Starting phenix.real_space_refine on Fri Mar 22 16:22:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jh7_22335/03_2024/7jh7_22335_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jh7_22335/03_2024/7jh7_22335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jh7_22335/03_2024/7jh7_22335.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jh7_22335/03_2024/7jh7_22335.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jh7_22335/03_2024/7jh7_22335_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jh7_22335/03_2024/7jh7_22335_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 198 5.16 5 C 21508 2.51 5 N 5791 2.21 5 O 6412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 39": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "F ARG 29": "NH1" <-> "NH2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 663": "NH1" <-> "NH2" Residue "F ARG 703": "NH1" <-> "NH2" Residue "F ARG 719": "NH1" <-> "NH2" Residue "F ARG 739": "NH1" <-> "NH2" Residue "F ARG 780": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "G ARG 29": "NH1" <-> "NH2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 663": "NH1" <-> "NH2" Residue "G ARG 703": "NH1" <-> "NH2" Residue "G ARG 719": "NH1" <-> "NH2" Residue "G ARG 739": "NH1" <-> "NH2" Residue "G ARG 780": "NH1" <-> "NH2" Residue "C ASP 11": "OD1" <-> "OD2" Residue "C ARG 39": "NH1" <-> "NH2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C ARG 335": "NH1" <-> "NH2" Residue "H ARG 29": "NH1" <-> "NH2" Residue "H ARG 54": "NH1" <-> "NH2" Residue "H PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 663": "NH1" <-> "NH2" Residue "H ARG 703": "NH1" <-> "NH2" Residue "H ARG 719": "NH1" <-> "NH2" Residue "H ARG 739": "NH1" <-> "NH2" Residue "H ARG 780": "NH1" <-> "NH2" Residue "E ASP 11": "OD1" <-> "OD2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 147": "NH1" <-> "NH2" Residue "E ARG 335": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 335": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33924 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2903 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Conformer: "B" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} bond proxies already assigned to first conformer: 2955 Chain: "F" Number of atoms: 5973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5973 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 28, 'TRANS': 713} Chain breaks: 3 Chain: "B" Number of atoms: 2903 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Conformer: "B" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} bond proxies already assigned to first conformer: 2955 Chain: "G" Number of atoms: 5973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5973 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 28, 'TRANS': 713} Chain breaks: 3 Chain: "C" Number of atoms: 2903 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Conformer: "B" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} bond proxies already assigned to first conformer: 2955 Chain: "H" Number of atoms: 5973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5973 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 28, 'TRANS': 713} Chain breaks: 3 Chain: "E" Number of atoms: 2903 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Conformer: "B" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} bond proxies already assigned to first conformer: 2955 Chain: "D" Number of atoms: 2903 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Conformer: "B" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} bond proxies already assigned to first conformer: 2955 Chain: "I" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "J" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 22.88, per 1000 atoms: 0.67 Number of scatterers: 33924 At special positions: 0 Unit cell: (144.672, 162.624, 239.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 198 16.00 P 10 15.00 Mg 5 11.99 O 6412 8.00 N 5791 7.00 C 21508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 12.78 Conformation dependent library (CDL) restraints added in 8.4 seconds 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8168 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 182 helices and 43 sheets defined 46.1% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.17 Creating SS restraints... Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 removed outlier: 3.788A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 143 removed outlier: 4.123A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 193 Processing helix chain 'A' and resid 203 through 215 removed outlier: 3.753A pdb=" N GLU A 207 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A 209 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 230 Processing helix chain 'A' and resid 254 through 261 Proline residue: A 258 - end of helix removed outlier: 4.640A pdb=" N LEU A 261 " --> pdb=" O CYS A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 254 through 261' Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 277 through 283 Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.545A pdb=" N GLN A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 346 removed outlier: 3.733A pdb=" N ILE A 341 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY A 