M 42 " --> pdb=" O TYR M 38 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER M 44 " --> pdb=" O ARG M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 61 Processing helix chain 'M' and resid 64 through 77 Processing helix chain 'M' and resid 86 through 124 Processing helix chain 'M' and resid 134 through 140 Processing helix chain 'N' and resid 5 through 10 removed outlier: 4.303A pdb=" N VAL N 8 " --> pdb=" O LEU N 5 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP N 10 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 22 removed outlier: 3.681A pdb=" N LEU N 20 " --> pdb=" O SER N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 28 removed outlier: 3.724A pdb=" N LEU N 27 " --> pdb=" O LEU N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 60 removed outlier: 3.854A pdb=" N LEU N 57 " --> pdb=" O ARG N 53 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU N 58 " --> pdb=" O GLU N 54 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY N 60 " --> pdb=" O SER N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 68 removed outlier: 3.768A pdb=" N ASN N 67 " --> pdb=" O PHE N 64 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE N 68 " --> pdb=" O GLY N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 83 Processing helix chain 'N' and resid 91 through 94 Processing helix chain 'N' and resid 95 through 118 removed outlier: 3.732A pdb=" N THR N 99 " --> pdb=" O HIS N 95 " (cutoff:3.500A) Proline residue: N 105 - end of helix removed outlier: 3.946A pdb=" N TYR N 113 " --> pdb=" O SER N 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 127 removed outlier: 4.104A pdb=" N VAL N 127 " --> pdb=" O LEU N 123 " (cutoff:3.500A) Processing helix chain 'N' and resid 135 through 149 Processing helix chain 'N' and resid 149 through 175 removed outlier: 3.755A pdb=" N ARG N 157 " --> pdb=" O THR N 153 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN N 161 " --> pdb=" O ARG N 157 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU N 172 " --> pdb=" O LEU N 168 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN N 175 " --> pdb=" O LEU N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 180 through 219 Processing helix chain 'O' and resid 12 through 29 Processing helix chain 'O' and resid 31 through 49 Processing helix chain 'O' and resid 49 through 57 removed outlier: 3.805A pdb=" N GLY O 53 " --> pdb=" O PHE O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 76 removed outlier: 3.839A pdb=" N GLU O 76 " --> pdb=" O SER O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 93 Processing helix chain 'O' and resid 95 through 97 No H-bonds generated for 'chain 'O' and resid 95 through 97' Processing helix chain 'O' and resid 98 through 109 removed outlier: 3.644A pdb=" N ILE O 103 " --> pdb=" O VAL O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 132 through 141 removed outlier: 3.719A pdb=" N GLY O 141 " --> pdb=" O VAL O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 157 through 160 Processing helix chain 'O' and resid 175 through 191 Processing helix chain 'P' and resid 5 through 12 Processing helix chain 'P' and resid 14 through 21 removed outlier: 4.204A pdb=" N UNK P 21 " --> pdb=" O UNK P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 45 Processing helix chain 'Q' and resid 9 through 28 Processing helix chain 'Q' and resid 41 through 46 removed outlier: 4.357A pdb=" N THR Q 46 " --> pdb=" O PHE Q 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 33 removed outlier: 3.671A pdb=" N VAL R 33 " --> pdb=" O LEU R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 45 Processing helix chain 'R' and resid 48 through 68 Processing helix chain 'R' and resid 75 through 93 Processing helix chain 'R' and resid 93 through 99 Processing helix chain 'S' and resid 27 through 37 Processing helix chain 'S' and resid 41 through 43 No H-bonds generated for 'chain 'S' and resid 41 through 43' Processing helix chain 'S' and resid 44 through 61 removed outlier: 3.572A pdb=" N THR S 61 " --> pdb=" O HIS S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 68 through 95 Processing helix chain 'T' and resid 10 through 77 removed outlier: 3.927A pdb=" N LYS T 37 " --> pdb=" O GLY T 33 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG T 38 " --> pdb=" O SER T 34 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG T 48 " --> pdb=" O VAL T 44 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 35 removed outlier: 7.032A pdb=" N ARG A 40 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ILE A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N MET A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.214A pdb=" N THR A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 108 removed outlier: 6.544A pdb=" N ARG A 106 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N SER A 233 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL A 108 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 146 removed outlier: 4.532A pdb=" N ILE A 159 " --> pdb=" O MET A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 28 through 35 removed outlier: 6.619A pdb=" N ARG B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.137A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.550A pdb=" N VAL B 108 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TYR B 200 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE B 267 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 202 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ASP B 269 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL B 204 " --> pdb=" O ASP B 269 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA B 264 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LEU B 324 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE B 266 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL B 326 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TYR B 268 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N GLU B 328 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.806A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS C 60 " --> pdb=" O PHE C 76 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N MET C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.233A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.741A pdb=" N CYS C 201 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N VAL C 232 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR C 203 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ALA C 234 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA C 205 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU C 166 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU C 352 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE C 168 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 13 through 20 removed outlier: 6.448A pdb=" N ASP D 25 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL D 19 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL D 23 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR D 60 " --> pdb=" O HIS D 55 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N HIS D 55 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG D 62 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 86 through 88 Processing sheet with id=AB4, first strand: chain 'D' and resid 97 through 98 removed outlier: 6.104A pdb=" N MET D 98 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N SER D 184 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N VAL D 221 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE D 186 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N GLY D 223 " --> pdb=" O PHE D 186 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLY D 188 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLY D 153 " --> pdb=" O SER D 309 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N GLN D 311 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE D 155 " --> pdb=" O GLN D 311 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE D 313 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU D 157 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS D 154 " --> pdb=" O ALA D 334 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N THR D 336 " --> pdb=" O LYS D 154 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY D 156 " --> pdb=" O THR D 336 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 135 through 136 removed outlier: 4.067A pdb=" N TYR D 149 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 13 through 20 removed outlier: 6.549A pdb=" N ASP E 25 " --> pdb=" O THR E 17 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL E 19 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL E 23 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N THR E 60 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N HIS E 55 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ARG E 62 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASN E 37 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA E 38 " --> pdb=" O THR E 81 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 86 through 89 removed outlier: 4.142A pdb=" N LYS E 115 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 97 through 98 removed outlier: 6.126A pdb=" N MET E 98 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL E 185 " --> pdb=" O PHE E 257 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE E 155 " --> pdb=" O GLN E 311 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LYS E 154 " --> pdb=" O ALA E 334 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N THR E 336 " --> pdb=" O LYS E 154 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY E 156 " --> pdb=" O THR E 336 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 13 through 20 removed outlier: 6.430A pdb=" N ASP F 25 " --> pdb=" O THR F 17 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL F 19 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL F 23 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N THR F 60 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N HIS F 55 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ARG F 62 " --> pdb=" O ALA F 53 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 86 through 89 removed outlier: 4.282A pdb=" N LYS F 115 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 135 through 136 removed outlier: 4.152A pdb=" N TYR F 149 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 157 through 158 Processing sheet with id=AC4, first strand: chain 'F' and resid 218 through 220 removed outlier: 7.327A pdb=" N GLY F 223 " --> pdb=" O PHE F 186 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLY F 188 " --> pdb=" O GLY F 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 218 through 220 removed outlier: 6.429A pdb=" N VAL F 254 " --> pdb=" O THR F 308 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL F 310 " --> pdb=" O VAL F 254 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU F 256 " --> pdb=" O VAL F 310 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 100 through 104 removed outlier: 6.502A pdb=" N ILE G 68 " --> pdb=" O ILE G 102 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL G 104 " --> pdb=" O ILE G 68 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA G 70 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ASN G 159 " --> pdb=" O ILE G 71 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 100 through 104 removed outlier: 6.502A pdb=" N ILE G 68 " --> pdb=" O ILE G 102 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL G 104 " --> pdb=" O ILE G 68 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA G 70 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ASN G 159 " --> pdb=" O ILE G 71 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 45 through 47 removed outlier: 5.556A pdb=" N ASN H 29 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE H 20 " --> pdb=" O ASN H 29 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA H 31 " --> pdb=" O PHE H 18 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR H 83 " --> pdb=" O GLN H 91 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 45 through 47 removed outlier: 6.815A pdb=" N TYR H 66 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL H 36 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N THR H 64 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL H 38 " --> pdb=" O VAL H 62 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL H 62 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 12 through 13 Processing sheet with id=AD2, first strand: chain 'O' and resid 148 through 155 2327 hydrogen bonds defined for protein. 6786 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: 7.58 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6574 1.32 - 1.44: 9629 1.44 - 1.56: 23206 1.56 - 1.69: 28 1.69 - 1.81: 309 Bond restraints: 39746 Sorted by residual: bond pdb=" O5' ATP B 601 " pdb=" PA ATP B 601 " ideal model delta sigma weight residual 1.579 1.609 -0.030 1.10e-02 8.26e+03 7.42e+00 bond pdb=" O5' ATP A 601 " pdb=" PA ATP A 601 " ideal model delta sigma weight residual 1.579 1.609 -0.030 1.10e-02 8.26e+03 7.28e+00 bond pdb=" O5' ATP C 601 " pdb=" PA ATP C 601 " ideal model delta sigma weight residual 1.579 1.608 -0.029 1.10e-02 8.26e+03 7.12e+00 bond pdb=" O5' ATP D 601 " pdb=" PA ATP D 601 " ideal model delta sigma weight residual 1.579 1.608 -0.029 1.10e-02 8.26e+03 6.91e+00 bond pdb=" CA TRP S 73 " pdb=" C TRP S 73 " ideal model delta sigma weight residual 1.524 1.491 0.032 1.32e-02 5.74e+03 6.02e+00 ... (remaining 39741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 53215 2.39 - 4.79: 422 4.79 - 7.18: 62 7.18 - 9.58: 6 9.58 - 11.97: 4 Bond angle restraints: 53709 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 127.90 11.97 1.00e+00 1.00e+00 1.43e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 127.91 11.96 1.00e+00 1.00e+00 1.43e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 128.57 11.30 1.00e+00 1.00e+00 1.28e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 129.10 10.77 1.00e+00 1.00e+00 1.16e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 128.97 7.86 1.00e+00 1.00e+00 6.18e+01 ... (remaining 53704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.60: 23125 21.60 - 43.19: 864 43.19 - 64.79: 171 64.79 - 86.39: 20 86.39 - 107.98: 4 Dihedral angle restraints: 24184 sinusoidal: 9670 harmonic: 14514 Sorted by residual: dihedral pdb=" CA PHE N 86 " pdb=" C PHE N 86 " pdb=" N PRO N 87 " pdb=" CA PRO N 87 " ideal model delta harmonic sigma weight residual -180.00 -153.01 -26.99 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA LYS I 36 " pdb=" C LYS I 36 " pdb=" N PRO I 37 " pdb=" CA PRO I 37 " ideal model delta harmonic sigma weight residual -180.00 -153.95 -26.05 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA SER E 45 " pdb=" C SER E 45 " pdb=" N PRO E 46 " pdb=" CA PRO E 46 " ideal model delta harmonic sigma weight residual 180.00 155.94 24.06 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 24181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3858 0.035 - 0.070: 1599 0.070 - 0.105: 484 0.105 - 0.140: 228 0.140 - 0.175: 9 Chirality restraints: 6178 Sorted by residual: chirality pdb=" CA PRO N 87 " pdb=" N PRO N 87 " pdb=" C PRO N 87 " pdb=" CB PRO N 87 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.64e-01 chirality pdb=" CB ILE D 87 " pdb=" CA ILE D 87 " pdb=" CG1 ILE D 87 " pdb=" CG2 ILE D 87 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA PRO I 37 " pdb=" N PRO I 37 " pdb=" C PRO I 37 " pdb=" CB PRO I 37 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.32e-01 ... (remaining 6175 not shown) Planarity restraints: 6879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN S 75 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.03e+01 pdb=" C ASN S 75 " 0.056 2.00e-02 2.50e+03 pdb=" O ASN S 75 " -0.021 2.00e-02 2.50e+03 pdb=" N THR S 76 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 464 " -0.048 5.00e-02 4.00e+02 7.24e-02 8.40e+00 pdb=" N PRO D 465 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 465 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 465 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 69 " 0.047 5.00e-02 4.00e+02 7.08e-02 8.01e+00 pdb=" N PRO R 70 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO R 70 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO R 70 " 0.039 5.00e-02 4.00e+02 ... (remaining 6876 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 93 2.41 - 3.03: 21623 3.03 - 3.66: 59167 3.66 - 4.28: 89204 4.28 - 4.90: 149387 Nonbonded interactions: 319474 Sorted by model distance: nonbonded pdb=" O2B ATP B 601 " pdb="MG MG B 602 " model vdw 1.789 2.170 nonbonded pdb=" O2B ATP A 601 " pdb="MG MG A 602 " model vdw 1.809 2.170 nonbonded pdb=" O2B ATP C 601 " pdb="MG MG C 602 " model vdw 1.857 2.170 nonbonded pdb=" O2G ATP B 601 " pdb="MG MG B 602 " model vdw 1.915 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 602 " model vdw 1.962 2.170 ... (remaining 319469 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' } ncs_group { reference = (chain 'A' and (resid 8 through 508 or resid 601 through 602)) selection = (chain 'B' and (resid 8 through 21 or (resid 22 through 23 and (name N or name C \ A or name C or name O or name CB )) or resid 24 through 405 or resid 410 through \ 602)) selection = (chain 'C' and (resid 8 through 21 or (resid 22 through 23 and (name N or name C \ A or name C or name O or name CB )) or resid 24 through 405 or resid 410 through \ 602)) } ncs_group { reference = (chain 'D' and (resid 12 through 315 or resid 330 through 476)) selection = (chain 'E' and resid 12 through 476) selection = (chain 'F' and (resid 12 through 315 or resid 330 through 476)) } 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=0.23 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 33.720 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.100 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:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 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 : 0.005 0.071 39746 Z= 0.217 Angle : 0.596 11.974 53709 Z= 0.336 Chirality : 0.045 0.175 6178 Planarity : 0.005 0.072 6879 Dihedral : 11.890 107.982 14880 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.52 % Allowed : 6.85 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.11), residues: 4987 helix: -0.24 (0.09), residues: 2630 sheet: 0.22 (0.23), residues: 537 loop : -0.70 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 70 TYR 0.012 0.002 TYR R 94 PHE 0.025 0.002 PHE K 25 TRP 0.023 0.002 TRP S 73 HIS 0.006 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00491 (39746) covalent geometry : angle 0.59609 (53709) hydrogen bonds : bond 0.14785 ( 2316) hydrogen bonds : angle 6.06391 ( 6786) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9974 Ramachandran restraints generated. 