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.901A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 369 removed outlier: 3.540A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'F' and resid 14 through 17 No H-bonds generated for 'chain 'F' and resid 14 through 17' Processing helix chain 'F' and resid 23 through 28 removed outlier: 4.865A pdb=" N THR F 28 " --> pdb=" O LEU F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 110 removed outlier: 4.367A pdb=" N ASN F 104 " --> pdb=" O ALA F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 154 through 167 Processing helix chain 'F' and resid 184 through 197 removed outlier: 4.060A pdb=" N TYR F 194 " --> pdb=" O ARG F 190 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE F 195 " --> pdb=" O VAL F 191 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA F 196 " --> pdb=" O ILE F 192 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL F 197 " --> pdb=" O GLN F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 231 Proline residue: F 225 - end of helix Processing helix chain 'F' and resid 270 through 274 Processing helix chain 'F' and resid 284 through 290 Processing helix chain 'F' and resid 295 through 300 Processing helix chain 'F' and resid 325 through 337 removed outlier: 3.566A pdb=" N ASN F 334 " --> pdb=" O MET F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 357 removed outlier: 3.918A pdb=" N TYR F 350 " --> pdb=" O LYS F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 388 Processing helix chain 'F' and resid 392 through 400 removed outlier: 3.744A pdb=" N LEU F 396 " --> pdb=" O SER F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 447 removed outlier: 4.187A pdb=" N ALA F 428 " --> pdb=" O THR F 424 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR F 446 " --> pdb=" O ARG F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 504 removed outlier: 4.124A pdb=" N THR F 481 " --> pdb=" O CYS F 477 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU F 496 " --> pdb=" O HIS F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 524 removed outlier: 5.188A pdb=" N ALA F 519 " --> pdb=" O ASP F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 537 Processing helix chain 'F' and resid 545 through 556 Processing helix chain 'F' and resid 593 through 596 No H-bonds generated for 'chain 'F' and resid 593 through 596' Processing helix chain 'F' and resid 603 through 611 Processing helix chain 'F' and resid 615 through 619 Processing helix chain 'F' and resid 647 through 662 Processing helix chain 'F' and resid 686 through 695 removed outlier: 3.847A pdb=" N ARG F 694 " --> pdb=" O MET F 690 " (cutoff:3.500A) Processing helix chain 'F' and resid 698 through 707 removed outlier: 3.727A pdb=" N CYS F 705 " --> pdb=" O GLY F 701 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG F 706 " --> pdb=" O ILE F 702 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS F 707 " --> pdb=" O ARG F 703 " (cutoff:3.500A) Processing helix chain 'F' and resid 715 through 721 removed outlier: 3.587A pdb=" N ARG F 721 " --> pdb=" O ASP F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 738 through 746 removed outlier: 3.870A pdb=" N LEU F 745 " --> pdb=" O GLY F 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 753 through 755 No H-bonds generated for 'chain 'F' and resid 753 through 755' Processing helix chain 'F' and resid 772 through 775 No H-bonds generated for 'chain 'F' and resid 772 through 775' Processing helix chain 'F' and resid 777 through 780 No H-bonds generated for 'chain 'F' and resid 777 through 780' Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.788A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 143 removed outlier: 4.123A pdb=" N SER B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 193 Processing helix chain 'B' and resid 203 through 215 removed outlier: 3.754A pdb=" N GLU B 207 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL B 209 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 230 Processing helix chain 'B' and resid 254 through 261 Proline residue: B 258 - end of helix removed outlier: 4.640A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 254 through 261' Processing helix chain 'B' and resid 264 through 266 No H-bonds generated for 'chain 'B' and resid 264 through 266' Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 309 through 320 removed outlier: 3.546A pdb=" N GLN B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 346 removed outlier: 3.733A pdb=" N ILE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY B 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 removed outlier: 3.901A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 369 removed outlier: 3.540A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Proline residue: B 367 - end of helix Processing helix chain 'G' and resid 14 through 17 No H-bonds generated for 'chain 'G' and resid 14 through 17' Processing helix chain 'G' and resid 23 through 28 removed outlier: 4.865A pdb=" N THR G 28 " --> pdb=" O LEU G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 110 removed outlier: 4.366A pdb=" N ASN G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 139 No H-bonds generated for 'chain 'G' and resid 136 through 139' Processing helix chain 'G' and resid 154 through 167 Processing helix chain 'G' and resid 184 through 197 removed outlier: 4.061A pdb=" N TYR G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE G 195 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL G 197 " --> pdb=" O GLN G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 231 Proline residue: G 225 - end of helix Processing helix chain 'G' and resid 270 through 274 Processing helix chain 'G' and resid 284 through 290 Processing helix chain 'G' and resid 295 through 300 Processing helix chain 'G' and resid 325 through 337 removed outlier: 3.565A pdb=" N ASN G 334 " --> pdb=" O MET G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 357 removed outlier: 3.918A pdb=" N TYR G 350 " --> pdb=" O LYS G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 388 Processing helix chain 'G' and resid 392 through 400 removed outlier: 3.743A pdb=" N LEU G 396 " --> pdb=" O SER G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 447 removed outlier: 4.187A pdb=" N ALA G 428 " --> pdb=" O THR G 424 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR G 446 " --> pdb=" O ARG G 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 473 through 504 removed outlier: 4.125A pdb=" N THR G 481 " --> pdb=" O CYS G 477 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU G 496 " --> pdb=" O HIS G 492 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 524 removed outlier: 5.187A pdb=" N ALA G 519 " --> pdb=" O ASP G 516 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 537 Processing helix chain 'G' and resid 545 through 556 Processing helix chain 'G' and resid 593 through 596 No H-bonds generated for 'chain 'G' and resid 593 through 596' Processing helix chain 'G' and resid 603 through 611 Processing helix chain 'G' and resid 615 through 619 Processing helix chain 'G' and resid 647 through 662 Processing helix chain 'G' and resid 686 through 695 removed outlier: 3.847A pdb=" N ARG G 694 " --> pdb=" O MET G 690 " (cutoff:3.500A) Processing helix chain 'G' and resid 698 through 707 removed outlier: 3.727A pdb=" N CYS G 705 " --> pdb=" O GLY G 701 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG G 706 " --> pdb=" O ILE G 702 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS G 707 " --> pdb=" O ARG G 703 " (cutoff:3.500A) Processing helix chain 'G' and resid 715 through 721 removed outlier: 3.586A pdb=" N ARG G 721 " --> pdb=" O ASP G 717 " (cutoff:3.500A) Processing helix chain 'G' and resid 738 through 746 removed outlier: 3.870A pdb=" N LEU G 745 " --> pdb=" O GLY G 741 " (cutoff:3.500A) Processing helix chain 'G' and resid 753 through 755 No H-bonds generated for 'chain 'G' and resid 753 through 755' Processing helix chain 'G' and resid 772 through 775 No H-bonds generated for 'chain 'G' and resid 772 through 775' Processing helix chain 'G' and resid 777 through 780 No H-bonds generated for 'chain 'G' and resid 777 through 780' Processing helix chain 'C' and resid 55 through 57 No H-bonds generated for 'chain 'C' and resid 55 through 57' Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 removed outlier: 3.788A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 143 removed outlier: 4.124A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 203 through 215 removed outlier: 3.754A pdb=" N GLU C 207 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL C 209 " --> pdb=" O ARG C 206 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG C 210 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 230 Processing helix chain 'C' and resid 254 through 261 Proline residue: C 258 - end of helix removed outlier: 4.639A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 254 through 261' Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 277 through 283 Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.546A pdb=" N GLN C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 346 removed outlier: 3.732A pdb=" N ILE C 341 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 355 removed outlier: 3.901A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 369 removed outlier: 3.539A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Proline residue: C 367 - end of helix Processing helix chain 'H' and resid 14 through 17 No H-bonds generated for 'chain 'H' and resid 14 through 17' Processing helix chain 'H' and resid 23 through 28 removed outlier: 4.865A pdb=" N THR H 28 " --> pdb=" O LEU H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 110 removed outlier: 4.366A pdb=" N ASN H 104 " --> pdb=" O ALA H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 139 No H-bonds generated for 'chain 'H' and resid 136 through 139' Processing helix chain 'H' and resid 154 through 167 Processing helix chain 'H' and resid 184 through 197 removed outlier: 4.060A pdb=" N TYR H 194 " --> pdb=" O ARG H 190 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE H 195 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA H 196 " --> pdb=" O ILE H 192 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL H 197 " --> pdb=" O GLN H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 231 Proline residue: H 225 - end of helix Processing helix chain 'H' and resid 270 through 274 Processing helix chain 'H' and resid 284 through 290 Processing helix chain 'H' and resid 295 through 300 Processing helix chain 'H' and resid 325 through 337 removed outlier: 3.565A pdb=" N ASN H 334 " --> pdb=" O MET H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 344 through 357 removed outlier: 3.917A pdb=" N TYR H 350 " --> pdb=" O LYS H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 388 Processing helix chain 'H' and resid 392 through 400 removed outlier: 3.744A pdb=" N LEU H 396 " --> pdb=" O SER H 392 " (cutoff:3.500A) Processing helix chain 'H' and resid 417 through 447 removed outlier: 4.186A pdb=" N ALA H 428 " --> pdb=" O THR H 424 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR H 446 " --> pdb=" O ARG H 442 " (cutoff:3.500A) Processing helix chain 'H' and resid 473 through 504 removed outlier: 4.125A pdb=" N THR H 481 " --> pdb=" O CYS H 477 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU H 496 " --> pdb=" O HIS H 492 " (cutoff:3.500A) Processing helix chain 'H' and resid 514 through 524 removed outlier: 5.188A pdb=" N ALA H 519 " --> pdb=" O ASP H 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 530 through 537 Processing helix chain 'H' and resid 545 through 556 Processing helix chain 'H' and resid 593 through 596 No H-bonds generated for 'chain 'H' and resid 593 through 596' Processing helix chain 'H' and resid 603 through 611 Processing helix chain 'H' and resid 615 through 619 Processing helix chain 'H' and resid 647 through 662 Processing helix chain 'H' and resid 686 through 695 removed outlier: 3.847A pdb=" N ARG H 694 " --> pdb=" O MET H 690 " (cutoff:3.500A) Processing helix chain 'H' and resid 698 through 707 removed outlier: 3.727A pdb=" N CYS H 705 " --> pdb=" O GLY H 701 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG H 706 " --> pdb=" O ILE H 702 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS H 707 " --> pdb=" O ARG H 703 " (cutoff:3.500A) Processing helix chain 'H' and resid 715 through 721 removed outlier: 3.587A pdb=" N ARG H 721 " --> pdb=" O ASP H 717 " (cutoff:3.500A) Processing helix chain 'H' and resid 738 through 746 removed outlier: 3.870A pdb=" N LEU H 745 " --> pdb=" O GLY H 741 " (cutoff:3.500A) Processing helix chain 'H' and resid 753 through 755 No H-bonds generated for 'chain 'H' and resid 753 through 755' Processing helix chain 'H' and resid 772 through 775 No H-bonds generated for 'chain 'H' and resid 772 through 775' Processing helix chain 'H' and resid 777 through 780 No H-bonds generated for 'chain 'H' and resid 777 through 780' Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 91 removed outlier: 3.787A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 143 removed outlier: 4.123A pdb=" N SER E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 193 Processing helix chain 'E' and resid 203 through 215 removed outlier: 3.754A pdb=" N GLU E 207 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL E 209 " --> pdb=" O ARG E 206 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG E 210 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 230 Processing helix chain 'E' and resid 254 through 261 Proline residue: E 258 - end of helix removed outlier: 4.640A pdb=" N LEU E 261 " --> pdb=" O CYS E 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 254 through 261' Processing helix chain 'E' and resid 264 through 266 No H-bonds generated for 'chain 'E' and resid 264 through 266' Processing helix chain 'E' and resid 277 through 283 Processing helix chain 'E' and resid 290 through 295 Processing helix chain 'E' and resid 303 through 305 No H-bonds generated for 'chain 'E' and resid 303 through 305' Processing helix chain 'E' and resid 309 through 320 removed outlier: 3.546A pdb=" N GLN E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 346 removed outlier: 3.732A pdb=" N ILE E 341 " --> pdb=" O SER E 338 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY E 342 " --> pdb=" O VAL E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 355 removed outlier: 3.901A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 369 removed outlier: 3.540A pdb=" N GLU E 364 " --> pdb=" O GLN E 360 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA E 365 " --> pdb=" O GLU E 361 " (cutoff:3.500A) Proline residue: E 367 - end of helix Processing helix chain 'D' and resid 55 through 57 No H-bonds generated for 'chain 'D' and resid 55 through 57' Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 91 removed outlier: 3.788A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 143 removed outlier: 4.124A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 193 Processing helix chain 'D' and resid 203 through 215 removed outlier: 3.755A pdb=" N GLU D 207 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL D 209 " --> pdb=" O ARG D 206 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG D 210 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 230 Processing helix chain 'D' and resid 254 through 261 Proline residue: D 258 - end of helix removed outlier: 4.639A pdb=" N LEU D 261 " --> pdb=" O CYS D 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 254 through 261' Processing helix chain 'D' and resid 264 through 266 No H-bonds generated for 'chain 'D' and resid 264 through 266' Processing helix chain 'D' and resid 277 through 283 Processing helix chain 'D' and resid 290 through 295 Processing helix chain 'D' and resid 303 through 305 No H-bonds generated for 'chain 'D' and resid 303 through 305' Processing helix chain 