4987 Oldfield, 0 Emsley, 4987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9974 Ramachandran restraints generated. 4987 Oldfield, 0 Emsley, 4987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 1104 time to evaluate : 1.609 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: 1 36 TYR cc_start: 0.7109 (t80) cc_final: 0.6749 (t80) REVERT: 2 60 MET cc_start: 0.6386 (mmt) cc_final: 0.5958 (mpt) REVERT: 3 60 MET cc_start: 0.6971 (mmp) cc_final: 0.6753 (mmt) REVERT: 6 7 LYS cc_start: 0.7785 (mtmt) cc_final: 0.7436 (mtpt) REVERT: 7 66 MET cc_start: 0.6433 (ttp) cc_final: 0.5652 (tmm) REVERT: A 26 GLU cc_start: 0.7896 (tp30) cc_final: 0.6988 (pt0) REVERT: A 50 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8096 (mt-10) REVERT: A 62 MET cc_start: 0.8973 (ttp) cc_final: 0.8658 (ttm) REVERT: A 143 ARG cc_start: 0.7573 (mtt180) cc_final: 0.7159 (pmm-80) REVERT: A 196 LYS cc_start: 0.7371 (tppt) cc_final: 0.6942 (tmmt) REVERT: A 226 MET cc_start: 0.8707 (tpt) cc_final: 0.8446 (mmt) REVERT: A 260 ASN cc_start: 0.8477 (m-40) cc_final: 0.8257 (m-40) REVERT: A 347 ASP cc_start: 0.7481 (m-30) cc_final: 0.7218 (m-30) REVERT: A 353 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7303 (mm-30) REVERT: A 355 GLU cc_start: 0.7548 (tt0) cc_final: 0.7193 (mm-30) REVERT: A 359 LYS cc_start: 0.7453 (mttm) cc_final: 0.7126 (mmtp) REVERT: A 362 ARG cc_start: 0.7951 (mtt90) cc_final: 0.7616 (mtt90) REVERT: A 366 ASN cc_start: 0.7867 (t0) cc_final: 0.7294 (t0) REVERT: A 369 LEU cc_start: 0.8213 (mt) cc_final: 0.7926 (mp) REVERT: A 381 ARG cc_start: 0.7948 (mmt180) cc_final: 0.7464 (mmm160) REVERT: A 389 SER cc_start: 0.7426 (t) cc_final: 0.7210 (t) REVERT: A 426 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6653 (tp30) REVERT: A 439 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7196 (pm20) REVERT: A 449 VAL cc_start: 0.7080 (t) cc_final: 0.6767 (m) REVERT: B 8 ILE cc_start: 0.6814 (tp) cc_final: 0.6614 (pt) REVERT: B 50 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7963 (mp0) REVERT: B 52 MET cc_start: 0.8228 (tpt) cc_final: 0.7833 (tpt) REVERT: B 59 LEU cc_start: 0.7525 (mt) cc_final: 0.7180 (mp) REVERT: B 62 MET cc_start: 0.8697 (ttp) cc_final: 0.8354 (ttm) REVERT: B 89 LYS cc_start: 0.8413 (mtpp) cc_final: 0.8048 (mtmm) REVERT: B 94 ILE cc_start: 0.7752 (pt) cc_final: 0.7370 (pt) REVERT: B 124 LYS cc_start: 0.8707 (mmtt) cc_final: 0.8317 (mmtm) REVERT: B 125 THR cc_start: 0.7480 (p) cc_final: 0.7255 (t) REVERT: B 127 GLN cc_start: 0.7476 (mt0) cc_final: 0.7120 (tt0) REVERT: B 172 GLN cc_start: 0.7724 (mt0) cc_final: 0.7299 (mm-40) REVERT: B 193 GLN cc_start: 0.7693 (tp40) cc_final: 0.7091 (mp10) REVERT: B 312 MET cc_start: 0.8600 (mmm) cc_final: 0.8298 (mmm) REVERT: B 335 SER cc_start: 0.8537 (m) cc_final: 0.8258 (p) REVERT: B 351 PHE cc_start: 0.7423 (t80) cc_final: 0.6725 (m-80) REVERT: B 355 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7676 (mp0) REVERT: B 371 VAL cc_start: 0.8625 (OUTLIER) cc_final: 0.8386 (p) REVERT: B 391 LYS cc_start: 0.8286 (ptmt) cc_final: 0.8032 (tptt) REVERT: B 396 GLN cc_start: 0.7426 (mm-40) cc_final: 0.6915 (pp30) REVERT: B 426 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7368 (tp30) REVERT: B 455 LYS cc_start: 0.8373 (mtpp) cc_final: 0.8076 (pptt) REVERT: B 470 GLN cc_start: 0.8377 (mt0) cc_final: 0.8170 (mp10) REVERT: B 498 LYS cc_start: 0.7575 (tmtm) cc_final: 0.7256 (tppt) REVERT: C 26 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7473 (mp0) REVERT: C 78 ASN cc_start: 0.7711 (m110) cc_final: 0.7412 (t0) REVERT: C 91 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8155 (p) REVERT: C 148 THR cc_start: 0.8935 (m) cc_final: 0.8640 (p) REVERT: C 170 ASP cc_start: 0.7955 (m-30) cc_final: 0.7393 (m-30) REVERT: C 171 ARG cc_start: 0.7141 (ptp90) cc_final: 0.6867 (mtm110) REVERT: C 196 LYS cc_start: 0.8554 (mttt) cc_final: 0.8150 (mmmt) REVERT: C 227 ARG cc_start: 0.7777 (mtt90) cc_final: 0.7554 (ptm-80) REVERT: C 286 ARG cc_start: 0.8028 (mmt90) cc_final: 0.7670 (mmp-170) REVERT: C 385 GLN cc_start: 0.8289 (tt0) cc_final: 0.8064 (pt0) REVERT: C 392 LEU cc_start: 0.7694 (tp) cc_final: 0.7302 (pp) REVERT: C 434 VAL cc_start: 0.7950 (t) cc_final: 0.7733 (m) REVERT: C 450 ARG cc_start: 0.7252 (mmm160) cc_final: 0.6959 (mmt90) REVERT: C 457 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7915 (tp30) REVERT: C 476 HIS cc_start: 0.7504 (m90) cc_final: 0.7071 (m90) REVERT: C 481 ASP cc_start: 0.8904 (t70) cc_final: 0.8646 (m-30) REVERT: D 45 SER cc_start: 0.8921 (m) cc_final: 0.8698 (p) REVERT: D 212 LYS cc_start: 0.8594 (mttm) cc_final: 0.8378 (mtmt) REVERT: D 213 ASP cc_start: 0.7858 (p0) cc_final: 0.7416 (p0) REVERT: D 214 LYS cc_start: 0.8371 (mttm) cc_final: 0.7849 (mmtt) REVERT: D 253 ASP cc_start: 0.8567 (m-30) cc_final: 0.8353 (m-30) REVERT: D 285 GLN cc_start: 0.8227 (pt0) cc_final: 0.7851 (pm20) REVERT: D 359 ARG cc_start: 0.7172 (ttm170) cc_final: 0.6791 (ttm-80) REVERT: D 385 LYS cc_start: 0.8401 (ttmm) cc_final: 0.8094 (ttpt) REVERT: D 422 GLN cc_start: 0.7973 (mt0) cc_final: 0.7770 (mp10) REVERT: D 446 MET cc_start: 0.7734 (mtt) cc_final: 0.7527 (mtp) REVERT: D 462 MET cc_start: 0.8245 (mmt) cc_final: 0.8042 (mmt) REVERT: E 15 GLN cc_start: 0.7646 (mt0) cc_final: 0.7106 (mt0) REVERT: E 31 GLN cc_start: 0.6872 (mt0) cc_final: 0.6628 (mt0) REVERT: E 79 LEU cc_start: 0.8170 (tp) cc_final: 0.7932 (tm) REVERT: E 191 GLU cc_start: 0.7640 (tt0) cc_final: 0.7057 (pp20) REVERT: E 259 ASP cc_start: 0.7466 (t0) cc_final: 0.7255 (t70) REVERT: E 277 ARG cc_start: 0.7296 (mtm180) cc_final: 0.6804 (mtp180) REVERT: E 296 GLN cc_start: 0.7989 (mm110) cc_final: 0.7568 (mm110) REVERT: E 378 GLN cc_start: 0.8018 (mt0) cc_final: 0.7660 (mt0) REVERT: E 442 LYS cc_start: 0.7864 (tptp) cc_final: 0.7593 (tppt) REVERT: E 460 PHE cc_start: 0.8671 (m-80) cc_final: 0.8421 (m-10) REVERT: E 463 VAL cc_start: 0.7400 (OUTLIER) cc_final: 0.7122 (t) REVERT: E 467 GLU cc_start: 0.7901 (mp0) cc_final: 0.7579 (pm20) REVERT: E 468 GLU cc_start: 0.6911 (tp30) cc_final: 0.6469 (tp30) REVERT: F 15 GLN cc_start: 0.7770 (mt0) cc_final: 0.7280 (mp10) REVERT: F 98 MET cc_start: 0.8559 (ptp) cc_final: 0.8280 (ptp) REVERT: F 122 ASP cc_start: 0.8152 (m-30) cc_final: 0.7931 (m-30) REVERT: F 125 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7488 (mm-30) REVERT: F 263 ARG cc_start: 0.7696 (mmt-90) cc_final: 0.6633 (mtt90) REVERT: F 266 GLN cc_start: 0.7468 (tt0) cc_final: 0.7189 (tt0) REVERT: F 292 MET cc_start: 0.7825 (tpp) cc_final: 0.7543 (tpt) REVERT: F 344 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8050 (mp0) REVERT: F 362 ASP cc_start: 0.8666 (t70) cc_final: 0.8350 (t0) REVERT: F 379 LYS cc_start: 0.8179 (ttmp) cc_final: 0.7782 (tttm) REVERT: F 382 GLN cc_start: 0.8419 (mt0) cc_final: 0.8006 (mm-40) REVERT: F 462 MET cc_start: 0.8302 (tpp) cc_final: 0.8042 (tpp) REVERT: F 475 LYS cc_start: 0.7659 (mmmt) cc_final: 0.7192 (mptm) REVERT: G 11 LYS cc_start: 0.8278 (tttt) cc_final: 0.8074 (ttpp) REVERT: G 146 GLU cc_start: 0.6282 (mt-10) cc_final: 0.6059 (tm-30) REVERT: G 224 ARG cc_start: 0.7246 (ttm110) cc_final: 0.6800 (tpt170) REVERT: H 137 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7272 (mt-10) REVERT: I 25 ASP cc_start: 0.7403 (m-30) cc_final: 0.7133 (m-30) REVERT: I 27 GLU cc_start: 0.6324 (mt-10) cc_final: 0.5075 (mt-10) REVERT: K 11 LYS cc_start: 0.8789 (mttt) cc_final: 0.8570 (mmtt) REVERT: K 19 GLU cc_start: 0.8439 (tt0) cc_final: 0.8209 (tp30) REVERT: K 98 ASP cc_start: 0.8043 (m-30) cc_final: 0.7599 (p0) REVERT: K 197 CYS cc_start: 0.7210 (m) cc_final: 0.6540 (t) REVERT: L 16 LYS cc_start: 0.9432 (mttt) cc_final: 0.9192 (ptpp) REVERT: M 45 TYR cc_start: 0.6774 (m-10) cc_final: 0.6188 (m-80) REVERT: M 78 LYS cc_start: 0.5705 (tttm) cc_final: 0.5496 (tptt) REVERT: M 85 LYS cc_start: 0.8468 (mttt) cc_final: 0.8111 (mptt) REVERT: M 105 ILE cc_start: 0.9182 (mt) cc_final: 0.8967 (pt) REVERT: M 107 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8578 (pt0) REVERT: M 112 ILE cc_start: 0.9375 (mt) cc_final: 0.9030 (mt) REVERT: M 142 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.4868 (pt0) REVERT: N 51 LEU cc_start: 0.8850 (mt) cc_final: 0.8628 (mt) REVERT: N 118 GLU cc_start: 0.7561 (mt-10) cc_final: 0.6986 (pp20) REVERT: N 168 LEU cc_start: 0.8581 (tp) cc_final: 0.8313 (tt) REVERT: N 219 GLU cc_start: 0.6669 (mt-10) cc_final: 0.5692 (tm-30) REVERT: O 33 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7195 (mp0) REVERT: O 94 ASN cc_start: 0.8793 (t0) cc_final: 0.8298 (t0) REVERT: O 120 GLU cc_start: 0.7742 (tt0) cc_final: 0.7108 (mm-30) REVERT: O 140 LYS cc_start: 0.8626 (tptt) cc_final: 0.8405 (mmtt) REVERT: O 142 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.7274 (t80) REVERT: O 149 ILE cc_start: 0.7590 (mp) cc_final: 0.6945 (mt) REVERT: O 154 LYS cc_start: 0.8589 (mtpt) cc_final: 0.8207 (mtpp) REVERT: O 174 MET cc_start: 0.5569 (ttm) cc_final: 0.5030 (ttp) REVERT: R 37 GLU cc_start: 0.6450 (mm-30) cc_final: 0.6222 (tm-30) REVERT: S 54 ASN cc_start: 0.9079 (t0) cc_final: 0.8852 (t0) REVERT: S 66 GLN cc_start: 0.7521 (mp10) cc_final: 0.7273 (mp10) REVERT: S 90 GLU cc_start: 0.7932 (tt0) cc_final: 0.6870 (tm-30) REVERT: T 35 LEU cc_start: 0.8536 (pp) cc_final: 0.8281 (mt) REVERT: T 48 ARG cc_start: 0.8906 (mtm180) cc_final: 0.8629 (ptt-90) REVERT: T 68 GLU cc_start: 0.8090 (tp30) cc_final: 0.7808 (tp30) REVERT: T 69 MET cc_start: 0.8059 (mmm) cc_final: 0.7156 (mmt) REVERT: T 74 LYS cc_start: 0.8690 (tttt) cc_final: 0.8217 (tptp) outliers start: 103 outliers final: 27 residues processed: 1174 average time/residue: 0.6596 time to fit residues: 929.3424 Evaluate side-chains 702 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 670 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 3 residue 28 VAL Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 5 residue 1 ASP Chi-restraints excluded: chain 5 residue 64 CYS Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 8 residue 2 ILE Chi-restraints excluded: chain 8 residue 15 THR Chi-restraints excluded: chain 8 residue 18 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain H residue 41 PHE Chi-restraints excluded: chain H residue 91 GLN Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain M residue 142 GLU Chi-restraints excluded: chain O residue 142 PHE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain S residue 79 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 432 optimal weight: 0.5980 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 494 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.0970 chunk 207 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 45 GLN ** 4 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 44 GLN ** 7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 ASN B 316 ASN C 113 ASN C 471 HIS D 27 GLN D 54 GLN D 77 ASN D 133 GLN D 180 HIS D 249 GLN D 252 GLN D 331 HIS E 31 GLN E 54 GLN E 132 GLN E 175 ASN E 249 GLN E 370 HIS E 419 GLN F 54 GLN F 175 ASN F 382 GLN F 388 GLN F 419 GLN G 234 ASN H 85 ASN H 91 GLN K 27 ASN K 121 GLN ** K 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 135 GLN ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 170 GLN N 18 ASN ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN T 40 ASN T 57 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.175438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.143176 restraints weight = 62696.796| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.55 r_work: 0.3873 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 39746 Z= 0.138 Angle : 0.579 10.287 53709 Z= 0.297 Chirality : 0.043 0.195 6178 Planarity : 0.005 0.085 6879 Dihedral : 8.641 96.024 5781 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.55 % Allowed : 16.93 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.12), residues: 4987 helix: 1.19 (0.10), residues: 2654 sheet: 0.29 (0.22), residues: 554 loop : -0.46 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 477 TYR 0.018 0.001 TYR T 30 PHE 0.025 0.001 PHE O 171 TRP 0.019 0.002 TRP S 85 HIS 0.005 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00302 (39746) covalent geometry : angle 0.57899 (53709) hydrogen bonds : bond 0.04518 ( 2316) hydrogen bonds : angle 4.51430 ( 6786) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9974 Ramachandran restraints generated. 4987 Oldfield, 0 Emsley, 4987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9974 Ramachandran restraints generated. 4987 Oldfield, 0 Emsley, 4987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 748 time to evaluate : 1.497 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: 1 36 TYR cc_start: 0.7013 (t80) cc_final: 0.6671 (t80) REVERT: 2 60 MET cc_start: 0.6501 (mmt) cc_final: 0.5916 (mmt) REVERT: 4 31 SER cc_start: 0.7825 (m) cc_final: 0.7583 (p) REVERT: 5 66 MET cc_start: 0.7445 (ttp) cc_final: 0.7097 (tmm) REVERT: 6 7 LYS cc_start: 0.7660 (mtmt) cc_final: 0.7300 (mtpt) REVERT: 7 54 PHE cc_start: 0.7906 (t80) cc_final: 0.7677 (t80) REVERT: A 26 GLU cc_start: 0.7710 (tp30) cc_final: 0.6831 (pm20) REVERT: A 30 ARG cc_start: 0.7553 (ttm110) cc_final: 0.7334 (ttm170) REVERT: A 40 ARG cc_start: 0.7701 (mmt-90) cc_final: 0.7426 (mmt180) REVERT: A 143 ARG cc_start: 0.7642 (mtt180) cc_final: 0.7124 (pmm-80) REVERT: A 195 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7522 (tp30) REVERT: A 196 LYS cc_start: 0.7402 (tppt) cc_final: 0.6996 (tmmt) REVERT: A 226 MET cc_start: 0.8899 (tpt) cc_final: 0.8628 (mmt) REVERT: A 355 GLU cc_start: 0.7321 (tt0) cc_final: 0.7066 (mm-30) REVERT: A 362 ARG cc_start: 0.7847 (mtt90) cc_final: 0.7610 (mtt90) REVERT: A 381 ARG cc_start: 0.7852 (mmt180) cc_final: 0.7520 (mmm160) REVERT: A 426 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6751 (tp30) REVERT: A 439 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7265 (pm20) REVERT: A 449 VAL cc_start: 0.7001 (t) cc_final: 0.6723 (m) REVERT: B 50 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7996 (mp0) REVERT: B 52 MET cc_start: 0.8099 (tpt) cc_final: 0.7870 (tpt) REVERT: B 62 MET cc_start: 0.8744 (ttp) cc_final: 0.8465 (ttm) REVERT: B 89 LYS cc_start: 0.8577 (mtpp) cc_final: 0.8182 (mtmm) REVERT: B 124 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8323 (mmtm) REVERT: B 125 THR cc_start: 0.7368 (p) cc_final: 0.7114 (t) REVERT: B 127 GLN cc_start: 0.7672 (mt0) cc_final: 0.7250 (tt0) REVERT: B 136 ILE cc_start: 0.7553 (pt) cc_final: 0.7091 (mt) REVERT: B 144 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7058 (mt-10) REVERT: B 172 GLN cc_start: 0.7757 (mt0) cc_final: 0.7230 (mm-40) REVERT: B 181 ASP cc_start: 0.7982 (m-30) cc_final: 0.7646 (m-30) REVERT: B 312 MET cc_start: 0.8582 (mmm) cc_final: 0.8287 (mmm) REVERT: B 335 SER cc_start: 0.8836 (m) cc_final: 0.8424 (p) REVERT: B 347 ASP cc_start: 0.8065 (m-30) cc_final: 0.7840 (m-30) REVERT: B 355 GLU cc_start: 0.8508 (mt-10) cc_final: 0.7934 (mp0) REVERT: B 381 ARG cc_start: 0.7471 (mmm160) cc_final: 0.7135 (mmm160) REVERT: B 391 LYS cc_start: 0.8205 (ptmt) cc_final: 0.7971 (tppt) REVERT: B 392 LEU cc_start: 0.8627 (tt) cc_final: 0.8407 (mt) REVERT: B 396 GLN cc_start: 0.7459 (mm-40) cc_final: 0.7094 (mt0) REVERT: B 426 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7541 (tp30) REVERT: B 436 MET cc_start: 0.8401 (mtp) cc_final: 0.8065 (ttm) REVERT: B 455 LYS cc_start: 0.8325 (mtpp) cc_final: 0.8012 (pptt) REVERT: C 26 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7681 (mp0) REVERT: C 40 ARG cc_start: 0.8186 (mtt-85) cc_final: 0.7690 (mmt180) REVERT: C 67 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.6542 (mt-10) REVERT: C 78 ASN cc_start: 0.7783 (m110) cc_final: 0.7432 (t0) REVERT: C 148 THR cc_start: 0.8991 (m) cc_final: 0.8721 (p) REVERT: C 170 ASP cc_start: 0.8213 (m-30) cc_final: 0.7719 (m-30) REVERT: C 171 ARG cc_start: 0.7530 (ptp90) cc_final: 0.7256 (mtm110) REVERT: C 196 LYS cc_start: 0.8656 (mttt) cc_final: 0.8313 (mmmt) REVERT: C 227 ARG cc_start: 0.8128 (mtt90) cc_final: 0.7921 (ptm-80) REVERT: C 286 ARG cc_start: 0.8289 (mmt90) cc_final: 0.7793 (mmp-170) REVERT: C 416 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8144 (pp30) REVERT: C 450 ARG cc_start: 0.7184 (mmm160) cc_final: 0.6795 (mmt90) REVERT: C 470 GLN cc_start: 0.7514 (mt0) cc_final: 0.7263 (pp30) REVERT: C 476 HIS cc_start: 0.7350 (m90) cc_final: 0.7045 (m90) REVERT: C 477 ARG cc_start: 0.6583 (mmm160) cc_final: 0.6380 (mmm160) REVERT: C 481 ASP cc_start: 0.8938 (t70) cc_final: 0.8636 (m-30) REVERT: D 45 SER cc_start: 0.8873 (m) cc_final: 0.8645 (p) REVERT: D 64 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8508 (mm) REVERT: D 151 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7585 (mtmm) REVERT: D 212 LYS cc_start: 0.8689 (mttm) cc_final: 0.8454 (mtmt) REVERT: D 213 ASP cc_start: 0.7877 (p0) cc_final: 0.7418 (p0) REVERT: D 214 LYS cc_start: 0.8318 (mttm) cc_final: 0.7850 (mmtt) REVERT: D 252 GLN cc_start: 0.7066 (mm-40) cc_final: 0.6483 (mm110) REVERT: D 253 ASP cc_start: 0.8734 (m-30) cc_final: 0.8499 (m-30) REVERT: D 285 GLN cc_start: 0.8075 (pt0) cc_final: 0.7851 (pm20) REVERT: D 302 THR cc_start: 0.8227 (m) cc_final: 0.7913 (p) REVERT: D 359 ARG