'D' and resid 309 through 320 removed outlier: 3.546A pdb=" N GLN D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 346 removed outlier: 3.733A pdb=" N ILE D 341 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY D 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 removed outlier: 3.901A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 369 removed outlier: 3.540A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Proline residue: D 367 - end of helix Processing helix chain 'I' and resid 63 through 195 removed outlier: 3.767A pdb=" N UNK I 93 " --> pdb=" O UNK I 89 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N UNK I 97 " --> pdb=" O UNK I 93 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N UNK I 106 " --> pdb=" O UNK I 102 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N UNK I 114 " --> pdb=" O UNK I 110 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N UNK I 162 " --> pdb=" O UNK I 158 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N UNK I 163 " --> pdb=" O UNK I 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 195 removed outlier: 4.145A pdb=" N UNK J 110 " --> pdb=" O UNK J 106 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N UNK J 111 " --> pdb=" O UNK J 107 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N UNK J 129 " --> pdb=" O UNK J 125 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N UNK J 131 " --> pdb=" O UNK J 127 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N UNK J 138 " --> pdb=" O UNK J 134 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N UNK J 139 " --> pdb=" O UNK J 135 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N UNK J 141 " --> pdb=" O UNK J 137 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N UNK J 142 " --> pdb=" O UNK J 138 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N UNK J 143 " --> pdb=" O UNK J 139 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N UNK J 152 " --> pdb=" O UNK J 148 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N UNK J 195 " --> pdb=" O UNK J 191 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 17 through 19 Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 removed outlier: 3.588A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 103 through 107 Processing sheet with id= D, first strand: chain 'A' and resid 160 through 163 removed outlier: 6.890A pdb=" N VAL A 298 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N SER A 155 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N SER A 300 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 238 through 240 Processing sheet with id= F, first strand: chain 'F' and resid 36 through 39 Processing sheet with id= G, first strand: chain 'F' and resid 58 through 60 Processing sheet with id= H, first strand: chain 'F' and resid 115 through 118 removed outlier: 3.574A pdb=" N PHE F 121 " --> pdb=" O SER F 118 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 670 through 672 removed outlier: 3.753A pdb=" N ILE F 462 " --> pdb=" O ILE F 176 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY F 178 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE F 250 " --> pdb=" O ILE F 457 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 403 through 406 Processing sheet with id= K, first strand: chain 'F' and resid 577 through 581 removed outlier: 3.588A pdb=" N PHE F 577 " --> pdb=" O TYR F 588 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 711 through 714 Processing sheet with id= M, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= N, first strand: chain 'B' and resid 35 through 38 removed outlier: 3.587A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 103 through 107 Processing sheet with id= P, first strand: chain 'B' and resid 160 through 163 removed outlier: 6.890A pdb=" N VAL B 298 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N SER B 155 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N SER B 300 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 238 through 240 Processing sheet with id= R, first strand: chain 'G' and resid 36 through 39 Processing sheet with id= S, first strand: chain 'G' and resid 58 through 60 Processing sheet with id= T, first strand: chain 'G' and resid 115 through 118 removed outlier: 3.574A pdb=" N PHE G 121 " --> pdb=" O SER G 118 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 670 through 672 removed outlier: 3.752A pdb=" N ILE G 462 " --> pdb=" O ILE G 176 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY G 178 " --> pdb=" O ILE G 462 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE G 250 " --> pdb=" O ILE G 457 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 403 through 406 Processing sheet with id= W, first strand: chain 'G' and resid 577 through 581 removed outlier: 3.588A pdb=" N PHE G 577 " --> pdb=" O TYR G 588 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 711 through 714 Processing sheet with id= Y, first strand: chain 'C' and resid 35 through 38 removed outlier: 3.587A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= AA, first strand: chain 'C' and resid 160 through 163 removed outlier: 6.890A pdb=" N VAL C 298 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N SER C 155 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N SER C 300 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 