cc_start: 0.7589 (ttm170) cc_final: 0.6972 (ttm-80) REVERT: D 368 GLU cc_start: 0.7711 (tp30) cc_final: 0.7507 (tp30) REVERT: D 396 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.7861 (mmm) REVERT: D 422 GLN cc_start: 0.8118 (mt0) cc_final: 0.7844 (mp10) REVERT: E 15 GLN cc_start: 0.7846 (mt0) cc_final: 0.6996 (mm-40) REVERT: E 17 THR cc_start: 0.8232 (m) cc_final: 0.7847 (p) REVERT: E 157 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7479 (tt) REVERT: E 191 GLU cc_start: 0.7634 (tt0) cc_final: 0.7011 (pp20) REVERT: E 259 ASP cc_start: 0.7550 (t0) cc_final: 0.7348 (OUTLIER) REVERT: E 277 ARG cc_start: 0.7312 (mtm180) cc_final: 0.6976 (mtp180) REVERT: E 296 GLN cc_start: 0.8121 (mm110) cc_final: 0.7833 (mm110) REVERT: E 368 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7398 (mm-30) REVERT: E 378 GLN cc_start: 0.8122 (mt0) cc_final: 0.7819 (mp10) REVERT: E 425 GLU cc_start: 0.7357 (pt0) cc_final: 0.6922 (pt0) REVERT: E 460 PHE cc_start: 0.8632 (m-80) cc_final: 0.8393 (m-10) REVERT: E 467 GLU cc_start: 0.7933 (mp0) cc_final: 0.7560 (pm20) REVERT: E 468 GLU cc_start: 0.7049 (tp30) cc_final: 0.6849 (tp30) REVERT: F 15 GLN cc_start: 0.8060 (mt0) cc_final: 0.7571 (mp10) REVERT: F 31 GLN cc_start: 0.7603 (pm20) cc_final: 0.7202 (pm20) REVERT: F 122 ASP cc_start: 0.8147 (m-30) cc_final: 0.7947 (m-30) REVERT: F 125 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7627 (mm-30) REVERT: F 263 ARG cc_start: 0.7980 (mmt-90) cc_final: 0.6782 (mtt90) REVERT: F 266 GLN cc_start: 0.7509 (tt0) cc_final: 0.7241 (tt0) REVERT: F 292 MET cc_start: 0.7739 (tpp) cc_final: 0.7438 (tpt) REVERT: F 344 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7943 (mp0) REVERT: F 362 ASP cc_start: 0.8728 (t70) cc_final: 0.8407 (t0) REVERT: F 379 LYS cc_start: 0.8131 (ttmp) cc_final: 0.7738 (tttm) REVERT: F 382 GLN cc_start: 0.8469 (mt0) cc_final: 0.7986 (mm-40) REVERT: F 462 MET cc_start: 0.8484 (tpp) cc_final: 0.8256 (tpp) REVERT: F 475 LYS cc_start: 0.7525 (mmmt) cc_final: 0.7128 (mptm) REVERT: G 4 LYS cc_start: 0.7933 (ttpp) cc_final: 0.7681 (pttp) REVERT: G 11 LYS cc_start: 0.8275 (tttt) cc_final: 0.8073 (ttpp) REVERT: H 109 ARG cc_start: 0.7831 (mtt90) cc_final: 0.7448 (mpt180) REVERT: H 112 LEU cc_start: 0.8608 (mt) cc_final: 0.8349 (mp) REVERT: H 140 GLU cc_start: 0.7737 (tp30) cc_final: 0.7457 (tp30) REVERT: I 19 ASP cc_start: 0.7912 (p0) cc_final: 0.7635 (p0) REVERT: I 27 GLU cc_start: 0.6166 (mt-10) cc_final: 0.5339 (mt-10) REVERT: I 31 MET cc_start: 0.7947 (tmm) cc_final: 0.7289 (tmm) REVERT: K 11 LYS cc_start: 0.8966 (mttt) cc_final: 0.8720 (mmtt) REVERT: K 98 ASP cc_start: 0.8043 (m-30) cc_final: 0.7558 (p0) REVERT: K 193 MET cc_start: 0.7738 (tmt) cc_final: 0.7416 (pp-130) REVERT: M 78 LYS cc_start: 0.5761 (tttm) cc_final: 0.5531 (tptt) REVERT: M 85 LYS cc_start: 0.8476 (mttt) cc_final: 0.8000 (mptt) REVERT: M 106 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8119 (mm110) REVERT: M 107 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8699 (pt0) REVERT: M 142 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.5738 (pm20) REVERT: N 113 TYR cc_start: 0.6304 (t80) cc_final: 0.6039 (t80) REVERT: N 118 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7165 (pp20) REVERT: N 142 MET cc_start: 0.6510 (mpt) cc_final: 0.5877 (mpt) REVERT: N 162 MET cc_start: 0.7658 (tpt) cc_final: 0.7451 (tpt) REVERT: O 33 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7270 (mp0) REVERT: O 92 GLU cc_start: 0.8451 (tp30) cc_final: 0.8032 (tp30) REVERT: O 94 ASN cc_start: 0.8614 (t0) cc_final: 0.8213 (t0) REVERT: O 120 GLU cc_start: 0.7645 (tt0) cc_final: 0.7230 (mm-30) REVERT: O 142 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7191 (t80) REVERT: O 154 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8325 (mtpp) REVERT: O 170 ARG cc_start: 0.6853 (mpp80) cc_final: 0.6554 (mpp80) REVERT: O 174 MET cc_start: 0.5614 (ttm) cc_final: 0.4696 (ppp) REVERT: Q 50 ASN cc_start: 0.8517 (m-40) cc_final: 0.8167 (m110) REVERT: Q 52 LYS cc_start: 0.8081 (mmmm) cc_final: 0.7843 (mmmm) REVERT: R 37 GLU cc_start: 0.6296 (mm-30) cc_final: 0.6066 (tm-30) REVERT: S 47 LYS cc_start: 0.8939 (tppp) cc_final: 0.8383 (tttm) REVERT: S 90 GLU cc_start: 0.8085 (tt0) cc_final: 0.7068 (tm-30) REVERT: T 49 ARG cc_start: 0.8435 (mmp80) cc_final: 0.7985 (mmp80) REVERT: T 53 ARG cc_start: 0.8618 (ttp-110) cc_final: 0.8294 (ttp-110) REVERT: T 57 ASN cc_start: 0.7795 (m-40) cc_final: 0.7578 (p0) REVERT: T 69 MET cc_start: 0.7811 (mmm) cc_final: 0.7264 (mmm) REVERT: T 74 LYS cc_start: 0.8679 (tttt) cc_final: 0.8200 (tptp) outliers start: 145 outliers final: 55 residues processed: 846 average time/residue: 0.7231 time to fit residues: 732.5277 Evaluate side-chains 680 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 617 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 28 VAL Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 65 LEU Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 5 residue 64 CYS Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 7 residue 21 SER Chi-restraints excluded: chain 8 residue 2 ILE Chi-restraints excluded: chain 8 residue 15 THR Chi-restraints excluded: chain 8 residue 18 VAL Chi-restraints excluded: chain 8 residue 34 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 416 GLN Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 172 ASN Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 124 GLN Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain M residue 142 GLU Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain O residue 142 PHE Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 304 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 316 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 280 optimal weight: 10.0000 chunk 327 optimal weight: 0.0870 chunk 282 optimal weight: 10.0000 chunk 288 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 357 optimal weight: 0.0370 chunk 481 optimal weight: 1.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 45 GLN 4 45 GLN ** 7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 ASN B 24 ASN B 65 ASN B 260 ASN F 54 GLN G 159 ASN G 234 ASN H 25 GLN K 27 ASN K 148 ASN ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN M 29 ASN ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.173050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.139661 restraints weight = 63307.417| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.76 r_work: 0.3815 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3815 r_free = 0.3815 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3815 r_free = 0.3815 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39746 Z= 0.139 Angle : 0.564 10.631 53709 Z= 0.289 Chirality : 0.043 0.230 6178 Planarity : 0.004 0.074 6879 Dihedral : 8.205 90.961 5762 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.06 % Allowed : 17.96 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.12), residues: 4987 helix: 1.61 (0.10), residues: 2705 sheet: 0.21 (0.22), residues: 559 loop : -0.41 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 340 TYR 0.018 0.001 TYR M 28 PHE 0.025 0.001 PHE O 171 TRP 0.018 0.001 TRP S 85 HIS 0.006 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00312 (39746) covalent geometry : angle 0.56351 (53709) hydrogen bonds : bond 0.04305 ( 2316) hydrogen bonds : angle 4.34188 ( 6786) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9974 Ramachandran restraints generated. 4987 Oldfield, 0 Emsley, 4987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9974 Ramachandran restraints generated. 4987 Oldfield, 0 Emsley, 4987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 673 time to evaluate : 1.573 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: 1 36 TYR cc_start: 0.6877 (t80) cc_final: 0.6521 (t80) REVERT: 2 60 MET cc_start: 0.6368 (mmt) cc_final: 0.5981 (mpt) REVERT: 4 31 SER cc_start: 0.7985 (m) cc_final: 0.7637 (p) REVERT: 4 58 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7918 (tm-30) REVERT: 5 21 SER cc_start: 0.8038 (m) cc_final: 0.7809 (t) REVERT: 5 66 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6654 (tmm) REVERT: 6 7 LYS cc_start: 0.7414 (mtmt) cc_final: 0.6955 (mtpt) REVERT: A 26 GLU cc_start: 0.7675 (tp30) cc_final: 0.6797 (pm20) REVERT: A 30 ARG cc_start: 0.7331 (ttm110) cc_final: 0.7043 (ttm110) REVERT: A 50 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7382 (pt0) REVERT: A 143 ARG cc_start: 0.7553 (mtt180) cc_final: 0.7046 (pmm-80) REVERT: A 196 LYS cc_start: 0.7399 (tppt) cc_final: 0.7007 (tmmt) REVERT: A 226 MET cc_start: 0.8798 (tpt) cc_final: 0.8505 (mmm) REVERT: A 362 ARG cc_start: 0.7799 (mtt90) cc_final: 0.7536 (mtt90) REVERT: A 426 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6704 (tp30) REVERT: A 439 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7184 (pm20) REVERT: B 52 MET cc_start: 0.7897 (tpt) cc_final: 0.7640 (tpt) REVERT: B 62 MET cc_start: 0.8548 (ttp) cc_final: 0.8258 (ttm) REVERT: B 89 LYS cc_start: 0.8376 (mtpp) cc_final: 0.7990 (mtmm) REVERT: B 124 LYS cc_start: 0.8754 (mmtt) cc_final: 0.8366 (mmtm) REVERT: B 125 THR cc_start: 0.7331 (p) cc_final: 0.7070 (t) REVERT: B 127 GLN cc_start: 0.7449 (mt0) cc_final: 0.7023 (tt0) REVERT: B 136 ILE cc_start: 0.7462 (pt) cc_final: 0.7070 (mt) REVERT: B 144 GLU cc_start: 0.7574 (mm-30) cc_final: 0.6964 (mt-10) REVERT: B 147 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7810 (mp10) REVERT: B 172 GLN cc_start: 0.7617 (mt0) cc_final: 0.7085 (mm-40) REVERT: B 181 ASP cc_start: 0.7854 (m-30) cc_final: 0.7391 (m-30) REVERT: B 297 ASP cc_start: 0.7840 (p0) cc_final: 0.7492 (p0) REVERT: B 312 MET cc_start: 0.8440 (mmm) cc_final: 0.8144 (mmm) REVERT: B 335 SER cc_start: 0.8813 (m) cc_final: 0.8378 (p) REVERT: B 347 ASP cc_start: 0.7838 (m-30) cc_final: 0.7568 (m-30) REVERT: B 355 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7838 (mp0) REVERT: B 381 ARG cc_start: 0.7355 (mmm160) cc_final: 0.6886 (mmm160) REVERT: B 391 LYS cc_start: 0.8175 (ptmt) cc_final: 0.7915 (tppt) REVERT: B 426 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7414 (tp30) REVERT: B 436 MET cc_start: 0.8358 (mtp) cc_final: 0.7684 (ttm) REVERT: B 455 LYS cc_start: 0.8396 (mtpp) cc_final: 0.7994 (pptt) REVERT: C 26 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7495 (mp0) REVERT: C 34 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8724 (tp) REVERT: C 40 ARG cc_start: 0.8047 (mtt-85) cc_final: 0.7628 (mmt180) REVERT: C 78 ASN cc_start: 0.7644 (m110) cc_final: 0.7292 (t0) REVERT: C 148 THR cc_start: 0.8865 (m) cc_final: 0.8606 (p) REVERT: C 170 ASP cc_start: 0.8028 (m-30) cc_final: 0.7550 (m-30) REVERT: C 171 ARG cc_start: 0.7415 (ptp90) cc_final: 0.7119 (mtm110) REVERT: C 196 LYS cc_start: 0.8656 (mttt) cc_final: 0.8295 (mmmt) REVERT: C 227 ARG cc_start: 0.8119 (mtt90) cc_final: 0.7816 (ptm-80) REVERT: C 286 ARG cc_start: 0.8066 (mmt90) cc_final: 0.7652 (mmp-170) REVERT: C 381 ARG cc_start: 0.7511 (mtm110) cc_final: 0.7309 (mtm110) REVERT: C 416 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8186 (pp30) REVERT: C 450 ARG cc_start: 0.7082 (mmm160) cc_final: 0.6541 (mmt90) REVERT: C 466 LYS cc_start: 0.7313 (mttt) cc_final: 0.6843 (tptm) REVERT: C 476 HIS cc_start: 0.7399 (m90) cc_final: 0.7122 (m90) REVERT: C 481 ASP cc_start: 0.8931 (t70) cc_final: 0.8601 (m-30) REVERT: D 45 SER cc_start: 0.8856 (m) cc_final: 0.8626 (p) REVERT: D 151 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7568 (mtmm) REVERT: D 170 MET cc_start: 0.8178 (mmm) cc_final: 0.7919 (mmt) REVERT: D 212 LYS cc_start: 0.8676 (mttm) cc_final: 0.8445 (mtmt) REVERT: D 213 ASP cc_start: 0.7856 (p0) cc_final: 0.7378 (p0) REVERT: D 214 LYS cc_start: 0.8343 (mttm) cc_final: 0.7872 (mmtt) REVERT: D 252 GLN cc_start: 0.6968 (mm-40) cc_final: 0.6344 (mm110) REVERT: D 253 ASP cc_start: 0.8723 (m-30) cc_final: 0.8502 (m-30) REVERT: D 285 GLN cc_start: 0.7911 (pt0) cc_final: 0.7606 (pm20) REVERT: D 302 THR cc_start: 0.8109 (m) cc_final: 0.7882 (p) REVERT: D 359 ARG cc_start: 0.7436 (ttm170) cc_final: 0.6922 (ttm-80) REVERT: D 368 GLU cc_start: 0.7554 (tp30) cc_final: 0.7344 (tp30) REVERT: D 396 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.7755 (mmm) REVERT: D 422 GLN cc_start: 0.8041 (mt0) cc_final: 0.7765 (mp10) REVERT: E 15 GLN cc_start: 0.7613 (mt0) cc_final: 0.6694 (mm-40) REVERT: E 17 THR cc_start: 0.8115 (m) cc_final: 0.7708 (p) REVERT: E 191 GLU cc_start: 0.7580 (tt0) cc_final: 0.6960 (pp20) REVERT: E 259 ASP cc_start: 0.7305 (t0) cc_final: 0.7051 (OUTLIER) REVERT: E 277 ARG cc_start: 0.7229 (mtm180) cc_final: 0.6914 (mtp180) REVERT: E 296 GLN cc_start: 0.8020 (mm110) cc_final: 0.7795 (mm110) REVERT: E 378 GLN cc_start: 0.8196 (mt0) cc_final: 0.7820 (mt0) REVERT: E 425 GLU cc_start: 0.7331 (pt0) cc_final: 0.6999 (pt0) REVERT: E 458 VAL cc_start: 0.7825 (t) cc_final: 0.7491 (p) REVERT: E 467 GLU cc_start: 0.7858 (mp0) cc_final: 0.7563 (pm20) REVERT: F 15 GLN cc_start: 0.7848 (mt0) cc_final: 0.7333 (mp10) REVERT: F 20 ILE cc_start: 0.6498 (OUTLIER) cc_final: 0.6227 (tp) REVERT: F 31 GLN cc_start: 0.7751 (pm20) cc_final: 0.7344 (pm20) REVERT: F 125 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7658 (mm-30) REVERT: F 263 ARG cc_start: 0.7808 (mmt-90) cc_final: 0.6521 (mtt180) REVERT: F 266 GLN cc_start: 0.7259 (tt0) cc_final: 0.6982 (tt0) REVERT: F 292 MET cc_start: 0.7579 (tpp) cc_final: 0.7231 (tpt) REVERT: F 344 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8014 (mp0) REVERT: F 362 ASP cc_start: 0.8664 (t70) cc_final: 0.8339 (t0) REVERT: F 379 LYS cc_start: 0.8095 (ttmp) cc_final: 0.7741 (tttm) REVERT: F 382 GLN cc_start: 0.8417 (mt0) cc_final: 0.7944 (mm-40) REVERT: F 475 LYS cc_start: 0.7516 (mmmt) cc_final: 0.7120 (mptm) REVERT: G 149 MET cc_start: 0.6615 (ppp) cc_final: 0.6244 (tmm) REVERT: G 159 ASN cc_start: 0.7780 (m-40) cc_final: 0.7063 (m-40) REVERT: H 140 GLU cc_start: 0.7726 (tp30) cc_final: 0.7510 (tp30) REVERT: I 19 ASP cc_start: 0.7777 (p0) cc_final: 0.7523 (p0) REVERT: I 27 GLU cc_start: 0.6216 (mt-10) cc_final: 0.5630 (mt-10) REVERT: I 31 MET cc_start: 0.7914 (tmm) cc_final: 0.7185 (tmm) REVERT: K 11 LYS cc_start: 0.8843 (mttt) cc_final: 0.8570 (mmtt) REVERT: K 19 GLU cc_start: 0.8425 (tt0) cc_final: 0.7772 (tp30) REVERT: K 43 THR cc_start: 0.8985 (m) cc_final: 0.8638 (t) REVERT: K 129 ARG cc_start: 0.8759 (ttp80) cc_final: 0.8458 (ttm-80) REVERT: L 11 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.8170 (m-80) REVERT: M 45 TYR cc_start: 0.7013 (m-10) cc_final: 0.6387 (m-80) REVERT: M 85 LYS cc_start: 0.8372 (mttt) cc_final: 0.8054 (mptt) REVERT: M 105 ILE cc_start: 0.8820 (mm) cc_final: 0.8575 (pt) REVERT: M 106 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8224 (mm110) REVERT: M 107 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8664 (pt0) REVERT: M 121 LYS cc_start: 0.9218 (ttpp) cc_final: 0.8993 (tppt) REVERT: M 142 GLU cc_start: 0.6159 (OUTLIER) cc_final: 0.5952 (pm20) REVERT: N 113 TYR cc_start: 0.6249 (t80) cc_final: 0.6037 (t80) REVERT: N 118 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7134 (pp20) REVERT: N 142 MET cc_start: 0.6802 (mpt) cc_final: 0.6253 (mpt) REVERT: N 162 MET cc_start: 0.7631 (tpt) cc_final: 0.7359 (tpt) REVERT: O 33 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7146 (mp0) REVERT: O 63 ARG cc_start: 0.7339 (ptp-170) cc_final: 0.7042 (ptp-170) REVERT: O 92 GLU cc_start: 0.8459 (tp30) cc_final: 0.7970 (tp30) REVERT: O 94 ASN cc_start: 0.8377 (t0) cc_final: 0.8078 (t0) REVERT: O 120 GLU cc_start: 0.7574 (tt0) cc_final: 0.7161 (mm-30) REVERT: O 142 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.7092 (t80) REVERT: O 154 LYS cc_start: 0.8498 (mtpt) cc_final: 0.8213 (mtpp) REVERT: O 174 MET cc_start: 0.5454 (ttm) cc_final: 0.4600 (ppp) REVERT: Q 52 LYS cc_start: 0.8236 (mmmm) cc_final: 0.7994 (mmmm) REVERT: S 47 LYS cc_start: 0.9088 (tppp) cc_final: 0.8591 (tttm) REVERT: S 49 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8013 (tp-100) REVERT: S 90 GLU cc_start: 0.7934 (tt0) cc_final: 0.6928 (tm-30) REVERT: T 48 ARG cc_start: 0.8862 (ptt90) cc_final: 0.8308 (ptt90) REVERT: T 49 ARG cc_start: 0.8424 (mmp80) cc_final: 0.8194 (mmp80) REVERT: T 74 LYS cc_start: 0.8651 (tttt) cc_final: 0.8150 (tptp) outliers start: 166 outliers final: 71 residues processed: 787 average time/residue: 0.6837 time to fit residues: 646.2863 Evaluate side-chains 689 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 608 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 28 VAL Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 65 LEU Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 45 GLN Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 57 SER Chi-restraints excluded: chain 4 residue 58 GLU Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 5 residue 64 CYS Chi-restraints excluded: chain 5 residue 66 MET Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 7 residue 15 THR Chi-restraints excluded: chain 7 residue 21 SER Chi-restraints excluded: chain 8 residue 2 ILE Chi-restraints excluded: chain 8 residue 15 THR Chi-restraints excluded: chain 8 residue 18 VAL Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 416 GLN Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain G residue 238 MET Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain K residue 173 MET Chi-restraints excluded: chain K residue 197 CYS Chi-restraints excluded: chain L residue 11 PHE Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 124 GLN Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 142 GLU Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain O residue 142 PHE Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 320 optimal weight: 2.9990 chunk 270 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 347 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 441 optimal weight: 1.9990 chunk 341 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 479 optimal weight: 1.9990 chunk 263 optimal weight: 6.9990 chunk 375 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 45 GLN 4 45 GLN ** 7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 GLN B 24 ASN B 65 ASN D 174 ASN F 54 GLN ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 ASN K 27 ASN ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.170613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.136442 restraints weight = 63097.729| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.77 r_work: 0.3774 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 39746 Z= 0.180 Angle : 0.607 13.508 53709 Z= 0.307 Chirality : 0.044 0.299 6178 Planarity : 0.005 0.084 6879 Dihedral : 8.077 89.960 5758 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.40 % Allowed : 18.72 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.12), residues: 4987 helix: 1.64 (0.10), residues: 2703 sheet: 0.21 (0.22), residues: 556 loop : -0.40 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 154 TYR 0.018 0.001 TYR A 42 PHE 0.029 0.002 PHE B 464 TRP 0.011 0.002 TRP R 61 HIS 0.007 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00418 (39746) covalent geometry : angle 0.60694 (53709) hydrogen bonds : bond 0.04462 ( 2316) hydrogen bonds : angle 4.33768 ( 6786) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9974 Ramachandran restraints generated. 4987 Oldfield, 0 Emsley, 4987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9974 Ramachandran restraints generated. 4987 Oldfield, 0 Emsley, 4987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 646 time to evaluate : 1.470 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: 1 36 TYR cc_start: 0.6989 (t80) cc_final: 0.6652 (t80) REVERT: 2 60 MET cc_start: 0.6416 (mmt) cc_final: 0.6019 (mpt) REVERT: 4 31 SER cc_start: 0.7983 (m) cc_final: 0.7635 (p) REVERT: 5 66 MET cc_start: 0.7012 (ttp) cc_final: 0.6747 (tmm) REVERT: 5 71 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7919 (mp) REVERT: 5 75 PHE cc_start: 0.5252 (OUTLIER) cc_final: 0.4272 (m-80) REVERT: 6 7 LYS cc_start: 0.7518 (mtmt) cc_final: 0.7020 (mtpt) REVERT: 8 67 MET cc_start: 0.8134 (mmm) cc_final: 0.7893 (tpt) REVERT: A 26 GLU cc_start: 0.7703 (tp30) cc_final: 0.6782 (pm20) REVERT: A 30 ARG cc_start: 0.7495 (ttm110) cc_final: 0.7174 (ttm110) REVERT: A 40 ARG cc_start: 0.7478 (mmt-90) cc_final: 0.7222 (mmt180) REVERT: A 143 ARG cc_start: 0.7469 (mtt180) cc_final: 0.6962 (pmm-80) REVERT: A 196 LYS cc_start: 0.7456 (tppt) cc_final: 0.7181 (ttpt) REVERT: A 226 MET cc_start: 0.8850 (tpt) cc_final: 0.8568 (mmm) REVERT: A 353 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7294 (mm-30) REVERT: A 362 ARG cc_start: 0.7842 (mtt90) cc_final: 0.7477 (mtt90) REVERT: A 426 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6728 (tp30) REVERT: A 439 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7150 (pm20) REVERT: B 52 MET cc_start: 0.7905 (tpt) cc_final: 0.7631 (tpt) REVERT: B 62 MET cc_start: 0.8612 (ttp) cc_final: 0.8324 (ttm) REVERT: B 89 LYS cc_start: 0.8346 (mtpp) cc_final: 0.7941 (mtmm) REVERT: B 124 LYS cc_start: 0.8807 (mmtt) cc_final: 0.8422 (mmtm) REVERT: B 125 THR cc_start: 0.7398 (p) cc_final: 0.7127 (t) REVERT: B 136 ILE cc_start: 0.7502 (pt) cc_final: 0.7173 (mt) REVERT: B 144 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7145 (mt-10) REVERT: B 147 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7716 (mp10) REVERT: B 172 GLN cc_start: 0.7637 (mt0) cc_final: 0.7087 (mm-40) REVERT: B 181 ASP cc_start: 0.7845 (m-30) cc_final: 0.7348 (m-30) REVERT: B 193 GLN cc_start: 0.7550 (mm-40) cc_final: 0.6813 (mp10) REVERT: B 297 ASP cc_start: 0.7818 (p0) cc_final: 0.7492 (p0) REVERT: B 312 MET cc_start: 0.8436 (mmm) cc_final: 0.8205 (mmm) REVERT: B 335 SER cc_start: 0.8794 (m) cc_final: 0.8374 (p) REVERT: B 355 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7798 (mp0) REVERT: B 381 ARG cc_start: 0.7355 (mmm160) cc_final: 0.6879 (mmm160) REVERT: B 391 LYS cc_start: 0.8188 (ptmt) cc_final: 0.7859 (tppt) REVERT: B 426 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7342 (tp30) REVERT: B 498 LYS cc_start: 0.7618 (tmtm) cc_final: 0.7297 (tppt) REVERT: C 26 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7506 (mp0) REVERT: C 34 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8712 (tp) REVERT: C 40 ARG cc_start: 0.8060 (mtt-85) cc_final: 0.7658 (mmt180) REVERT: C 78 ASN cc_start: 0.7667 (m110) cc_final: 0.7245 (t0) REVERT: C 170 ASP cc_start: 0.8017 (m-30) cc_final: 0.7557 (m-30) REVERT: C 171 ARG cc_start: 0.7391 (ptp90) cc_final: 0.6972 (mtm110) REVERT: C 196 LYS cc_start: 0.8659 (mttt) cc_final: 0.8284 (mmmt) REVERT: C 286 ARG cc_start: 0.8109 (mmt90) cc_final: 0.7670 (mmp-170) REVERT: C 355 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8121 (pm20) REVERT: C 416 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8156 (pp30) REVERT: C 450 ARG cc_start: 0.7079 (mmm160) cc_final: 0.6545 (mmt90) REVERT: C 466 LYS cc_start: 0.7392 (mttt) cc_final: 0.6972 (mtpm) REVERT: C 467 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7475 (mm-30) REVERT: C 476 HIS cc_start: 0.7545 (m90) cc_final: 0.7306 (m90) REVERT: C 477 ARG cc_start: 0.6864 (mmm160) cc_final: 0.6313 (mmm160) REVERT: C 481 ASP cc_start: 0.9004 (t70) cc_final: 0.8601 (m-30) REVERT: D 151 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7650 (mtmm) REVERT: D 202 GLU cc_start: 0.7631 (tt0) cc_final: 0.7270 (pt0) REVERT: D 212 LYS cc_start: 0.8710 (mttm) cc_final: 0.8487 (mtmt) REVERT: D 213 ASP cc_start: 0.7875 (p0) cc_final: 0.7401 (p0) REVERT: D 214 LYS cc_start: 0.8380 (mttm) cc_final: 0.7847 (mmtt) REVERT: D 252 GLN cc_start: 0.6999 (mm-40) cc_final: 0.6410 (mm-40) REVERT: D 253 ASP cc_start: 0.8724 (m-30) cc_final: 0.8493 (m-30) REVERT: D 285 GLN cc_start: 0.7979 (pt0) cc_final: 0.7659 (pm20) REVERT: D 302 THR cc_start: 0.8085 (m) cc_final: 0.7860 (p) REVERT: D 359 ARG cc_start: 0.7446 (ttm170) cc_final: 0.6956 (ttm-80) REVERT: D 368 GLU cc_start: 0.7587 (tp30) cc_final: 0.7374 (tp30) REVERT: D 422 GLN cc_start: 0.8051 (mt0) cc_final: 0.7747 (mp10) REVERT: E 15 GLN cc_start: 0.7539 (mt0) cc_final: 0.7025 (mt0) REVERT: E 191 GLU cc_start: 0.7627 (tt0) cc_final: 0.7019 (pp20) REVERT: E 259 ASP cc_start: 0.7366 (t0) cc_final: 0.7120 (OUTLIER) REVERT: E 277 ARG cc_start: 0.7295 (mtm180) cc_final: 0.6966 (mtp180) REVERT: E 296 GLN cc_start: 0.8098 (mm110) cc_final: 0.7882 (mm110) REVERT: E 378 GLN cc_start: 0.8230 (mt0) cc_final: 0.7710 (mp10) REVERT: E 458 VAL cc_start: 0.7911 (t) cc_final: 0.7572 (p) REVERT: E 467 GLU cc_start: 0.7986 (mp0) cc_final: 0.7641 (pm20) REVERT: F 15 GLN cc_start: 0.7864 (mt0) cc_final: 0.7319 (mp10) REVERT: F 20 ILE cc_start: 0.6423 (OUTLIER) cc_final: 0.6150 (tp) REVERT: F 31 GLN cc_start: 0.7902 (pm20) cc_final: 0.7488 (pm20) REVERT: F 125 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7577 (mm-30) REVERT: F 263 ARG cc_start: 0.7876 (mmt-90) cc_final: 0.6602 (mtt180) REVERT: F 266 GLN cc_start: 0.7326 (tt0) cc_final: 0.7003 (tt0) REVERT: F 292 MET cc_start: 0.7699 (tpp) cc_final: 0.7326 (tpt) REVERT: F 297 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8304 (mt-10) REVERT: F 340 ARG cc_start: 0.7644 (tpt170) cc_final: 0.7394 (tpt90) REVERT: F 344 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8062 (mp0) REVERT: F 362 ASP cc_start: 0.8664 (t70) cc_final: 0.8333 (t0) REVERT: F 379 LYS cc_start: 0.8074 (ttmp) cc_final: 0.7720 (tttm) REVERT: F 382 GLN cc_start: 0.8410 (mt0) cc_final: 0.7952 (mm-40) REVERT: F 475 LYS cc_start: 0.7519 (mmmt) cc_final: 0.7052 (mptm) REVERT: G 33 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8087 (tppt) REVERT: H 140 GLU cc_start: 0.7773 (tp30) cc_final: 0.7527 (tp30) REVERT: I 19 ASP cc_start: 0.7864 (p0) cc_final: 0.7594 (p0) REVERT: I 27 GLU cc_start: 0.6616 (mt-10) cc_final: 0.5906 (mt-10) REVERT: I 31 MET cc_start: 0.8127 (tmm) cc_final: 0.7337 (tmm) REVERT: K 11 LYS cc_start: 0.8828 (mttt) cc_final: 0.8596 (mmtt) REVERT: K 19 GLU cc_start: 0.8472 (tt0) cc_final: 0.7827 (tp30) REVERT: K 43 THR cc_start: 0.9087 (m) cc_final: 0.8728 (t) REVERT: K 129 ARG cc_start: 0.8875 (ttp80) cc_final: 0.8617 (ttm-80) REVERT: L 11 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.8197 (t80) REVERT: M 45 TYR cc_start: 0.7186 (m-10) cc_final: 0.6534 (m-80) REVERT: M 85 LYS cc_start: 0.8403 (mttt) cc_final: 0.8074 (mptt) REVERT: M 105 ILE cc_start: 0.8854 (mm) cc_final: 0.8567 (pt) REVERT: M 106 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8398 (mm110) REVERT: M 107 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8639 (pt0) REVERT: M 121 LYS cc_start: 0.9207 (ttpp) cc_final: 0.9004 (tppt) REVERT: M 142 GLU cc_start: 0.6240 (OUTLIER) cc_final: 0.6030 (pm20) REVERT: N 118 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7147 (pp20) REVERT: N 142 MET cc_start: 0.6973 (OUTLIER) cc_final: 0.6325 (mpt) REVERT: N 145 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8316 (mm) REVERT: N 162 MET cc_start: 0.7700 (tpt) cc_final: 0.7403 (tpt) REVERT: O 33 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7149 (mp0) REVERT: O 63 ARG cc_start: 0.7316 (ptp-170) cc_final: 0.7078 (ptp-170) REVERT: O 92 GLU cc_start: 0.8502 (tp30) cc_final: 0.8068 (tp30) REVERT: O 94 ASN cc_start: 0.8354 (t0) cc_final: 0.8083 (t0) REVERT: O 98 MET cc_start: 0.7984 (ptp) cc_final: 0.7361 (ptp) REVERT: O 104 ASN cc_start: 0.8490 (t0) cc_final: 0.8214 (m-40) REVERT: O 120 GLU cc_start: 0.7581 (tt0) cc_final: 0.7162 (mm-30) REVERT: O 142 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7276 (t80) REVERT: O 154 LYS cc_start: 0.8499 (mtpt) cc_final: 0.8212 (mtpp) REVERT: O 174 MET cc_start: 0.5325 (ttm) cc_final: 0.4565 (ppp) REVERT: Q 52 LYS cc_start: 0.8340 (mmmm) cc_final: 0.8018 (mmmm) REVERT: S 47 LYS cc_start: 0.9094 (tppp) cc_final: 0.8617 (tttm) REVERT: S 49 GLN cc_start: 0.8500 (mm-40) cc_final: 0.8012 (tp-100) REVERT: S 90 GLU cc_start: 0.7996 (tt0) cc_final: 0.6916 (tm-30) REVERT: T 48 ARG cc_start: 0.8888 (ptt90) cc_final: 0.8316 (ptt90) REVERT: T 49 ARG cc_start: 0.8537 (mmp80) cc_final: 0.8230 (mmp80) REVERT: T 74 LYS cc_start: 0.8635 (tttt) cc_final: 0.8124 (tptp) outliers start: 180 outliers final: 81 residues processed: 768 average time/residue: 0.6424 time to fit residues: 596.7145 Evaluate side-chains 703 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 607 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 28 VAL Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 65 LEU Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 57 SER Chi-restraints excluded: chain 4 residue 67 MET Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 5 residue 64 CYS Chi-restraints excluded: chain 5 residue 71 LEU Chi-restraints excluded: chain 5 residue 75 PHE Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 7 residue 15 THR Chi-restraints excluded: chain 7 residue 21 SER Chi-restraints excluded: chain 8 residue 2 ILE Chi-restraints excluded: chain 8 residue 15 THR Chi-restraints excluded: chain 8 residue 18 VAL Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 416 GLN Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 470 VAL Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain K residue 173 MET Chi-restraints excluded: chain K residue 197 CYS Chi-restraints excluded: chain L residue 11 PHE Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 124 GLN Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 142 GLU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 142 MET Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain O residue 73 MET Chi-restraints excluded: chain O residue 142 PHE Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 452 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 363 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 453 optimal weight: 5.9990 chunk 210 optimal weight: 6.9990 chunk 467 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 18 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 264 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 45 GLN ** 7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 ASN B 65 ASN B 476 HIS E 174 ASN F 54 GLN ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 ASN ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 ASN K 27 ASN K 149 ASN M 93 GLN ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 GLN ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.172185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.138412 restraints weight = 63192.202| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.69 r_work: 0.3805 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3810 r_free = 0.3810 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3810 r_free = 0.3810 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 39746 Z= 0.136 Angle : 0.572 10.921 53709 Z= 0.290 Chirality : 0.043 0.273 6178 Planarity : 0.004 0.073 6879 Dihedral : 7.821 88.945 5756 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.79 % Allowed : 20.14 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.12), residues: 4987 helix: 1.67 (0.10), residues: 2659 sheet: 0.22 (0.22), residues: 560 loop : -0.36 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 340 TYR 0.019 0.001 TYR A 42 PHE 0.034 0.001 PHE G 167 TRP 0.030 0.002 TRP S 85 HIS 0.005 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00306 (39746) covalent geometry : angle 0.57186 (53709) hydrogen bonds : bond 0.04180 ( 2316) hydrogen bonds : angle 4.22344 ( 6786) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9974 Ramachandran restraints generated. 4987 Oldfield, 0 Emsley, 4987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9974 Ramachandran restraints generated. 4987 Oldfield, 0 Emsley, 4987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 658 time to evaluate : 1.277 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: 1 36 TYR cc_start: 0.6924 (t80) cc_final: 0.6542 (t80) REVERT: 4 31 SER cc_start: 0.7980 (m) cc_final: 0.7636 (p) REVERT: 5 71 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7931 (mp) REVERT: 5 75 PHE cc_start: 0.5354 (OUTLIER) cc_final: 0.4450 (m-80) REVERT: 6 7 LYS cc_start: 0.7488 (mtmt) cc_final: 0.6983 (mtpt) REVERT: A 26 GLU cc_start: 0.7732 (tp30) cc_final: 0.6841 (pm20) REVERT: A 143 ARG cc_start: 0.7588 (mtt180) cc_final: 0.7077 (pmm-80) REVERT: A 196 LYS cc_start: 0.7440 (tppt) cc_final: 0.7170 (ttpt) REVERT: A 226 MET cc_start: 0.8831 (tpt) cc_final: 0.8563 (mmm) REVERT: A 353 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7278 (mm-30) REVERT: A 362 ARG cc_start: 0.7819 (mtt90) cc_final: 0.7455 (mtt90) REVERT: A 426 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6705 (tp30) REVERT: A 439 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7304 (pm20) REVERT: A 465 GLU cc_start: 0.6717 (tt0) cc_final: 0.6448 (tm-30) REVERT: B 62 MET cc_start: 0.8563 (ttp) cc_final: 0.8304 (ttm) REVERT: B 89 LYS cc_start: 0.8325 (mtpp) cc_final: 0.7901 (mtmm) REVERT: B 124 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8340 (mmtm) REVERT: B 125 THR cc_start: 0.7341 (p) cc_final: 0.7072 (t) REVERT: B 136 ILE cc_start: 0.7444 (pt) cc_final: 0.7152 (mt) REVERT: B 144 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7137 (mt-10) REVERT: B 172 GLN cc_start: 0.7602 (mt0) cc_final: 0.7058 (mm-40) REVERT: B 181 ASP cc_start: 0.7830 (m-30) cc_final: 0.7328 (m-30) REVERT: B 193 GLN cc_start: 0.7556 (mm-40) cc_final: 0.6817 (mp10) REVERT: B 297 ASP cc_start: 0.7879 (p0) cc_final: 0.7570 (p0) REVERT: B 312 MET cc_start: 0.8435 (mmm) cc_final: 0.8211 (mmm) REVERT: B 335 SER cc_start: 0.8789 (m) cc_final: 0.8367 (p) REVERT: B 355 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7744 (mp0) REVERT: B 381 ARG cc_start: 0.7341 (mmm160) cc_final: 0.6851 (mmm160) REVERT: B 391 LYS cc_start: 0.8180 (ptmt) cc_final: 0.7832 (tppt) REVERT: B 396 GLN cc_start: 0.7432 (mm110) cc_final: 0.6954 (tm130) REVERT: B 426 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7369 (tp30) REVERT: B 436 MET cc_start: 0.7927 (ttp) cc_final: 0.7280 (ttm) REVERT: B 458 PRO cc_start: 0.7645 (Cg_exo) cc_final: 0.7046 (Cg_endo) REVERT: C 26 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7509 (mp0) REVERT: C 40 ARG cc_start: 0.8049 (mtt-85) cc_final: 0.7619 (mmt180) REVERT: C 78 ASN cc_start: 0.7634 (m110) cc_final: 0.7222 (t0) REVERT: C 170 ASP cc_start: 0.7971 (m-30) cc_final: 0.7494 (m-30) REVERT: C 171 ARG cc_start: 0.7341 (ptp90) cc_final: 0.6977 (mtm110) REVERT: C 196 LYS cc_start: 0.8647 (mttt) cc_final: 0.8273 (mmmt) REVERT: C 286 ARG cc_start: 0.8124 (mmt90) cc_final: 0.7673 (mmp-170) REVERT: C 355 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8116 (pm20) REVERT: C 381 ARG cc_start: 0.7595 (mtm110) cc_final: 0.7355 (mtm110) REVERT: C 383 MET cc_start: 0.7379 (tpt) cc_final: 0.6895 (tpt) REVERT: C 385 GLN cc_start: 0.8227 (pt0) cc_final: 0.7811 (pt0) REVERT: C 416 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8184 (pp30) REVERT: C 450 ARG cc_start: 0.7023 (mmm160) cc_final: 0.6507 (mmt90) REVERT: C 466 LYS cc_start: 0.7482 (mttt) cc_final: 0.7172 (mtpm) REVERT: C 467 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7544 (mm-30) REVERT: C 477 ARG cc_start: 0.6790 (mmm160) cc_final: 0.6467 (mmm160) REVERT: C 481 ASP cc_start: 0.9009 (t70) cc_final: 0.8631 (m-30) REVERT: D 151 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7367 (mtmm) REVERT: D 212 LYS cc_start: 0.8691 (mttm) cc_final: 0.8471 (mtmt) REVERT: D 213 ASP cc_start: 0.7869 (p0) cc_final: 0.7435 (p0) REVERT: D 214 LYS cc_start: 0.8383 (mttm) cc_final: 0.7831 (mmtt) REVERT: D 252 GLN cc_start: 0.7005 (mm-40) cc_final: 0.6426 (mm-40) REVERT: D 253 ASP cc_start: 0.8709 (m-30) cc_final: 0.8498 (m-30) REVERT: D 285 GLN cc_start: 0.7874 (pt0) cc_final: 0.7577 (pm20) REVERT: D 302 THR cc_start: 0.8002 (m) cc_final: 0.7786 (p) REVERT: D 359 ARG cc_start: 0.7378 (ttm170) cc_final: 0.6883 (ttm-80) REVERT: D 368 GLU cc_start: 0.7537 (tp30) cc_final: 0.7315 (tp30) REVERT: D 396 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.7926 (mmm) REVERT: D 422 GLN cc_start: 0.8045 (mt0) cc_final: 0.7735 (mp10) REVERT: E 15 