238 through 240 Processing sheet with id= AC, first strand: chain 'H' and resid 36 through 39 Processing sheet with id= AD, first strand: chain 'H' and resid 58 through 60 Processing sheet with id= AE, first strand: chain 'H' and resid 115 through 118 removed outlier: 3.574A pdb=" N PHE H 121 " --> pdb=" O SER H 118 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 670 through 672 removed outlier: 3.752A pdb=" N ILE H 462 " --> pdb=" O ILE H 176 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY H 178 " --> pdb=" O ILE H 462 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE H 250 " --> pdb=" O ILE H 457 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'H' and resid 403 through 406 Processing sheet with id= AH, first strand: chain 'H' and resid 577 through 581 removed outlier: 3.588A pdb=" N PHE H 577 " --> pdb=" O TYR H 588 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 711 through 714 Processing sheet with id= AJ, first strand: chain 'E' and resid 35 through 38 removed outlier: 3.587A pdb=" N ARG E 37 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'E' and resid 103 through 107 Processing sheet with id= AL, first strand: chain 'E' and resid 160 through 163 removed outlier: 6.891A pdb=" N VAL E 298 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N SER E 155 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N SER E 300 " --> pdb=" O SER E 155 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'E' and resid 238 through 240 Processing sheet with id= AN, first strand: chain 'D' and resid 35 through 38 removed outlier: 3.587A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'D' and resid 103 through 107 Processing sheet with id= AP, first strand: chain 'D' and resid 160 through 163 removed outlier: 6.890A pdb=" N VAL D 298 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N SER D 155 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N SER D 300 " --> pdb=" O SER D 155 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'D' and resid 238 through 240 1230 hydrogen bonds defined for protein. 3279 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: 12.49 Time building geometry restraints manager: 13.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7277 1.33 - 1.45: 7642 1.45 - 1.57: 19343 1.57 - 1.69: 10 1.69 - 1.81: 347 Bond restraints: 34619 Sorted by residual: bond pdb=" C LYS E 18 " pdb=" O LYS E 18 " ideal model delta sigma weight residual 1.236 1.206 0.030 1.19e-02 7.06e+03 6.33e+00 bond pdb=" C LYS C 18 " pdb=" O LYS C 18 " ideal model delta sigma weight residual 1.235 1.207 0.029 1.14e-02 7.69e+03 6.27e+00 bond pdb=" CA LYS E 18 " pdb=" C LYS E 18 " ideal model delta sigma weight residual 1.523 1.493 0.029 1.23e-02 6.61e+03 5.64e+00 bond pdb=" CB GLN G 288 " pdb=" CG GLN G 288 " ideal model delta sigma weight residual 1.520 1.449 0.071 3.00e-02 1.11e+03 5.60e+00 bond pdb=" CB GLN H 288 " pdb=" CG GLN H 288 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.51e+00 ... (remaining 34614 not shown) Histogram of bond angle deviations from ideal: 95.42 - 103.39: 472 103.39 - 111.36: 13500 111.36 - 119.33: 14960 119.33 - 127.30: 17628 127.30 - 135.26: 298 Bond angle restraints: 46858 Sorted by residual: angle pdb=" N ILE H 457 " pdb=" CA ILE H 457 " pdb=" C ILE H 457 " ideal model delta sigma weight residual 109.34 95.42 13.92 2.08e+00 2.31e-01 4.48e+01 angle pdb=" N ILE F 457 " pdb=" CA ILE F 457 " pdb=" C ILE F 457 " ideal model delta sigma weight residual 109.34 95.46 13.88 2.08e+00 2.31e-01 4.45e+01 angle pdb=" N ILE G 457 " pdb=" CA ILE G 457 " pdb=" C ILE G 457 " ideal model delta sigma weight residual 109.34 95.51 13.83 2.08e+00 2.31e-01 4.42e+01 angle pdb=" N ALA H 136 " pdb=" CA ALA H 136 " pdb=" C ALA H 136 " ideal model delta sigma weight residual 111.07 116.77 -5.70 1.07e+00 8.73e-01 2.84e+01 angle pdb=" N ALA G 136 " pdb=" CA ALA G 136 " pdb=" C ALA G 136 " ideal model delta sigma weight residual 111.07 116.77 -5.70 1.07e+00 8.73e-01 2.84e+01 ... (remaining 46853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.98: 20400 24.98 - 49.96: 490 49.96 - 74.95: 26 74.95 - 99.93: 11 99.93 - 124.91: 5 Dihedral angle restraints: 20932 sinusoidal: 8249 harmonic: 12683 Sorted by residual: dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 64.91 -124.91 1 2.00e+01 2.50e-03 3.77e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 64.84 -124.84 1 2.00e+01 2.50e-03 3.77e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 64.84 -124.83 1 2.00e+01 2.50e-03 3.77e+01 ... (remaining 20929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 4435 0.079 - 0.158: 682 0.158 - 0.238: 55 0.238 - 0.317: 18 0.317 - 0.396: 7 Chirality restraints: 5197 Sorted by residual: chirality pdb=" CB ILE G 580 " pdb=" CA ILE G 580 " pdb=" CG1 ILE G 580 " pdb=" CG2 ILE G 580 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" CB ILE H 580 " pdb=" CA ILE H 580 " pdb=" CG1 ILE H 580 " pdb=" CG2 ILE H 580 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CB ILE F 580 " pdb=" CA ILE F 580 " pdb=" CG1 ILE F 580 " pdb=" CG2 ILE F 580 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 5194 not shown) Planarity restraints: 6060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU F 88 " -0.014 2.00e-02 2.50e+03 2.96e-02 8.78e+00 pdb=" CD GLU F 88 " 0.051 2.00e-02 2.50e+03 