GLN cc_start: 0.7530 (mt0) cc_final: 0.7001 (mt0) REVERT: E 17 THR cc_start: 0.8140 (m) cc_final: 0.7754 (p) REVERT: E 191 GLU cc_start: 0.7668 (tt0) cc_final: 0.7068 (pp20) REVERT: E 259 ASP cc_start: 0.7432 (t0) cc_final: 0.7198 (OUTLIER) REVERT: E 277 ARG cc_start: 0.7345 (mtm180) cc_final: 0.7090 (mtp180) REVERT: E 296 GLN cc_start: 0.8063 (mm110) cc_final: 0.7795 (mm110) REVERT: E 375 ARG cc_start: 0.8430 (mmm160) cc_final: 0.8193 (mmm160) REVERT: E 378 GLN cc_start: 0.8199 (mt0) cc_final: 0.7620 (mp10) REVERT: E 425 GLU cc_start: 0.7348 (pt0) cc_final: 0.6889 (pt0) REVERT: E 446 MET cc_start: 0.5100 (ptp) cc_final: 0.4854 (ptp) REVERT: E 458 VAL cc_start: 0.7918 (t) cc_final: 0.7587 (p) REVERT: E 467 GLU cc_start: 0.7892 (mp0) cc_final: 0.7610 (pm20) REVERT: F 15 GLN cc_start: 0.7846 (mt0) cc_final: 0.7306 (mp10) REVERT: F 20 ILE cc_start: 0.6468 (OUTLIER) cc_final: 0.6195 (tp) REVERT: F 31 GLN cc_start: 0.7920 (pm20) cc_final: 0.7645 (pm20) REVERT: F 125 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7571 (mm-30) REVERT: F 222 TYR cc_start: 0.8006 (m-10) cc_final: 0.7756 (m-80) REVERT: F 263 ARG cc_start: 0.7841 (mmt-90) cc_final: 0.6557 (mtt180) REVERT: F 266 GLN cc_start: 0.7253 (tt0) cc_final: 0.6961 (tt0) REVERT: F 292 MET cc_start: 0.7603 (tpp) cc_final: 0.7222 (tpt) REVERT: F 340 ARG cc_start: 0.7641 (tpt170) cc_final: 0.7392 (tpt90) REVERT: F 344 GLU cc_start: 0.8247 (mm-30) cc_final: 0.8012 (mp0) REVERT: F 362 ASP cc_start: 0.8666 (t70) cc_final: 0.8332 (t0) REVERT: F 379 LYS cc_start: 0.8052 (ttmp) cc_final: 0.7697 (tttm) REVERT: F 382 GLN cc_start: 0.8387 (mt0) cc_final: 0.7942 (mm-40) REVERT: F 409 ARG cc_start: 0.7706 (mtm-85) cc_final: 0.7498 (mtm-85) REVERT: F 475 LYS cc_start: 0.7491 (mmmt) cc_final: 0.7092 (mptm) REVERT: G 149 MET cc_start: 0.6725 (ppp) cc_final: 0.6259 (tmm) REVERT: H 140 GLU cc_start: 0.7782 (tp30) cc_final: 0.7518 (tp30) REVERT: I 19 ASP cc_start: 0.7878 (p0) cc_final: 0.7623 (p0) REVERT: I 27 GLU cc_start: 0.6399 (mt-10) cc_final: 0.5757 (mt-10) REVERT: I 31 MET cc_start: 0.8027 (tmm) cc_final: 0.7207 (tmm) REVERT: K 11 LYS cc_start: 0.8822 (mttt) cc_final: 0.8540 (mmtt) REVERT: K 19 GLU cc_start: 0.8443 (tt0) cc_final: 0.7838 (tp30) REVERT: K 43 THR cc_start: 0.9067 (m) cc_final: 0.8709 (t) REVERT: K 129 ARG cc_start: 0.8862 (ttp80) cc_final: 0.8612 (ttm-80) REVERT: L 29 LEU cc_start: 0.7815 (mm) cc_final: 0.7476 (tp) REVERT: M 45 TYR cc_start: 0.7070 (m-10) cc_final: 0.6486 (m-80) REVERT: M 85 LYS cc_start: 0.8383 (mttt) cc_final: 0.8061 (mptt) REVERT: M 105 ILE cc_start: 0.8837 (mm) cc_final: 0.8548 (pt) REVERT: M 106 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8291 (mm110) REVERT: M 107 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8661 (pt0) REVERT: M 126 ILE cc_start: 0.7554 (tp) cc_final: 0.7139 (pp) REVERT: N 10 ASP cc_start: 0.8373 (t0) cc_final: 0.8077 (t70) REVERT: N 113 TYR cc_start: 0.6312 (t80) cc_final: 0.6057 (t80) REVERT: N 118 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7123 (pp20) REVERT: N 136 MET cc_start: 0.5246 (mmt) cc_final: 0.5036 (mpm) REVERT: N 142 MET cc_start: 0.6933 (OUTLIER) cc_final: 0.6299 (mpt) REVERT: N 145 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8313 (mm) REVERT: N 162 MET cc_start: 0.7769 (tpt) cc_final: 0.7393 (tpt) REVERT: O 33 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7125 (mp0) REVERT: O 92 GLU cc_start: 0.8479 (tp30) cc_final: 0.8023 (tp30) REVERT: O 94 ASN cc_start: 0.8407 (t0) cc_final: 0.8126 (t0) REVERT: O 98 MET cc_start: 0.8114 (ptp) cc_final: 0.7420 (ptp) REVERT: O 104 ASN cc_start: 0.8381 (t0) cc_final: 0.8106 (m-40) REVERT: O 120 GLU cc_start: 0.7525 (tt0) cc_final: 0.6806 (tm-30) REVERT: O 142 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7232 (t80) REVERT: O 174 MET cc_start: 0.5336 (ttm) cc_final: 0.4561 (pp-130) REVERT: Q 48 TYR cc_start: 0.7217 (OUTLIER) cc_final: 0.6753 (m-80) REVERT: Q 52 LYS cc_start: 0.8437 (mmmm) cc_final: 0.8110 (mmmm) REVERT: R 105 TYR cc_start: 0.8341 (m-80) cc_final: 0.8106 (m-80) REVERT: S 49 GLN cc_start: 0.8468 (mm-40) cc_final: 0.7989 (tp-100) REVERT: S 90 GLU cc_start: 0.7963 (tt0) cc_final: 0.6907 (tm-30) REVERT: T 41 GLU cc_start: 0.8172 (pp20) cc_final: 0.7959 (pp20) REVERT: T 74 LYS cc_start: 0.8647 (tttt) cc_final: 0.8127 (tptp) outliers start: 155 outliers final: 85 residues processed: 768 average time/residue: 0.7295 time to fit residues: 673.1846 Evaluate side-chains 710 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 614 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 4 SER Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 45 GLN Chi-restraints excluded: chain 2 residue 51 ILE Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 21 SER Chi-restraints excluded: chain 3 residue 28 VAL Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 56 LEU Chi-restraints excluded: chain 3 residue 65 LEU Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 5 residue 48 SER Chi-restraints excluded: chain 5 residue 64 CYS Chi-restraints excluded: chain 5 residue 71 LEU Chi-restraints excluded: chain 5 residue 75 PHE Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 7 residue 21 SER Chi-restraints excluded: chain 8 residue 2 ILE Chi-restraints excluded: chain 8 residue 18 VAL Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 416 GLN Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 284 TYR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 197 CYS Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 114 ASN Chi-restraints excluded: chain M residue 124 GLN Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 142 MET Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain O residue 142 PHE Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain Q residue 48 TYR Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain S residue 64 TRP Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 356 optimal weight: 5.9990 chunk 232 optimal weight: 0.9990 chunk 448 optimal weight: 5.9990 chunk 434 optimal weight: 3.9990 chunk 146 optimal weight: 0.0050 chunk 252 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 324 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 45 GLN ** 7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 ASN B 65 ASN F 54 GLN ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 ASN ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 ASN K 27 ASN ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 161 ASN ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.170160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.136492 restraints weight = 62733.946| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.55 r_work: 0.3776 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 39746 Z= 0.184 Angle : 0.614 13.249 53709 Z= 0.311 Chirality : 0.044 0.343 6178 Planarity : 0.005 0.081 6879 Dihedral : 7.839 89.585 5752 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.82 % Allowed : 20.04 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.12), residues: 4987 helix: 1.60 (0.10), residues: 2658 sheet: 0.22 (0.22), residues: 555 loop : -0.40 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 340 TYR 0.019 0.001 TYR A 42 PHE 0.029 0.002 PHE G 161 TRP 0.031 0.002 TRP S 85 HIS 0.007 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00429 (39746) covalent geometry : angle 0.61438 (53709) hydrogen bonds : bond 0.04454 ( 2316) hydrogen bonds : angle 4.31142 ( 6786) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9974 Ramachandran restraints generated. 4987 Oldfield, 0 Emsley, 4987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9974 Ramachandran restraints generated. 4987 Oldfield, 0 Emsley, 4987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 621 time to evaluate : 1.106 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: 1 36 TYR cc_start: 0.7083 (t80) cc_final: 0.6759 (t80) REVERT: 4 31 SER cc_start: 0.8106 (m) cc_final: 0.7778 (p) REVERT: 5 71 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7873 (mp) REVERT: 5 75 PHE cc_start: 0.5484 (OUTLIER) cc_final: 0.4537 (m-80) REVERT: 6 7 LYS cc_start: 0.7703 (mtmt) cc_final: 0.7210 (mtpt) REVERT: 8 66 MET cc_start: 0.7370 (tmm) cc_final: 0.7049 (pp-130) REVERT: A 26 GLU cc_start: 0.7731 (tp30) cc_final: 0.6786 (pm20) REVERT: A 40 ARG cc_start: 0.7591 (mmt-90) cc_final: 0.7385 (mmt180) REVERT: A 143 ARG cc_start: 0.7593 (mtt180) cc_final: 0.6985 (pmm-80) REVERT: A 196 LYS cc_start: 0.7538 (tppt) cc_final: 0.7108 (tmmt) REVERT: A 226 MET cc_start: 0.8900 (tpt) cc_final: 0.8625 (mmt) REVERT: A 353 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7436 (mm-30) REVERT: A 362 ARG cc_start: 0.7855 (mtt90) cc_final: 0.7619 (mtt90) REVERT: A 381 ARG cc_start: 0.7874 (mmt180) cc_final: 0.7550 (mmm160) REVERT: A 426 GLU cc_start: 0.7519 (mm-30) cc_final: 0.6833 (tp30) REVERT: A 439 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7268 (pm20) REVERT: A 449 VAL cc_start: 0.6711 (OUTLIER) cc_final: 0.6452 (m) REVERT: A 465 GLU cc_start: 0.6467 (tt0) cc_final: 0.6192 (tm-30) REVERT: B 62 MET cc_start: 0.8634 (ttp) cc_final: 0.8428 (ttm) REVERT: B 89 LYS cc_start: 0.8442 (mtpp) cc_final: 0.8073 (mtmm) REVERT: B 124 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8313 (mmtm) REVERT: B 125 THR cc_start: 0.7373 (p) cc_final: 0.7095 (t) REVERT: B 136 ILE cc_start: 0.7510 (pt) cc_final: 0.7247 (mt) REVERT: B 144 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7182 (mt-10) REVERT: B 172 GLN cc_start: 0.7708 (mt0) cc_final: 0.7155 (mm-40) REVERT: B 181 ASP cc_start: 0.7982 (m-30) cc_final: 0.7494 (m-30) REVERT: B 193 GLN cc_start: 0.7555 (mm-40) cc_final: 0.6792 (mp10) REVERT: B 195 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6544 (tm-30) REVERT: B 297 ASP cc_start: 0.7819 (p0) cc_final: 0.7521 (p0) REVERT: B 312 MET cc_start: 0.8531 (mmm) cc_final: 0.8326 (mmm) REVERT: B 335 SER cc_start: 0.8686 (m) cc_final: 0.8284 (p) REVERT: B 355 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7801 (mp0) REVERT: B 381 ARG cc_start: 0.7417 (mmm160) cc_final: 0.6922 (mmm160) REVERT: B 391 LYS cc_start: 0.8160 (ptmt) cc_final: 0.7789 (tppt) REVERT: B 396 GLN cc_start: 0.7479 (mm110) cc_final: 0.6966 (tm130) REVERT: B 426 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7409 (tp30) REVERT: B 436 MET cc_start: 0.7984 (ttp) cc_final: 0.7243 (ttm) REVERT: B 458 PRO cc_start: 0.7885 (Cg_exo) cc_final: 0.7395 (Cg_endo) REVERT: B 486 GLU cc_start: 0.7394 (tp30) cc_final: 0.7007 (mt-10) REVERT: C 26 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7590 (mp0) REVERT: C 40 ARG cc_start: 0.8228 (mtt-85) cc_final: 0.7837 (mmt180) REVERT: C 78 ASN cc_start: 0.7758 (m110) cc_final: 0.7261 (t0) REVERT: C 171 ARG cc_start: 0.7482 (ptp90) cc_final: 0.7051 (mtm110) REVERT: C 196 LYS cc_start: 0.8705 (mttt) cc_final: 0.8324 (mmmt) REVERT: C 286 ARG cc_start: 0.8228 (mmt90) cc_final: 0.7754 (mmp-170) REVERT: C 355 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8069 (pm20) REVERT: C 381 ARG cc_start: 0.7631 (mtm110) cc_final: 0.7351 (mtm110) REVERT: C 385 GLN cc_start: 0.8212 (pt0) cc_final: 0.7788 (pt0) REVERT: C 416 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8097 (pp30) REVERT: C 450 ARG cc_start: 0.7174 (mmm160) cc_final: 0.6626 (mmt90) REVERT: C 462 THR cc_start: 0.8309 (OUTLIER) cc_final: 0.8069 (p) REVERT: C 466 LYS cc_start: 0.7584 (mttt) cc_final: 0.7215 (mtpm) REVERT: C 467 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7508 (mm-30) REVERT: C 477 ARG cc_start: 0.6849 (mmm160) cc_final: 0.6470 (mmm160) REVERT: C 481 ASP cc_start: 0.9034 (t70) cc_final: 0.8613 (m-30) REVERT: D 37 ASN cc_start: 0.7805 (OUTLIER) cc_final: 0.7506 (t0) REVERT: D 151 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7475 (mtmm) REVERT: D 214 LYS cc_start: 0.8388 (mttm) cc_final: 0.7962 (mmtt) REVERT: D 253 ASP cc_start: 0.8787 (m-30) cc_final: 0.8571 (m-30) REVERT: D 285 GLN cc_start: 0.8039 (pt0) cc_final: 0.7721 (pm20) REVERT: D 302 THR cc_start: 0.8109 (m) cc_final: 0.7859 (p) REVERT: D 359 ARG cc_start: 0.7487 (ttm170) cc_final: 0.6814 (tpp-160) REVERT: D 366 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7523 (pp) REVERT: D 368 GLU cc_start: 0.7695 (tp30) cc_final: 0.7444 (tp30) REVERT: D 396 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8009 (mmm) REVERT: D 422 GLN cc_start: 0.8170 (mt0) cc_final: 0.7798 (mp10) REVERT: E 15 GLN cc_start: 0.7638 (mt0) cc_final: 0.6900 (mm-40) REVERT: E 58 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8273 (pp20) REVERT: E 191 GLU cc_start: 0.7666 (tt0) cc_final: 0.7273 (pm20) REVERT: E 203 MET cc_start: 0.7546 (mtt) cc_final: 0.7295 (mtt) REVERT: E 259 ASP cc_start: 0.7443 (t0) cc_final: 0.7139 (OUTLIER) REVERT: E 296 GLN cc_start: 0.8082 (mm110) cc_final: 0.7866 (mm110) REVERT: E 375 ARG cc_start: 0.8452 (mmm160) cc_final: 0.8214 (mmm160) REVERT: E 378 GLN cc_start: 0.8229 (mt0) cc_final: 0.7646 (mp10) REVERT: E 425 GLU cc_start: 0.7324 (pt0) cc_final: 0.6861 (pt0) REVERT: E 446 MET cc_start: 0.5149 (ptp) cc_final: 0.4890 (ptp) REVERT: E 458 VAL cc_start: 0.7918 (OUTLIER) cc_final: 0.7579 (p) REVERT: E 467 GLU cc_start: 0.7903 (mp0) cc_final: 0.7600 (pm20) REVERT: F 15 GLN cc_start: 0.8022 (mt0) cc_final: 0.7512 (mp10) REVERT: F 20 ILE cc_start: 0.6429 (OUTLIER) cc_final: 0.6141 (tp) REVERT: F 31 GLN cc_start: 0.8036 (pm20) cc_final: 0.7640 (pm20) REVERT: F 125 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7540 (mm-30) REVERT: F 263 ARG cc_start: 0.8050 (mmt-90) cc_final: 0.6760 (mtt180) REVERT: F 292 MET cc_start: 0.7740 (tpp) cc_final: 0.7346 (tpt) REVERT: F 297 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8305 (mt-10) REVERT: F 340 ARG cc_start: 0.7854 (tpt170) cc_final: 0.7622 (tpt90) REVERT: F 344 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8092 (mp0) REVERT: F 362 ASP cc_start: 0.8654 (t70) cc_final: 0.8339 (t0) REVERT: F 379 LYS cc_start: 0.8129 (ttmp) cc_final: 0.7813 (tttm) REVERT: F 382 GLN cc_start: 0.8417 (mt0) cc_final: 0.7990 (mm-40) REVERT: F 409 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7656 (mtm-85) REVERT: F 475 LYS cc_start: 0.7522 (mmmt) cc_final: 0.7053 (mptm) REVERT: G 33 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8128 (tppt) REVERT: G 149 MET cc_start: 0.6803 (ppp) cc_final: 0.6391 (tmm) REVERT: G 248 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7016 (mtp180) REVERT: H 104 ASP cc_start: 0.6211 (p0) cc_final: 0.5903 (p0) REVERT: H 140 GLU cc_start: 0.7846 (tp30) cc_final: 0.7615 (tp30) REVERT: I 19 ASP cc_start: 0.8048 (p0) cc_final: 0.7764 (p0) REVERT: I 27 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6201 (mt-10) REVERT: I 31 MET cc_start: 0.8251 (tmm) cc_final: 0.7340 (tmm) REVERT: K 2 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.7101 (ttm-80) REVERT: K 11 LYS cc_start: 0.8967 (mttt) cc_final: 0.8658 (mmtt) REVERT: K 19 GLU cc_start: 0.8612 (tt0) cc_final: 0.8014 (tp30) REVERT: K 129 ARG cc_start: 0.8918 (ttp80) cc_final: 0.8697 (ttm-80) REVERT: L 11 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8193 (t80) REVERT: L 29 LEU cc_start: 0.7811 (mm) cc_final: 0.7519 (mm) REVERT: L 31 GLU cc_start: 0.7438 (pm20) cc_final: 0.7010 (pm20) REVERT: M 43 LEU cc_start: 0.8039 (pp) cc_final: 0.7741 (mm) REVERT: M 85 LYS cc_start: 0.8366 (mttt) cc_final: 0.8062 (mptt) REVERT: M 105 ILE cc_start: 0.8834 (mm) cc_final: 0.8550 (pt) REVERT: M 106 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8376 (mm110) REVERT: M 107 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8665 (pt0) REVERT: N 10 ASP cc_start: 0.8434 (t0) cc_final: 0.8090 (t70) REVERT: N 113 TYR cc_start: 0.6463 (t80) cc_final: 0.6231 (t80) REVERT: N 118 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7150 (pp20) REVERT: N 142 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6391 (mpt) REVERT: N 145 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8351 (mm) REVERT: N 162 MET cc_start: 0.7896 (tpt) cc_final: 0.7610 (tpt) REVERT: O 33 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7185 (mp0) REVERT: O 92 GLU cc_start: 0.8546 (tp30) cc_final: 0.8223 (tp30) REVERT: O 94 ASN cc_start: 0.8437 (t0) cc_final: 0.8154 (t0) REVERT: O 98 MET cc_start: 0.8226 (ptp) cc_final: 0.7433 (ptp) REVERT: O 104 ASN cc_start: 0.8460 (t0) cc_final: 0.8191 (m-40) REVERT: O 142 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.7320 (t80) REVERT: O 174 MET cc_start: 0.5294 (ttm) cc_final: 0.4494 (pp-130) REVERT: Q 48 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.6881 (m-80) REVERT: Q 52 LYS cc_start: 0.8482 (mmmm) cc_final: 0.8144 (mmmm) REVERT: S 49 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8053 (tp-100) REVERT: S 90 GLU cc_start: 0.8172 (tt0) cc_final: 0.7099 (tm-30) REVERT: T 74 LYS cc_start: 0.8711 (tttt) cc_final: 0.8174 (tptp) outliers start: 197 outliers final: 101 residues processed: 759 average time/residue: 0.6977 time to fit residues: 638.5282 Evaluate side-chains 705 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 582 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 4 SER Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 1 residue 58 GLU Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 51 ILE Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 21 SER Chi-restraints excluded: chain 3 residue 28 VAL Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 65 LEU Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 57 SER Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 5 residue 48 SER Chi-restraints excluded: chain 5 residue 64 CYS Chi-restraints excluded: chain 5 residue 71 LEU Chi-restraints excluded: chain 5 residue 75 PHE Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 7 residue 21 SER Chi-restraints excluded: chain 8 residue 2 ILE Chi-restraints excluded: chain 8 residue 15 THR Chi-restraints excluded: chain 8 residue 18 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 416 GLN Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 284 TYR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 458 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 470 VAL Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain G residue 248 ARG Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain K residue 2 ARG Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 194 LEU Chi-restraints excluded: chain K residue 197 CYS Chi-restraints excluded: chain L residue 11 PHE Chi-restraints excluded: chain L residue 43 GLU Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 114 ASN Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 142 MET Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 167 LEU Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain O residue 142 PHE Chi-restraints excluded: chain O residue 167 ILE Chi-restraints excluded: chain Q residue 48 TYR Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 71 ARG Chi-restraints excluded: chain S residue 64 TRP Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 286 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 330 optimal weight: 0.5980 chunk 158 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 354 optimal weight: 9.9990 chunk 357 optimal weight: 0.9980 chunk 464 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 45 GLN ** 7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 ASN B 65 ASN B 147 GLN F 54 GLN ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 ASN ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 ASN K 27 ASN ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 GLN O 93 ASN ** Q 50 ASN ** 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 = 0.4278 r_free = 0.4278 target = 0.172351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.138428 restraints weight = 63282.756| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.72 r_work: 0.3796 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 39746 Z= 0.135 Angle : 0.601 12.707 53709 Z= 0.302 Chirality : 0.043 0.287 6178 Planarity : 0.004 0.073 6879 Dihedral : 7.655 87.481 5752 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.74 % Allowed : 21.24 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.12), residues: 4987 helix: 1.68 (0.10), residues: 2662 sheet: 0.19 (0.22), residues: 562 loop : -0.36 (0.15), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 340 TYR 0.023 0.001 TYR T 30 PHE 0.036 0.001 PHE G 167 TRP 0.032 0.002 TRP S 85 HIS 0.005 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00304 (39746) covalent geometry : angle 0.60070 (53709) hydrogen bonds : bond 0.04202 ( 2316) hydrogen bonds : angle 4.22596 ( 6786) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9974 Ramachandran restraints generated. 4987 Oldfield, 0 Emsley, 4987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9974 Ramachandran restraints generated. 4987 Oldfield, 0 Emsley, 4987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 626 time to evaluate : 1.682 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: 1 36 TYR cc_start: 0.6942 (t80) cc_final: 0.6564 (t80) REVERT: 2 58 GLU cc_start: 0.7444 (tp30) cc_final: 0.7127 (mm-30) REVERT: 4 31 SER cc_start: 0.7977 (m) cc_final: 0.7653 (p) REVERT: 4 72 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8807 (mt) REVERT: 5 71 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7858 (mp) REVERT: 5 75 PHE cc_start: 0.5043 (OUTLIER) cc_final: 0.4094 (m-80) REVERT: 6 7 LYS cc_start: 0.7488 (mtmt) cc_final: 0.6964 (mtpt) REVERT: 8 66 MET cc_start: 0.7338 (tmm) cc_final: 0.7135 (pp-130) REVERT: A 26 GLU cc_start: 0.7749 (tp30) cc_final: 0.6826 (pm20) REVERT: A 143 ARG cc_start: 0.7625 (mtt180) cc_final: 0.7090 (pmm-80) REVERT: A 196 LYS cc_start: 0.7447 (tppt) cc_final: 0.7172 (ttpt) REVERT: A 353 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7257 (mm-30) REVERT: A 362 ARG cc_start: 0.7905 (mtt90) cc_final: 0.7682 (mtt90) REVERT: A 426 GLU cc_start: 0.7493 (mm-30) cc_final: 0.6802 (tp30) REVERT: A 439 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7326 (pm20) REVERT: A 449 VAL cc_start: 0.6710 (OUTLIER) cc_final: 0.6458 (m) REVERT: A 460 LYS cc_start: 0.7552 (mttt) cc_final: 0.7025 (tptp) REVERT: A 465 GLU cc_start: 0.6420 (tt0) cc_final: 0.6194 (tm-30) REVERT: B 62 MET cc_start: 0.8553 (ttp) cc_final: 0.8298 (ttm) REVERT: B 89 LYS cc_start: 0.8241 (mtpp) cc_final: 0.7911 (mtmm) REVERT: B 124 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8323 (mmtm) REVERT: B 125 THR cc_start: 0.7348 (p) cc_final: 0.7073 (t) REVERT: B 144 GLU cc_start: 0.7612 (mm-30) cc_final: 0.6942 (mt-10) REVERT: B 172 GLN cc_start: 0.7614 (mt0) cc_final: 0.7081 (mm-40) REVERT: B 181 ASP cc_start: 0.7891 (m-30) cc_final: 0.7342 (m-30) REVERT: B 193 GLN cc_start: 0.7404 (mm-40) cc_final: 0.6680 (mp10) REVERT: B 195 GLU cc_start: 0.6796 (mm-30) cc_final: 0.6418 (tm-30) REVERT: B 297 ASP cc_start: 0.7908 (p0) cc_final: 0.7603 (p0) REVERT: B 312 MET cc_start: 0.8502 (mmm) cc_final: 0.8292 (mmm) REVERT: B 335 SER cc_start: 0.8708 (m) cc_final: 0.8275 (p) REVERT: B 355 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7769 (mp0) REVERT: B 381 ARG cc_start: 0.7304 (mmm160) cc_final: 0.6798 (mmm160) REVERT: B 391 LYS cc_start: 0.8060 (ptmt) cc_final: 0.7653 (tppt) REVERT: B 396 GLN cc_start: 0.7440 (mm110) cc_final: 0.6969 (tm130) REVERT: B 426 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7325 (tp30) REVERT: B 436 MET cc_start: 0.7972 (ttp) cc_final: 0.7256 (ttm) REVERT: B 458 PRO cc_start: 0.7941 (Cg_exo) cc_final: 0.7404 (Cg_endo) REVERT: B 486 GLU cc_start: 0.7398 (tp30) cc_final: 0.7007 (mt-10) REVERT: C 26 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7447 (mp0) REVERT: C 27 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.6879 (mm-30) REVERT: C 40 ARG cc_start: 0.8114 (mtt-85) cc_final: 0.7733 (mmt180) REVERT: C 78 ASN cc_start: 0.7627 (m110) cc_final: 0.7190 (t0) REVERT: C 170 ASP cc_start: 0.7753 (m-30) cc_final: 0.7154 (m-30) REVERT: C 171 ARG cc_start: 0.7318 (ptp90) cc_final: 0.6935 (mtm110) REVERT: C 196 LYS cc_start: 0.8680 (mttt) cc_final: 0.8302 (mmmt) REVERT: C 286 ARG cc_start: 0.8155 (mmt90) cc_final: 0.7718 (mmp-170) REVERT: C 314 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8252 (mm-30) REVERT: C 355 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8136 (pm20) REVERT: C 381 ARG cc_start: 0.7611 (mtm110) cc_final: 0.7195 (mtm110) REVERT: C 383 MET cc_start: 0.7369 (tpt) cc_final: 0.6890 (tpt) REVERT: C 385 GLN cc_start: 0.8160 (pt0) cc_final: 0.7743 (pt0) REVERT: C 416 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8024 (pp30) REVERT: C 450 ARG cc_start: 0.7085 (mmm160) cc_final: 0.6546 (mmt90) REVERT: C 462 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.8083 (p) REVERT: C 466 LYS cc_start: 0.7578 (mttt) cc_final: 0.7199 (mtpm) REVERT: C 467 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7512 (mm-30) REVERT: C 477 ARG cc_start: 0.6810 (mmm160) cc_final: 0.6504 (mmm160) REVERT: C 481 ASP cc_start: 0.9034 (t70) cc_final: 0.8632 (m-30) REVERT: D 151 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7377 (mtmm) REVERT: D 214 LYS cc_start: 0.8375 (mttm) cc_final: 0.7953 (mmtt) REVERT: D 252 GLN cc_start: 0.6994 (mm-40) cc_final: 0.6434 (mm-40) REVERT: D 253 ASP cc_start: 0.8714 (m-30) cc_final: 0.8467 (m-30) REVERT: D 285 GLN cc_start: 0.7872 (pt0) cc_final: 0.7575 (pm20) REVERT: D 302 THR cc_start: 0.8042 (m) cc_final: 0.7780 (p) REVERT: D 359 ARG cc_start: 0.7266 (ttm170) cc_final: 0.6777 (tpp-160) REVERT: D 368 GLU cc_start: 0.7557 (tp30) cc_final: 0.7326 (tp30) REVERT: D 396 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.7981 (mmm) REVERT: D 422 GLN cc_start: 0.8059 (mt0) cc_final: 0.7721 (mp10) REVERT: E 15 GLN cc_start: 0.7538 (mt0) cc_final: 0.6795 (mm-40) REVERT: E 191 GLU cc_start: 0.7649 (tt0) cc_final: 0.7325 (pm20) REVERT: E 259 ASP cc_start: 0.7417 (t0) cc_final: 0.7186 (OUTLIER) REVERT: E 277 ARG cc_start: 0.7471 (mtm180) cc_final: 0.6722 (ptt-90) REVERT: E 296 GLN cc_start: 0.8057 (mm110) cc_final: 0.7844 (mm110) REVERT: E 375 ARG cc_start: 0.8442 (mmm160) cc_final: 0.8170 (mmm160) REVERT: E 378 GLN cc_start: 0.8207 (mt0) cc_final: 0.7614 (mp10) REVERT: E 425 GLU cc_start: 0.7322 (pt0) cc_final: 0.6868 (pt0) REVERT: E 446 MET cc_start: 0.5085 (ptp) cc_final: 0.4797 (ptp) REVERT: E 458 VAL cc_start: 0.7907 (OUTLIER) cc_final: 0.7578 (p) REVERT: E 467 GLU cc_start: 0.7845 (mp0) cc_final: 0.7479 (pm20) REVERT: F 15 GLN cc_start: 0.7881 (mt0) cc_final: 0.7354 (mp10) REVERT: F 20 ILE cc_start: 0.6433 (OUTLIER) cc_final: 0.6143 (tp) REVERT: F 125 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7570 (mm-30) REVERT: F 263 ARG cc_start: 0.7835 (mmt-90) cc_final: 0.6576 (mtt180) REVERT: F 292 MET cc_start: 0.7638 (tpp) cc_final: 0.7232 (tpt) REVERT: F 340 ARG cc_start: 0.7705 (tpt170) cc_final: 0.7436 (tpt90) REVERT: F 344 GLU cc_start: 0.8236 (mm-30) cc_final: 0.8032 (mp0) REVERT: F 362 ASP cc_start: 0.8604 (t70) cc_final: 0.8300 (t0) REVERT: F 379 LYS cc_start: 0.8084 (ttmp) cc_final: 0.7767 (tttm) REVERT: F 382 GLN cc_start: 0.8375 (mt0) cc_final: 0.7948 (mm-40) REVERT: F 409 ARG cc_start: 0.7755 (mtm-85) cc_final: 0.7532 (mtm-85) REVERT: F 475 LYS cc_start: 0.7501 (mmmt) cc_final: 0.7104 (mptm) REVERT: G 33 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8109 (tppt) REVERT: G 149 MET cc_start: 0.6826 (ppp) cc_final: 0.6446 (tmm) REVERT: G 159 ASN cc_start: 0.7816 (m-40) cc_final: 0.7133 (m-40) REVERT: G 248 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6916 (mtp180) REVERT: H 140 GLU cc_start: 0.7745 (tp30) cc_final: 0.7494 (tp30) REVERT: I 14 ARG cc_start: 0.6103 (mmt-90) cc_final: 0.4142 (mtt-85) REVERT: I 27 GLU cc_start: 0.6381 (mt-10) cc_final: 0.5752 (mt-10) REVERT: I 31 MET cc_start: 0.8168 (tmm) cc_final: 0.7282 (tmm) REVERT: K 11 LYS cc_start: 0.8813 (mttt) cc_final: 0.8528 (mmtt) REVERT: K 19 GLU cc_start: 0.8418 (tt0) cc_final: 0.7773 (tp30) REVERT: L 29 LEU cc_start: 0.7800 (mm) cc_final: 0.7506 (mm) REVERT: L 31 GLU cc_start: 0.7338 (pm20) cc_final: 0.6868 (pm20) REVERT: M 43 LEU cc_start: 0.8029 (pp) cc_final: 0.7756 (mm) REVERT: M 85 LYS cc_start: 0.8265 (mttt) cc_final: 0.7999 (mptt) REVERT: M 105 ILE cc_start: 0.8819 (mm) cc_final: 0.8532 (pt) REVERT: M 106 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8297 (mm110) REVERT: M 107 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8832 (mp0) REVERT: M 121 LYS cc_start: 0.9210 (ttpp) cc_final: 0.8980 (tppt) REVERT: M 122 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7838 (tm) REVERT: M 126 ILE cc_start: 0.7566 (tp) cc_final: 0.7138 (pp) REVERT: N 10 ASP cc_start: 0.8433 (t0) cc_final: 0.8080 (t70) REVERT: N 113 TYR cc_start: 0.6130 (t80) cc_final: 0.5896 (t80) REVERT: N 118 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7091 (pp20) REVERT: N 145 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8334 (mm) REVERT: N 162 MET cc_start: 0.7772 (tpt) cc_final: 0.7487 (tpt) REVERT: O 33 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7127 (mp0) REVERT: O 92 GLU cc_start: 0.8525 (tp30) cc_final: 0.8237 (tp30) REVERT: O 94 ASN cc_start: 0.8446 (t0) cc_final: 0.8157 (t0) REVERT: O 98 MET cc_start: 0.8140 (ptp) cc_final: 0.7370 (ptp) REVERT: O 104 ASN cc_start: 0.8437 (t0) cc_final: 0.8169 (m-40) REVERT: O 127 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6655 (pp) REVERT: O 142 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.7337 (t80) REVERT: O 174 MET cc_start: 0.5062 (ttm) cc_final: 0.4401 (pp-130) REVERT: R 32 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6892 (mp-120) REVERT: S 49 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8044 (tp-100) REVERT: S 90 GLU cc_start: 0.8054 (tt0) cc_final: 0.6970 (tm-30) REVERT: T 46 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8743 (tm-30) REVERT: T 74 LYS cc_start: 0.8645 (tttt) cc_final: 0.8120 (tptp) outliers start: 153 outliers final: 85 residues processed: 733 average time/residue: 0.7674 time to fit residues: 673.8867 Evaluate side-chains 689 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 585 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 4 SER Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 1 residue 58 GLU Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 45 GLN Chi-restraints excluded: chain 2 residue 51 ILE Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 28 VAL Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 65 LEU Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 4 residue 69 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 5 residue 48 SER Chi-restraints excluded: chain 5 residue 64 CYS Chi-restraints excluded: chain 5 residue 71 LEU Chi-restraints excluded: chain 5 residue 75 PHE Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 7 residue 21 SER Chi-restraints excluded: chain 8 residue 18 VAL Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 98 MET Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 284 TYR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 458 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain G residue 248 ARG Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 194 LEU Chi-restraints excluded: chain K residue 197 CYS Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 114 ASN Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain M residue 124 GLN Chi-restraints excluded: chain M residue 130 HIS Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 167 LEU Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain O residue 142 PHE Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain R residue 71 ARG Chi-restraints excluded: chain S residue 64 TRP Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 398 optimal weight: 5.9990 chunk 334 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 0.0270 chunk 148 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 214 optimal weight: 0.5980 chunk 297 optimal weight: 6.9990 chunk 464 optimal weight: 9.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 45 GLN 2 45 GLN ** 7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 ASN B 65 ASN B 147 GLN ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 ASN K 27 ASN ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 GLN ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 8 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.171224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.137447 restraints weight = 62483.741| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.66 r_work: 0.3799 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 39746 Z= 0.147 Angle : 0.613 12.378 53709 Z= 0.310 Chirality : 0.043 0.230 6178 Planarity : 0.004 0.075 6879 Dihedral : 7.594 86.479 5750 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.91 % Allowed : 21.63 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.12), residues: 4987 helix: 1.67 (0.10), residues: 2664 sheet: 0.22 (0.22), residues: 550 loop : -0.37 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 340 TYR 0.025 0.001 TYR L 18 PHE 0.034 0.001 PHE G 167 TRP 0.051 0.002 TRP Q 51 HIS 0.006 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00335 (39746) covalent geometry : angle 0.61297 (53709) hydrogen bonds : bond 0.04252 ( 2316) hydrogen bonds : angle 4.24422 ( 6786) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9974 Ramachandran restraints generated. 4987 Oldfield, 0 Emsley, 4987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9974 Ramachandran restraints generated. 