pdb=" OE1 GLU F 88 " -0.018 2.00e-02 2.50e+03 pdb=" OE2 GLU F 88 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU G 88 " -0.014 2.00e-02 2.50e+03 2.95e-02 8.73e+00 pdb=" CD GLU G 88 " 0.051 2.00e-02 2.50e+03 pdb=" OE1 GLU G 88 " -0.018 2.00e-02 2.50e+03 pdb=" OE2 GLU G 88 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 88 " -0.014 2.00e-02 2.50e+03 2.95e-02 8.68e+00 pdb=" CD GLU H 88 " 0.051 2.00e-02 2.50e+03 pdb=" OE1 GLU H 88 " -0.018 2.00e-02 2.50e+03 pdb=" OE2 GLU H 88 " -0.018 2.00e-02 2.50e+03 ... (remaining 6057 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 120 2.47 - 3.08: 21662 3.08 - 3.69: 53660 3.69 - 4.29: 78166 4.29 - 4.90: 124962 Nonbonded interactions: 278570 Sorted by model distance: nonbonded pdb=" OD1 ASP C 157 " pdb=" O3' ADP C 401 " model vdw 1.864 2.440 nonbonded pdb=" OD1 ASN C 12 " pdb=" CE MET C 119 " model vdw 1.901 3.460 nonbonded pdb=" OG SER C 14 " pdb=" CA GLY C 158 " model vdw 1.939 3.440 nonbonded pdb=" OD1 ASP E 157 " pdb=" O3' ADP E 401 " model vdw 1.945 2.440 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 1.995 2.170 ... (remaining 278565 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 46 or resid 48 through 375 or resid 401 through \ 402)) selection = (chain 'B' and (resid 5 through 46 or resid 48 through 375 or resid 401 through \ 402)) selection = (chain 'C' and (resid 5 through 46 or resid 48 through 375 or resid 401 through \ 402)) selection = (chain 'D' and (resid 5 through 46 or resid 48 through 375 or resid 401 through \ 402)) selection = (chain 'E' and (resid 5 through 46 or resid 48 through 375 or resid 401 through \ 402)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 3.420 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 96.330 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.320 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 34619 Z= 0.413 Angle : 1.030 13.916 46858 Z= 0.548 Chirality : 0.059 0.396 5197 Planarity : 0.008 0.057 6060 Dihedral : 10.791 124.912 12764 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.43 % Allowed : 2.48 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.11), residues: 4052 helix: -3.19 (0.08), residues: 1641 sheet: -3.21 (0.19), residues: 534 loop : -1.99 (0.13), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.005 TRP D 340 HIS 0.016 0.003 HIS F 492 PHE 0.037 0.004 PHE C 262 TYR 0.037 0.004 TYR A 294 ARG 0.014 0.001 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 3497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1155 time to evaluate : 4.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 SER cc_start: 0.9060 (t) cc_final: 0.8794 (p) REVERT: A 57 GLU cc_start: 0.7283 (tt0) cc_final: 0.7032 (tt0) REVERT: A 132 MET cc_start: 0.9020 (ppp) cc_final: 0.8503 (ppp) REVERT: A 167 GLU cc_start: 0.7853 (tp30) cc_final: 0.7652 (tp30) REVERT: A 180 LEU cc_start: 0.8826 (tt) cc_final: 0.8398 (tp) REVERT: A 191 LYS cc_start: 0.7534 (ttmt) cc_final: 0.7265 (ttpp) REVERT: A 291 LYS cc_start: 0.8432 (tttt) cc_final: 0.7996 (ttpp) REVERT: A 296 ASN cc_start: 0.8693 (m-40) cc_final: 0.8315 (m-40) REVERT: A 320 LEU cc_start: 0.9071 (mt) cc_final: 0.8771 (mt) REVERT: A 325 MET cc_start: 0.8877 (tpp) cc_final: 0.8490 (tpp) REVERT: A 328 LYS cc_start: 0.7876 (tttt) cc_final: 0.7455 (tptm) REVERT: A 330 ILE cc_start: 0.8964 (mp) cc_final: 0.8702 (mm) REVERT: F 63 THR cc_start: 0.4276 (t) cc_final: 0.3662 (m) REVERT: F 99 PRO cc_start: 0.6655 (Cg_endo) cc_final: 0.6430 (Cg_exo) REVERT: F 177 THR cc_start: 0.6903 (m) cc_final: 0.6656 (m) REVERT: F 239 ASP cc_start: 0.8459 (m-30) cc_final: 0.7864 (t70) REVERT: F 272 ARG cc_start: 0.7168 (tpp-160) cc_final: 0.6002 (tpt170) REVERT: F 422 TYR cc_start: 0.7358 (m-80) cc_final: 0.5238 (m-10) REVERT: F 478 ILE cc_start: 0.8811 (mm) cc_final: 0.8547 (mm) REVERT: F 484 LYS cc_start: 0.8247 (tptt) cc_final: 0.7828 (ttmt) REVERT: F 488 PHE cc_start: 0.8026 (t80) cc_final: 0.7807 (t80) REVERT: F 506 ILE cc_start: 0.7011 (mm) cc_final: 0.6633 (mm) REVERT: F 580 ILE cc_start: 0.7499 (tt) cc_final: 0.6979 (pt) REVERT: F 614 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6186 (tp) REVERT: F 653 GLU cc_start: 0.7702 (tp30) cc_final: 0.7320 (tp30) REVERT: F 673 ILE cc_start: 0.8183 (pt) cc_final: 0.7666 (pt) REVERT: F 700 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7334 (mm-30) REVERT: F 776 MET cc_start: 0.4449 (ttm) cc_final: 0.4220 (mtm) REVERT: B 60 SER cc_start: 0.8907 (t) cc_final: 0.8665 (t) REVERT: B 78 ASN cc_start: 0.8088 (t0) cc_final: 0.7744 (t0) REVERT: B 91 TYR cc_start: 0.8442 (m-80) cc_final: 0.8178 (m-80) REVERT: B 136 ILE cc_start: 0.8206 (mt) cc_final: 0.7920 (tt) REVERT: B 157 ASP cc_start: 0.7179 (t0) cc_final: 0.6864 (t0) REVERT: B 203 THR cc_start: 0.7889 (p) cc_final: 0.7630 (t) REVERT: B 205 GLU cc_start: 0.7112 (mp0) cc_final: 0.6437 (mp0) REVERT: B 263 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7765 (mm110) REVERT: B 291 LYS cc_start: 0.8893 (tttt) cc_final: 0.7851 (mptt) REVERT: B 326 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7704 (tmtt) REVERT: G 282 ASP cc_start: 0.7171 (t0) cc_final: 0.6922 (t0) REVERT: G 345 GLU cc_start: 0.7626 (pp20) cc_final: 0.6863 (tt0) REVERT: G 370 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7209 (mt-10) REVERT: G 417 VAL cc_start: 0.8566 (p) cc_final: 