4987 Oldfield, 0 Emsley, 4987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 621 time to evaluate : 1.641 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: 1 36 TYR cc_start: 0.6960 (t80) cc_final: 0.6587 (t80) REVERT: 2 58 GLU cc_start: 0.7436 (tp30) cc_final: 0.7198 (mm-30) REVERT: 4 31 SER cc_start: 0.7974 (m) cc_final: 0.7644 (p) REVERT: 4 58 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: 4 72 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8798 (mt) REVERT: 5 71 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7869 (mp) REVERT: 5 75 PHE cc_start: 0.5164 (OUTLIER) cc_final: 0.4224 (m-80) REVERT: 6 7 LYS cc_start: 0.7428 (mtmt) cc_final: 0.6965 (mtpt) REVERT: A 26 GLU cc_start: 0.7760 (tp30) cc_final: 0.6820 (pm20) REVERT: A 143 ARG cc_start: 0.7652 (mtt180) cc_final: 0.7092 (pmm-80) REVERT: A 196 LYS cc_start: 0.7436 (tppt) cc_final: 0.7167 (ttpt) REVERT: A 353 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7254 (mm-30) REVERT: A 362 ARG cc_start: 0.7914 (mtt90) cc_final: 0.7463 (mtt90) REVERT: A 426 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6735 (tp30) REVERT: A 439 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7328 (pm20) REVERT: A 449 VAL cc_start: 0.6713 (OUTLIER) cc_final: 0.6462 (m) REVERT: A 460 LYS cc_start: 0.7586 (mttt) cc_final: 0.7033 (tptp) REVERT: B 62 MET cc_start: 0.8538 (ttp) cc_final: 0.8280 (ttm) REVERT: B 89 LYS cc_start: 0.8244 (mtpp) cc_final: 0.7912 (mtmm) REVERT: B 124 LYS cc_start: 0.8712 (mmtt) cc_final: 0.8321 (mmtm) REVERT: B 125 THR cc_start: 0.7365 (p) cc_final: 0.7089 (t) REVERT: B 143 ARG cc_start: 0.8383 (ttm110) cc_final: 0.7648 (mtp-110) REVERT: B 144 GLU cc_start: 0.7662 (mm-30) cc_final: 0.6961 (mt-10) REVERT: B 172 GLN cc_start: 0.7653 (mt0) cc_final: 0.7113 (mm-40) REVERT: B 181 ASP cc_start: 0.7866 (m-30) cc_final: 0.7314 (m-30) REVERT: B 193 GLN cc_start: 0.7396 (mm-40) cc_final: 0.6716 (mp10) REVERT: B 195 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6383 (tm-30) REVERT: B 297 ASP cc_start: 0.7961 (p0) cc_final: 0.7680 (p0) REVERT: B 312 MET cc_start: 0.8470 (mmm) cc_final: 0.8260 (mmm) REVERT: B 355 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7742 (mp0) REVERT: B 381 ARG cc_start: 0.7282 (mmm160) cc_final: 0.6782 (mmm160) REVERT: B 391 LYS cc_start: 0.8059 (ptmt) cc_final: 0.7671 (tppt) REVERT: B 396 GLN cc_start: 0.7408 (mm110) cc_final: 0.6927 (tm130) REVERT: B 398 ARG cc_start: 0.7023 (ttm110) cc_final: 0.6676 (ptp-110) REVERT: B 426 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7279 (tp30) REVERT: B 436 MET cc_start: 0.7994 (ttp) cc_final: 0.7215 (ttm) REVERT: B 458 PRO cc_start: 0.8019 (Cg_exo) cc_final: 0.7620 (Cg_endo) REVERT: B 486 GLU cc_start: 0.7387 (tp30) cc_final: 0.7001 (mt-10) REVERT: C 26 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7443 (mp0) REVERT: C 27 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.6907 (mm-30) REVERT: C 40 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7724 (mmt180) REVERT: C 78 ASN cc_start: 0.7620 (m110) cc_final: 0.7184 (t0) REVERT: C 170 ASP cc_start: 0.7753 (m-30) cc_final: 0.7169 (m-30) REVERT: C 171 ARG cc_start: 0.7339 (ptp90) cc_final: 0.6930 (mtm110) REVERT: C 196 LYS cc_start: 0.8678 (mttt) cc_final: 0.8295 (mmmt) REVERT: C 286 ARG cc_start: 0.8133 (mmt90) cc_final: 0.7703 (mmp-170) REVERT: C 314 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8217 (mm-30) REVERT: C 355 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8095 (pm20) REVERT: C 381 ARG cc_start: 0.7610 (mtm110) cc_final: 0.7311 (mtm110) REVERT: C 385 GLN cc_start: 0.8123 (pt0) cc_final: 0.7702 (pt0) REVERT: C 416 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8089 (pp30) REVERT: C 450 ARG cc_start: 0.7079 (mmm160) cc_final: 0.6559 (mmt90) REVERT: C 462 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.8117 (p) REVERT: C 466 LYS cc_start: 0.7604 (mttt) cc_final: 0.7330 (mtpm) REVERT: C 467 GLU cc_start: 0.7743 (mt-10) cc_final: 0.6793 (mm-30) REVERT: C 470 GLN cc_start: 0.7483 (mt0) cc_final: 0.7146 (pp30) REVERT: C 477 ARG cc_start: 0.6845 (mmm160) cc_final: 0.6544 (mmm160) REVERT: C 481 ASP cc_start: 0.9043 (t70) cc_final: 0.8639 (m-30) REVERT: D 214 LYS cc_start: 0.8354 (mttm) cc_final: 0.7959 (mmtt) REVERT: D 252 GLN cc_start: 0.6981 (mm-40) cc_final: 0.6417 (mm-40) REVERT: D 253 ASP cc_start: 0.8712 (m-30) cc_final: 0.8467 (m-30) REVERT: D 285 GLN cc_start: 0.7877 (pt0) cc_final: 0.7578 (pm20) REVERT: D 302 THR cc_start: 0.8047 (m) cc_final: 0.7754 (p) REVERT: D 359 ARG cc_start: 0.7312 (ttm170) cc_final: 0.6886 (tpp-160) REVERT: D 366 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7452 (pp) REVERT: D 368 GLU cc_start: 0.7563 (tp30) cc_final: 0.7332 (tp30) REVERT: D 396 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8020 (mmm) REVERT: D 422 GLN cc_start: 0.8071 (mt0) cc_final: 0.7697 (mp10) REVERT: E 15 GLN cc_start: 0.7555 (mt0) cc_final: 0.6810 (mm-40) REVERT: E 191 GLU cc_start: 0.7637 (tt0) cc_final: 0.7326 (pm20) REVERT: E 259 ASP cc_start: 0.7380 (t0) cc_final: 0.7148 (OUTLIER) REVERT: E 277 ARG cc_start: 0.7422 (mtm180) cc_final: 0.6707 (ptt-90) REVERT: E 296 GLN cc_start: 0.8009 (mm110) cc_final: 0.7793 (mm110) REVERT: E 375 ARG cc_start: 0.8441 (mmm160) cc_final: 0.8152 (mmm160) REVERT: E 378 GLN cc_start: 0.8206 (mt0) cc_final: 0.7604 (mp10) REVERT: E 425 GLU cc_start: 0.7338 (pt0) cc_final: 0.6953 (pt0) REVERT: E 458 VAL cc_start: 0.7946 (OUTLIER) cc_final: 0.7621 (p) REVERT: E 467 GLU cc_start: 0.7894 (mp0) cc_final: 0.7517 (pm20) REVERT: F 15 GLN cc_start: 0.7879 (mt0) cc_final: 0.7360 (mp10) REVERT: F 20 ILE cc_start: 0.6440 (OUTLIER) cc_final: 0.6154 (tp) REVERT: F 125 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7567 (mm-30) REVERT: F 263 ARG cc_start: 0.7830 (mmt-90) cc_final: 0.6568 (mtt180) REVERT: F 292 MET cc_start: 0.7718 (tpp) cc_final: 0.7296 (tpt) REVERT: F 340 ARG cc_start: 0.7707 (tpt170) cc_final: 0.7342 (tpt90) REVERT: F 344 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7870 (mp0) REVERT: F 362 ASP cc_start: 0.8607 (t70) cc_final: 0.8285 (t0) REVERT: F 379 LYS cc_start: 0.8079 (ttmp) cc_final: 0.7763 (tttm) REVERT: F 382 GLN cc_start: 0.8383 (mt0) cc_final: 0.7941 (mm-40) REVERT: F 409 ARG cc_start: 0.7764 (mtm-85) cc_final: 0.7537 (mtm-85) REVERT: F 475 LYS cc_start: 0.7512 (mmmt) cc_final: 0.7116 (mptm) REVERT: G 33 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8122 (tppt) REVERT: G 149 MET cc_start: 0.6764 (ppp) cc_final: 0.6371 (tmm) REVERT: G 248 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6914 (mtp180) REVERT: H 140 GLU cc_start: 0.7717 (tp30) cc_final: 0.7455 (tp30) REVERT: I 27 GLU cc_start: 0.6536 (mt-10) cc_final: 0.5940 (mt-10) REVERT: I 31 MET cc_start: 0.8207 (tmm) cc_final: 0.7325 (tmm) REVERT: K 11 LYS cc_start: 0.8833 (mttt) cc_final: 0.8536 (mmtt) REVERT: K 19 GLU cc_start: 0.8406 (tt0) cc_final: 0.7754 (tp30) REVERT: K 131 ASN cc_start: 0.8387 (p0) cc_final: 0.8114 (p0) REVERT: L 29 LEU cc_start: 0.7816 (mm) cc_final: 0.7469 (mm) REVERT: M 43 LEU cc_start: 0.8028 (pp) cc_final: 0.7749 (mm) REVERT: M 85 LYS cc_start: 0.8301 (mttt) cc_final: 0.8027 (mptt) REVERT: M 105 ILE cc_start: 0.8794 (mm) cc_final: 0.8498 (pt) REVERT: M 106 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8322 (mm110) REVERT: M 107 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8837 (mp0) REVERT: M 121 LYS cc_start: 0.9222 (ttpp) cc_final: 0.9003 (tppt) REVERT: N 10 ASP cc_start: 0.8434 (t0) cc_final: 0.8081 (t70) REVERT: N 113 TYR cc_start: 0.6194 (t80) cc_final: 0.5984 (t80) REVERT: N 118 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7086 (pp20) REVERT: N 145 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8358 (mm) REVERT: N 162 MET cc_start: 0.7764 (tpt) cc_final: 0.7470 (tpt) REVERT: O 33 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7132 (mp0) REVERT: O 63 ARG cc_start: 0.7525 (ptp-110) cc_final: 0.7283 (ptp-110) REVERT: O 92 GLU cc_start: 0.8436 (tp30) cc_final: 0.8032 (tp30) REVERT: O 94 ASN cc_start: 0.8429 (t0) cc_final: 0.8106 (t0) REVERT: O 98 MET cc_start: 0.8161 (ptp) cc_final: 0.7536 (ptp) REVERT: O 104 ASN cc_start: 0.8415 (t0) cc_final: 0.8144 (m-40) REVERT: O 127 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6674 (pp) REVERT: O 142 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.7342 (t80) REVERT: O 174 MET cc_start: 0.5070 (ttm) cc_final: 0.4405 (pp-130) REVERT: R 32 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.7246 (mp10) REVERT: R 37 GLU cc_start: 0.7959 (mp0) cc_final: 0.7746 (mp0) REVERT: S 49 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8034 (tp-100) REVERT: S 90 GLU cc_start: 0.8034 (tt0) cc_final: 0.6953 (tm-30) REVERT: T 74 LYS cc_start: 0.8652 (tttt) cc_final: 0.8122 (tptp) outliers start: 160 outliers final: 99 residues processed: 735 average time/residue: 0.8256 time to fit residues: 728.3737 Evaluate side-chains 712 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 593 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 4 SER Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 1 residue 58 GLU Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 51 ILE Chi-restraints excluded: chain 2 residue 60 MET Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 21 SER Chi-restraints excluded: chain 3 residue 28 VAL Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 56 LEU Chi-restraints excluded: chain 3 residue 65 LEU Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 57 SER Chi-restraints excluded: chain 4 residue 58 GLU Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 5 residue 48 SER Chi-restraints excluded: chain 5 residue 64 CYS Chi-restraints excluded: chain 5 residue 71 LEU Chi-restraints excluded: chain 5 residue 75 PHE Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 7 residue 15 THR Chi-restraints excluded: chain 7 residue 21 SER Chi-restraints excluded: chain 8 residue 2 ILE Chi-restraints excluded: chain 8 residue 15 THR Chi-restraints excluded: chain 8 residue 18 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 416 GLN Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 98 MET Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 284 TYR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 458 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 470 VAL Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain G residue 248 ARG Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 194 LEU Chi-restraints excluded: chain K residue 197 CYS Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 114 ASN Chi-restraints excluded: chain M residue 124 GLN Chi-restraints excluded: chain M residue 130 HIS Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 167 LEU Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain O residue 142 PHE Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain R residue 71 ARG Chi-restraints excluded: chain S residue 64 TRP Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 36 optimal weight: 0.9990 chunk 201 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 489 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 350 optimal weight: 0.8980 chunk 259 optimal weight: 0.6980 chunk 218 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 45 GLN ** 7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN B 24 ASN B 65 ASN B 147 GLN B 471 HIS F 311 GLN G 159 ASN ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 ASN K 27 ASN ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 175 GLN O 77 GLN ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 8 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.171184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.137978 restraints weight = 63328.551| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.65 r_work: 0.3796 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 39746 Z= 0.146 Angle : 0.642 12.977 53709 Z= 0.322 Chirality : 0.043 0.275 6178 Planarity : 0.005 0.073 6879 Dihedral : 7.533 86.290 5750 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.55 % Allowed : 22.31 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.12), residues: 4987 helix: 1.64 (0.10), residues: 2662 sheet: 0.22 (0.22), residues: 550 loop : -0.36 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 340 TYR 0.025 0.001 TYR T 30 PHE 0.039 0.001 PHE 7 54 TRP 0.042 0.002 TRP S 85 HIS 0.006 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00332 (39746) covalent geometry : angle 0.64157 (53709) hydrogen bonds : bond 0.04283 ( 2316) hydrogen bonds : angle 4.27547 ( 6786) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9974 Ramachandran restraints generated. 4987 Oldfield, 0 Emsley, 4987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9974 Ramachandran restraints generated. 4987 Oldfield, 0 Emsley, 4987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 634 time to evaluate : 1.642 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: 1 36 TYR cc_start: 0.6956 (t80) cc_final: 0.6587 (t80) REVERT: 4 31 SER cc_start: 0.7905 (m) cc_final: 0.7609 (p) REVERT: 5 71 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7951 (mp) REVERT: 5 75 PHE cc_start: 0.5045 (OUTLIER) cc_final: 0.4076 (m-80) REVERT: 6 7 LYS cc_start: 0.7440 (mtmt) cc_final: 0.6978 (mtpt) REVERT: A 26 GLU cc_start: 0.7761 (tp30) cc_final: 0.6827 (pm20) REVERT: A 143 ARG cc_start: 0.7679 (mtt180) cc_final: 0.7092 (pmm-80) REVERT: A 196 LYS cc_start: 0.7453 (tppt) cc_final: 0.7200 (ttpt) REVERT: A 353 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7282 (mm-30) REVERT: A 362 ARG cc_start: 0.7948 (mtt90) cc_final: 0.7501 (mtt90) REVERT: A 426 GLU cc_start: 0.7458 (mm-30) cc_final: 0.6741 (tm-30) REVERT: A 439 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7367 (pm20) REVERT: A 449 VAL cc_start: 0.6770 (OUTLIER) cc_final: 0.6506 (m) REVERT: A 460 LYS cc_start: 0.7629 (mttt) cc_final: 0.7074 (tptp) REVERT: B 62 MET cc_start: 0.8565 (ttp) cc_final: 0.8316 (ttm) REVERT: B 89 LYS cc_start: 0.8264 (mtpp) cc_final: 0.7930 (mtmm) REVERT: B 124 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8366 (mmtm) REVERT: B 125 THR cc_start: 0.7349 (p) cc_final: 0.7085 (t) REVERT: B 143 ARG cc_start: 0.8389 (ttm110) cc_final: 0.7661 (mtp-110) REVERT: B 144 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7047 (mt-10) REVERT: B 172 GLN cc_start: 0.7734 (mt0) cc_final: 0.7212 (mm-40) REVERT: B 181 ASP cc_start: 0.7925 (m-30) cc_final: 0.7371 (m-30) REVERT: B 193 GLN cc_start: 0.7361 (mm-40) cc_final: 0.6687 (mp10) REVERT: B 195 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6410 (tm-30) REVERT: B 267 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8190 (mp) REVERT: B 297 ASP cc_start: 0.8002 (p0) cc_final: 0.7731 (p0) REVERT: B 312 MET cc_start: 0.8530 (mmm) cc_final: 0.8325 (mmm) REVERT: B 355 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7836 (mp0) REVERT: B 381 ARG cc_start: 0.7325 (mmm160) cc_final: 0.6828 (mmm160) REVERT: B 391 LYS cc_start: 0.8074 (ptmt) cc_final: 0.7669 (tppt) REVERT: B 396 GLN cc_start: 0.7419 (mm110) cc_final: 0.6939 (tm130) REVERT: B 398 ARG cc_start: 0.7026 (ttm110) cc_final: 0.6672 (ptp-110) REVERT: B 436 MET cc_start: 0.8025 (ttp) cc_final: 0.7295 (ttm) REVERT: B 486 GLU cc_start: 0.7392 (tp30) cc_final: 0.6979 (mt-10) REVERT: C 26 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7461 (mp0) REVERT: C 27 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.6947 (mm-30) REVERT: C 40 ARG cc_start: 0.8142 (mtt-85) cc_final: 0.7761 (mmt180) REVERT: C 78 ASN cc_start: 0.7620 (m110) cc_final: 0.7208 (t0) REVERT: C 170 ASP cc_start: 0.7812 (m-30) cc_final: 0.7231 (m-30) REVERT: C 171 ARG cc_start: 0.7378 (ptp90) cc_final: 0.6973 (mtm110) REVERT: C 196 LYS cc_start: 0.8700 (mttt) cc_final: 0.8331 (mmmt) REVERT: C 286 ARG cc_start: 0.8170 (mmt90) cc_final: 0.7717 (mmp-170) REVERT: C 314 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8250 (mm-30) REVERT: C 355 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8108 (pm20) REVERT: C 381 ARG cc_start: 0.7677 (mtm110) cc_final: 0.7361 (mtm110) REVERT: C 383 MET cc_start: 0.7407 (tpt) cc_final: 0.6936 (tpt) REVERT: C 385 GLN cc_start: 0.8104 (pt0) cc_final: 0.7626 (pt0) REVERT: C 416 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8179 (pp30) REVERT: C 450 ARG cc_start: 0.7159 (mmm160) cc_final: 0.6643 (mmt90) REVERT: C 462 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8261 (p) REVERT: C 466 LYS cc_start: 0.7597 (mttt) cc_final: 0.7336 (mtpm) REVERT: C 467 GLU cc_start: 0.7784 (mt-10) cc_final: 0.6850 (mm-30) REVERT: C 470 GLN cc_start: 0.7501 (mt0) cc_final: 0.7163 (pp30) REVERT: C 477 ARG cc_start: 0.6884 (mmm160) cc_final: 0.6588 (mmm160) REVERT: C 481 ASP cc_start: 0.9056 (t70) cc_final: 0.8640 (m-30) REVERT: D 214 LYS cc_start: 0.8379 (mttm) cc_final: 0.7993 (mmtt) REVERT: D 252 GLN cc_start: 0.7033 (mm-40) cc_final: 0.6475 (mm-40) REVERT: D 253 ASP cc_start: 0.8744 (m-30) cc_final: 0.8517 (m-30) REVERT: D 285 GLN cc_start: 0.7908 (pt0) cc_final: 0.7636 (pm20) REVERT: D 302 THR cc_start: 0.8139 (m) cc_final: 0.7723 (p) REVERT: D 359 ARG cc_start: 0.7281 (ttm170) cc_final: 0.6914 (tpp-160) REVERT: D 366 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7578 (pp) REVERT: D 368 GLU cc_start: 0.7607 (tp30) cc_final: 0.7403 (tp30) REVERT: D 396 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8054 (mmm) REVERT: D 422 GLN cc_start: 0.8078 (mt0) cc_final: 0.7734 (mp10) REVERT: E 15 GLN cc_start: 0.7598 (mt0) cc_final: 0.6846 (mm-40) REVERT: E 191 GLU cc_start: 0.7639 (tt0) cc_final: 0.7344 (pm20) REVERT: E 202 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7123 (tp30) REVERT: E 259 ASP cc_start: 0.7409 (t0) cc_final: 0.7187 (OUTLIER) REVERT: E 277 ARG cc_start: 0.7420 (mtm180) cc_final: 0.6725 (ptt-90) REVERT: E 296 GLN cc_start: 0.8054 (mm110) cc_final: 0.7838 (mm110) REVERT: E 375 ARG cc_start: 0.8458 (mmm160) cc_final: 0.8160 (mmm160) REVERT: E 378 GLN cc_start: 0.8227 (mt0) cc_final: 0.7616 (mp10) REVERT: E 425 GLU cc_start: 0.7337 (pt0) cc_final: 0.6953 (pt0) REVERT: E 458 VAL cc_start: 0.7962 (OUTLIER) cc_final: 0.7634 (p) REVERT: E 467 GLU cc_start: 0.7899 (mp0) cc_final: 0.7515 (pm20) REVERT: F 15 GLN cc_start: 0.7935 (mt0) cc_final: 0.7434 (mp10) REVERT: F 20 ILE cc_start: 0.6533 (OUTLIER) cc_final: 0.6233 (tp) REVERT: F 125 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7642 (mm-30) REVERT: F 263 ARG cc_start: 0.7865 (mmt-90) cc_final: 0.6622 (mtt180) REVERT: F 266 GLN cc_start: 0.7268 (tt0) cc_final: 0.6981 (tt0) REVERT: F 292 MET cc_start: 0.7806 (tpp) cc_final: 0.7368 (tpt) REVERT: F 340 ARG cc_start: 0.7750 (tpt170) cc_final: 0.7403 (tpt90) REVERT: F 344 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7912 (mp0) REVERT: F 362 ASP cc_start: 0.8631 (t70) cc_final: 0.8327 (t0) REVERT: F 379 LYS cc_start: 0.8091 (ttmp) cc_final: 0.7780 (tttm) REVERT: F 382 GLN cc_start: 0.8394 (mt0) cc_final: 0.7962 (mm-40) REVERT: F 409 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7557 (mtm-85) REVERT: F 475 LYS cc_start: 0.7568 (mmmt) cc_final: 0.7174 (mptm) REVERT: G 33 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8162 (tppt) REVERT: G 149 MET cc_start: 0.6715 (ppp) cc_final: 0.6175 (tmm) REVERT: G 159 ASN cc_start: 0.7886 (m-40) cc_final: 0.7202 (m-40) REVERT: G 168 ARG cc_start: 0.7383 (tmm-80) cc_final: 0.7033 (ttp80) REVERT: G 248 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6917 (mtp180) REVERT: I 14 ARG cc_start: 0.6141 (mmt-90) cc_final: 0.4364 (mmt-90) REVERT: I 27 GLU cc_start: 0.6482 (mt-10) cc_final: 0.5925 (mt-10) REVERT: I 31 MET cc_start: 0.8227 (tmm) cc_final: 0.7597 (tmm) REVERT: K 11 LYS cc_start: 0.8797 (mttt) cc_final: 0.8538 (mmtt) REVERT: K 19 GLU cc_start: 0.8331 (tt0) cc_final: 0.7737 (tp30) REVERT: K 26 TYR cc_start: 0.7849 (t80) cc_final: 0.7561 (t80) REVERT: K 131 ASN cc_start: 0.8336 (p0) cc_final: 0.8081 (p0) REVERT: L 29 LEU cc_start: 0.7822 (mm) cc_final: 0.7454 (mm) REVERT: L 31 GLU cc_start: 0.7437 (pm20) cc_final: 0.6972 (pm20) REVERT: L 76 MET cc_start: 0.4470 (mmt) cc_final: 0.3520 (mpm) REVERT: M 43 LEU cc_start: 0.7975 (pp) cc_final: 0.7705 (mm) REVERT: M 45 TYR cc_start: 0.7089 (m-10) cc_final: 0.6607 (m-80) REVERT: M 85 LYS cc_start: 0.8359 (mttt) cc_final: 0.7997 (mptt) REVERT: M 105 ILE cc_start: 0.8791 (mm) cc_final: 0.8502 (pt) REVERT: M 106 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8312 (mm110) REVERT: M 107 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8844 (mp0) REVERT: M 121 LYS cc_start: 0.9186 (ttpp) cc_final: 0.8752 (pptt) REVERT: M 126 ILE cc_start: 0.7405 (tp) cc_final: 0.7146 (tp) REVERT: N 10 ASP cc_start: 0.8404 (t0) cc_final: 0.8079 (t70) REVERT: N 118 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7084 (pp20) REVERT: O 33 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7174 (mp0) REVERT: O 92 GLU cc_start: 0.8490 (tp30) cc_final: 0.8114 (tp30) REVERT: O 94 ASN cc_start: 0.8459 (t0) cc_final: 0.8138 (t0) REVERT: O 98 MET cc_start: 0.8195 (ptp) cc_final: 0.7434 (ptp) REVERT: O 104 ASN cc_start: 0.8461 (t0) cc_final: 0.8184 (m-40) REVERT: O 127 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6683 (pp) REVERT: O 142 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7316 (t80) REVERT: O 174 MET cc_start: 0.5056 (ttm) cc_final: 0.4402 (pp-130) REVERT: R 32 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7263 (mp10) REVERT: R 37 GLU cc_start: 0.7891 (mp0) cc_final: 0.7465 (pm20) REVERT: S 49 GLN cc_start: 0.8485 (mm-40) cc_final: 0.8015 (tp-100) REVERT: S 90 GLU cc_start: 0.8041 (tt0) cc_final: 0.7001 (tm-30) REVERT: T 46 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8540 (tm-30) REVERT: T 50 LYS cc_start: 0.9427 (tppt) cc_final: 0.9194 (tppt) REVERT: T 53 ARG cc_start: 0.8612 (ttm110) cc_final: 0.8265 (ptp-170) REVERT: T 74 LYS cc_start: 0.8624 (tttt) cc_final: 0.8090 (tptp) outliers start: 145 outliers final: 100 residues processed: 744 average time/residue: 0.8128 time to fit residues: 726.4789 Evaluate side-chains 706 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 589 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 4 SER Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 1 residue 58 GLU Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 45 GLN Chi-restraints excluded: chain 2 residue 51 ILE Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 21 SER Chi-restraints excluded: chain 3 residue 28 VAL Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 56 LEU Chi-restraints excluded: chain 3 residue 65 LEU Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 5 residue 48 SER Chi-restraints excluded: chain 5 residue 64 CYS Chi-restraints excluded: chain 5 residue 71 LEU Chi-restraints excluded: chain 5 residue 75 PHE Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 7 residue 15 THR Chi-restraints excluded: chain 7 residue 21 SER Chi-restraints excluded: chain 8 residue 2 ILE Chi-restraints excluded: chain 8 residue 15 THR Chi-restraints excluded: chain 8 residue 18 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 98 MET Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 284 TYR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 458 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 470 VAL Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain G residue 248 ARG Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 194 LEU Chi-restraints excluded: chain K residue 197 CYS Chi-restraints excluded: chain K residue 204 MET Chi-restraints excluded: chain L residue 43 GLU Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain M residue 91 ASP Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 114 ASN Chi-restraints excluded: chain M residue 124 GLN Chi-restraints excluded: chain M residue 130 HIS Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 167 LEU Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain O residue 142 PHE Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain S residue 64 TRP Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 216 optimal weight: 4.9990 chunk 440 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 305 optimal weight: 1.9990 chunk 339 optimal weight: 3.9990 chunk 386 optimal weight: 0.3980 chunk 472 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 45 GLN ** 7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 HIS B 65 ASN B 147 GLN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 ASN K 27 ASN ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 GLN ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 8 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.169746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.136124 restraints weight = 62622.918| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.63 r_work: 0.3783 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 39746 Z= 0.178 Angle : 0.674 15.657 53709 Z= 0.340 Chirality : 0.045 0.320 6178 Planarity : 0.005 0.076 6879 Dihedral : 7.616 87.313 5750 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.35 % Allowed : 22.63 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.12), residues: 4987 helix: 1.55 (0.10), residues: 2659 sheet: 0.20 (0.22), residues: 554 loop : -0.39 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 340 TYR 0.021 0.001 TYR A 42 PHE 0.039 0.002 PHE B 464 TRP 0.051 0.002 TRP S 85 HIS 0.011 0.001 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00413 (39746) covalent geometry : angle 0.67432 (53709) hydrogen bonds : bond 0.04457 ( 2316) hydrogen bonds : angle 4.34688 ( 6786) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9974 Ramachandran restraints generated. 4987 Oldfield, 0 Emsley, 4987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9974 Ramachandran restraints generated. 4987 Oldfield, 0 Emsley, 4987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 592 time to evaluate : 1.593 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: 1 36 TYR cc_start: 0.6964 (t80) cc_final: 0.6600 (t80) REVERT: 1 38 ARG cc_start: 0.8124 (tpt90) cc_final: 0.7859 (tpt90) REVERT: 4 31 SER cc_start: 0.7928 (m) cc_final: 0.7640 (p) REVERT: 4 67 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7931 (ttt) REVERT: 5 75 PHE cc_start: 0.5087 (OUTLIER) cc_final: 0.4095 (m-80) REVERT: 6 7 LYS cc_start: 0.7544 (mtmt) cc_final: 0.7029 (mtpt) REVERT: A 26 GLU cc_start: 0.7805 (tp30) cc_final: 0.6831 (pm20) REVERT: A 143 ARG cc_start: 0.7673 (mtt180) cc_final: 0.7317 (ptp-110) REVERT: A 196 LYS cc_start: 0.7485 (tppt) cc_final: 0.7056 (tmmt) REVERT: A 353 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7271 (mm-30) REVERT: A 362 ARG cc_start: 0.7885 (mtt90) cc_final: 0.7408 (mtt90) REVERT: A 426 GLU cc_start: 0.7433 (mm-30) cc_final: 0.6743 (tm-30) REVERT: A 439 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7367 (pm20) REVERT: A 449 VAL cc_start: 0.6733 (OUTLIER) cc_final: 0.6478 (m) REVERT: A 460 LYS cc_start: 0.7682 (mttt) cc_final: 0.6705 (tttt) REVERT: A 465 GLU cc_start: 0.6013 (tt0) cc_final: 0.5680 (tm-30) REVERT: B 62 MET cc_start: 0.8532 (ttp) cc_final: 0.8288 (ttm) REVERT: B 89 LYS cc_start: 0.8256 (mtpp) cc_final: 0.7925 (mtmm) REVERT: B 124 LYS cc_start: 0.8723 (mmtt) cc_final: 0.8353 (mmtm) REVERT: B 125 THR cc_start: 0.7448 (p) cc_final: 0.7169 (t) REVERT: B 144 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7008 (mt-10) REVERT: B 147 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.6739 (mp-120) REVERT: B 172 GLN cc_start: 0.7723 (mt0) cc_final: 0.7204 (mm-40) REVERT: B 181 ASP cc_start: 0.7945 (m-30) cc_final: 0.7396 (m-30) REVERT: B 193 GLN cc_start: 0.7363 (mm-40) cc_final: 0.6682 (mp10) REVERT: B 195 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6380 (tm-30) REVERT: B 297 ASP cc_start: 0.7935 (p0) cc_final: 0.7652 (p0) REVERT: B 312 MET cc_start: 0.8506 (mmm) cc_final: 0.8293 (mmm) REVERT: B 355 GLU cc_start: 0.8456 (mt-10) cc_final: 0.7844 (mp0) REVERT: B 381 ARG cc_start: 0.7315 (mmm160) cc_final: 0.6815 (mmm160) REVERT: B 391 LYS cc_start: 0.8061 (ptmt) cc_final: 0.7657 (tppt) REVERT: B 398 ARG cc_start: 0.7027 (ttm110) cc_final: 0.6671 (ptp-110) REVERT: B 436 MET cc_start: 0.8066 (ttp) cc_final: 0.7252 (ttm) REVERT: B 486 GLU cc_start: 0.7383 (tp30) cc_final: 0.6967 (mt-10) REVERT: C 26 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7466 (mp0) REVERT: C 27 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.6923 (mm-30) REVERT: C 40 ARG cc_start: 0.8067 (mtt-85) cc_final: 0.7697 (mmt180) REVERT: C 78 ASN cc_start: 0.7629 (m110) cc_final: 0.7215 (t0) REVERT: C 170 ASP cc_start: 0.7841 (m-30) cc_final: 0.7267 (m-30) REVERT: C 171 ARG cc_start: 0.7411 (ptp90) cc_final: 0.6988 (mtm110) REVERT: C 196 LYS cc_start: 0.8711 (mttt) cc_final: 0.8336 (mmmt) REVERT: C 286 ARG cc_start: 0.8213 (mmt90) cc_final: 0.7745 (mmp-170) REVERT: C 314 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8293 (mm-30) REVERT: C 355 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8121 (pm20) REVERT: C 381 ARG cc_start: 0.7651 (mtm110) cc_final: 0.7285 (mtm110) REVERT: C 385 GLN cc_start: 0.8105 (pt0) cc_final: 0.7691 (pt0) REVERT: C 416 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8176 (pp30) REVERT: C 450 ARG cc_start: 0.7154 (mmm160) cc_final: 0.6637 (mmt90) REVERT: C 462 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8246 (p) REVERT: C 466 LYS cc_start: 0.7599 (mttt) cc_final: 0.7270 (mtpm) REVERT: C 467 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7531 (mm-30) REVERT: C 488 GLN cc_start: 0.6029 (tp40) cc_final: 0.5193 (tp40) REVERT: D 214 LYS cc_start: 0.8360 (mttm) cc_final: 0.7968 (mmtt) REVERT: D 253 ASP cc_start: 0.8732 (m-30) cc_final: 0.8518 (m-30) REVERT: D 285 GLN cc_start: 0.7944 (pt0) cc_final: 0.7672 (pm20) REVERT: D 302 THR cc_start: 0.8139 (m) cc_final: 0.7713 (p) REVERT: D 359 ARG cc_start: 0.7208 (ttm170) cc_final: 0.6827 (tpp-160) REVERT: D 366 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7577 (pp) REVERT: D 368 GLU cc_start: 0.7608 (tp30) cc_final: 0.7406 (tp30) REVERT: D 396 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8126 (mmm) REVERT: D 422 GLN cc_start: 0.8081 (mt0) cc_final: 0.7720 (mp10) REVERT: E 15 GLN cc_start: 0.7619 (mt0) cc_final: 0.6876 (mm-40) REVERT: E 191 GLU cc_start: 0.7632 (tt0) cc_final: 0.7343 (pm20) REVERT: E 202 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7063 (tp30) REVERT: E 259 ASP cc_start: 0.7430 (t0) cc_final: 0.7201 (OUTLIER) REVERT: E 277 ARG cc_start: 0.7475 (mtm180) cc_final: 0.6741 (ptt-90) REVERT: E 296 GLN cc_start: 0.8040 (mm110) cc_final: 0.7831 (mm110) REVERT: E 375 ARG cc_start: 0.8469 (mmm160) cc_final: 0.8161 (mmm160) REVERT: E 378 GLN cc_start: 0.8207 (mt0) cc_final: 0.7575 (mp10) REVERT: E 425 GLU cc_start: 0.7324 (pt0) cc_final: 0.6940 (pt0) REVERT: E 458 VAL cc_start: 0.7967 (OUTLIER) cc_final: 0.7640 (p) REVERT: E 467 GLU cc_start: 0.7858 (mp0) cc_final: 0.7533 (pm20) REVERT: F 15 GLN cc_start: 0.7924 (mt0) cc_final: 0.7442 (mp10) REVERT: F 20 ILE cc_start: 0.6502 (OUTLIER) cc_final: 0.6210 (tp) REVERT: F 125 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7625 (mm-30) REVERT: F 212 LYS cc_start: 0.8643 (mtmt) cc_final: 0.8406 (mptt) REVERT: F 263 ARG cc_start: 0.7910 (mmt-90) cc_final: 0.6685 (mtt180) REVERT: F 266 GLN cc_start: 0.7289 (tt0) cc_final: 0.7012 (tt0) REVERT: F 292 MET cc_start: 0.7858 (tpp) cc_final: 0.7437 (tpt) REVERT: F 297 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8204 (mt-10) REVERT: F 340 ARG cc_start: 0.7753 (tpt170) cc_final: 0.7489 (tpt90) REVERT: F 344 GLU cc_start: 0.8238 (mm-30) cc_final: 0.8027 (mp0) REVERT: F 362 ASP cc_start: 0.8630 (t70) cc_final: 0.8328 (t0) REVERT: F 379 LYS cc_start: 0.8107 (ttmp) cc_final: 0.7804 (tttm) REVERT: F 382 GLN cc_start: 0.8386 (mt0) cc_final: 0.7957 (mm-40) REVERT: F 409 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7523 (mtm-85) REVERT: F 475 LYS cc_start: 0.7560 (mmmt) cc_final: 0.7094 (mptm) REVERT: G 33 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8158 (tppt) REVERT: G 149 MET cc_start: 0.6743 (ppp) cc_final: 0.6109 (tmm) REVERT: G 168 ARG cc_start: 0.7333 (tmm-80) cc_final: 0.7020 (ttp80) REVERT: G 248 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6881 (mtp180) REVERT: I 14 ARG cc_start: 0.6229 (mmt-90) cc_final: 0.4412 (mmt-90) REVERT: I 27 GLU cc_start: 0.6550 (mt-10) cc_final: 0.5930 (mt-10) REVERT: I 31 MET cc_start: 0.8288 (tmm) cc_final: 0.7703 (tmm) REVERT: K 11 LYS cc_start: 0.8822 (mttt) cc_final: 0.8619 (mmtt) REVERT: K 26 TYR cc_start: 0.7930 (t80) cc_final: 0.7592 (t80) REVERT: K 131 ASN cc_start: 0.8342 (p0) cc_final: 0.8085 (p0) REVERT: L 29 LEU cc_start: 0.7814 (mm) cc_final: 0.7450 (mm) REVERT: L 31 GLU cc_start: 0.7512 (pm20) cc_final: 0.7016 (pm20) REVERT: L 76 MET cc_start: 0.4421 (mmt) cc_final: 0.3363 (mpm) REVERT: M 43 LEU cc_start: 0.7950 (pp) cc_final: 0.7652 (mm) REVERT: M 85 LYS cc_start: 0.8351 (mttt) cc_final: 0.8057 (mptt) REVERT: M 105 ILE cc_start: 0.8788 (mm) cc_final: 0.8494 (pt) REVERT: M 106 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8306 (mm110) REVERT: M 107 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8846 (mp0) REVERT: M 121 LYS cc_start: 0.9188 (ttpp) cc_final: 0.8872 (tmmt) REVERT: M 126 ILE cc_start: 0.7520 (tp) cc_final: 0.7235 (tp) REVERT: N 10 ASP cc_start: 0.8475 (t0) cc_final: 0.8157 (t70) REVERT: N 118 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7067 (pp20) REVERT: O 33 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7163 (mp0) REVERT: O 63 ARG cc_start: 0.7373 (ptp-110) cc_final: 0.6623 (ttm170) REVERT: O 92 GLU cc_start: 0.8461 (tp30) cc_final: 0.8054 (tp30) REVERT: O 94 ASN cc_start: 0.8421 (t0) cc_final: 0.8192 (t0) REVERT: O 98 MET cc_start: 0.8205 (ptp) cc_final: 0.7434 (ptp) REVERT: O 104 ASN cc_start: 0.8477 (t0) cc_final: 0.8182 (m-40) REVERT: O 127 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6776 (pp) REVERT: O 142 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.7331 (t80) REVERT: O 174 MET cc_start: 0.5065 (ttm) cc_final: 0.4398 (pp-130) REVERT: Q 48 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.6766 (m-80) REVERT: R 32 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7360 (mp10) REVERT: R 37 GLU cc_start: 0.7885 (mp0) cc_final: 0.7447 (pm20) REVERT: S 49 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8049 (tp-100) REVERT: S 90 GLU cc_start: 0.8023 (tt0) cc_final: 0.6983 (tm-30) REVERT: T 46 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8659 (tm-30) REVERT: T 53 ARG cc_start: 0.8590 (ttm110) cc_final: 0.8375 (ptp-170) REVERT: T 74 LYS cc_start: 0.8652 (tttt) cc_final: 0.8109 (tptp) outliers start: 137 outliers final: 99 residues processed: 692 average time/residue: 0.8312 time to fit residues: 687.3045 Evaluate side-chains 688 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 569 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 4 SER Chi-restraints excluded: chain 1 residue 34 ILE Chi-restraints excluded: chain 1 residue 48 SER Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 1 residue 58 GLU Chi-restraints excluded: chain 1 residue 66 MET Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 51 ILE Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 21 SER Chi-restraints excluded: chain 3 residue 28 VAL Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 3 residue 65 LEU Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 67 MET Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 5 residue 48 SER Chi-restraints excluded: chain 5 residue 64 CYS Chi-restraints excluded: chain 5 residue 75 PHE Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 7 residue 15 THR Chi-restraints excluded: chain 7 residue 21 SER Chi-restraints excluded: chain 7 residue 54 PHE Chi-restraints excluded: chain 8 residue 2 ILE Chi-restraints excluded: chain 8 residue 15 THR Chi-restraints excluded: chain 8 residue 18 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 416 GLN Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 98 MET Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 284 TYR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 458 VAL Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 430 HIS Chi-restraints excluded: chain F residue 470 VAL Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain G residue 248 ARG Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 127 LEU Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 194 LEU Chi-restraints excluded: chain K residue 197 CYS Chi-restraints excluded: chain L residue 43 GLU Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 114 ASN Chi-restraints excluded: chain M residue 130 HIS Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 167 LEU Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain O residue 142 PHE Chi-restraints excluded: chain Q residue 48 TYR Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain R residue 71 ARG Chi-restraints excluded: chain S residue 64 TRP Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 329 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 321 optimal weight: 1.9990 chunk 424 optimal weight: 2.9990 chunk 328 optimal weight: 0.9980 chunk 386 optimal weight: 0.3980 chunk 339 optimal weight: 2.9990 chunk 438 optimal weight: 0.7980 chunk 187 optimal weight: 0.8980 chunk 263 optimal weight: 3.9990 chunk 340 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN B 147 GLN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 ASN ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 ASN ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 GLN ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 40 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.170810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.138350 restraints weight = 63076.036| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.53 r_work: 0.3802 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 39746 Z= 0.152 Angle : 0.664 13.656 53709 Z= 0.335 Chirality : 0.044 0.328 6178 Planarity : 0.005 0.074 6879 Dihedral : 7.546 88.040 5750 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.23 % Allowed : 22.88 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.12), residues: 4987 helix: 1.52 (0.10), residues: 2678 sheet: 0.23 (0.22), residues: 552 loop : -0.37 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 340 TYR 0.028 0.001 TYR N 113 PHE 0.042 0.002 PHE B 464 TRP 0.051 0.002 TRP S 85 HIS 0.009 0.001 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00348 (39746) covalent geometry : angle 0.66367 (53709) hydrogen bonds : bond 0.04362 ( 2316) hydrogen bonds : angle 4.35048 ( 6786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19913.46 seconds wall clock time: 338 minutes 28.22 seconds (20308.22 seconds total)