0.8350 (p) REVERT: G 429 LYS cc_start: 0.7390 (ptpt) cc_final: 0.7150 (ptpp) REVERT: G 478 ILE cc_start: 0.7245 (mm) cc_final: 0.6976 (mm) REVERT: G 482 ASN cc_start: 0.6352 (m-40) cc_final: 0.6097 (m110) REVERT: G 487 GLN cc_start: 0.7900 (tp-100) cc_final: 0.7696 (tp40) REVERT: G 691 HIS cc_start: 0.6862 (t70) cc_final: 0.6506 (t-170) REVERT: G 710 PRO cc_start: 0.8111 (Cg_endo) cc_final: 0.7810 (Cg_exo) REVERT: G 765 PHE cc_start: 0.6776 (m-80) cc_final: 0.6471 (m-80) REVERT: G 778 ASP cc_start: 0.7137 (m-30) cc_final: 0.6835 (m-30) REVERT: C 191 LYS cc_start: 0.7984 (ttmt) cc_final: 0.7711 (ttmm) REVERT: C 215 LYS cc_start: 0.8894 (mttm) cc_final: 0.8537 (mttm) REVERT: C 291 LYS cc_start: 0.7346 (tttt) cc_final: 0.7104 (tttt) REVERT: C 328 LYS cc_start: 0.7832 (tttt) cc_final: 0.7307 (tptt) REVERT: C 351 THR cc_start: 0.8477 (p) cc_final: 0.8110 (t) REVERT: H 155 PHE cc_start: 0.6350 (m-10) cc_final: 0.5890 (m-10) REVERT: H 163 GLN cc_start: 0.6618 (tp40) cc_final: 0.6403 (tp40) REVERT: H 357 MET cc_start: 0.7258 (mmm) cc_final: 0.7041 (mtt) REVERT: H 451 GLN cc_start: 0.6455 (mp-120) cc_final: 0.6174 (mp-120) REVERT: H 536 GLU cc_start: 0.8351 (pp20) cc_final: 0.7799 (pp20) REVERT: H 657 LYS cc_start: 0.7365 (tmtm) cc_final: 0.6783 (tptp) REVERT: H 690 MET cc_start: 0.5738 (mmm) cc_final: 0.5501 (mmm) REVERT: H 702 ILE cc_start: 0.8169 (mm) cc_final: 0.7881 (mm) REVERT: H 762 LYS cc_start: 0.7130 (mttt) cc_final: 0.6927 (mttt) REVERT: E 53 TYR cc_start: 0.7764 (m-80) cc_final: 0.7407 (m-80) REVERT: E 113 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7723 (tppt) REVERT: E 127 PHE cc_start: 0.7683 (m-80) cc_final: 0.7347 (m-80) REVERT: E 155 SER cc_start: 0.8215 (t) cc_final: 0.7733 (m) REVERT: E 258 PRO cc_start: 0.7337 (Cg_endo) cc_final: 0.6688 (Cg_exo) REVERT: E 296 ASN cc_start: 0.8431 (m-40) cc_final: 0.8074 (m-40) REVERT: E 316 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6670 (mm-30) REVERT: E 354 GLN cc_start: 0.7312 (pt0) cc_final: 0.7094 (pt0) REVERT: E 363 ASP cc_start: 0.8023 (m-30) cc_final: 0.7602 (m-30) REVERT: D 9 VAL cc_start: 0.8914 (t) cc_final: 0.8691 (t) REVERT: D 16 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8358 (mp) REVERT: D 50 LYS cc_start: 0.8765 (mtmm) cc_final: 0.8451 (mtpt) REVERT: D 54 VAL cc_start: 0.8555 (m) cc_final: 0.7931 (m) REVERT: D 91 TYR cc_start: 0.8248 (m-80) cc_final: 0.7956 (m-10) REVERT: D 118 LYS cc_start: 0.7743 (tptt) cc_final: 0.7234 (ttmm) REVERT: D 125 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7779 (mt-10) REVERT: D 136 ILE cc_start: 0.8611 (mt) cc_final: 0.8345 (tt) REVERT: D 161 HIS cc_start: 0.8747 (p-80) cc_final: 0.8432 (p90) REVERT: D 167 GLU cc_start: 0.8430 (tp30) cc_final: 0.8134 (tp30) REVERT: D 249 THR cc_start: 0.7286 (p) cc_final: 0.7017 (p) REVERT: D 291 LYS cc_start: 0.8775 (tttt) cc_final: 0.8183 (ttpp) REVERT: D 296 ASN cc_start: 0.8687 (m-40) cc_final: 0.8083 (m-40) REVERT: D 313 MET cc_start: 0.7695 (tpp) cc_final: 0.7327 (tpt) REVERT: D 328 LYS cc_start: 0.7541 (tttt) cc_final: 0.7026 (tttt) REVERT: D 360 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8196 (tm-30) REVERT: D 361 GLU cc_start: 0.7992 (tt0) cc_final: 0.7513 (tt0) outliers start: 10 outliers final: 3 residues processed: 1164 average time/residue: 0.4995 time to fit residues: 899.6934 Evaluate side-chains 834 residues out of total 3497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 829 time to evaluate : 3.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 614 LEU Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain D residue 16 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 365 optimal weight: 0.0980 chunk 328 optimal weight: 0.4980 chunk 182 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 221 optimal weight: 0.7980 chunk 175 optimal weight: 9.9990 chunk 339 optimal weight: 8.9990 chunk 131 optimal weight: 0.7980 chunk 206 optimal weight: 5.9990 chunk 252 optimal weight: 10.0000 chunk 393 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 40 HIS A 73 HIS ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS F 79 GLN F 160 ASN F 171 ASN ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 391 ASN ** F 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN B 162 ASN B 275 HIS G 171 ASN ** G 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 372 GLN G 401 HIS ** G 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 711 ASN C 12 ASN C 49 GLN C 73 HIS C 111 ASN C 121 GLN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 HIS H 104 ASN ** H 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN ** H 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 ASN ** H 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 711 ASN E 12 ASN E 121 GLN E 137 GLN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 ASN E 275 HIS ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN D 162 ASN D 173 HIS D 314 GLN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34619 Z= 0.169 Angle : 0.630 10.526 46858 Z= 0.314 Chirality : 0.042 0.260 5197 Planarity : 0.005 0.048 6060 Dihedral : 6.682 88.902 4776 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.74 % Allowed : 11.15 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.12), residues: 4052 helix: -1.80 (0.11), residues: 1665 sheet: -2.50 (0.22), residues: 492 loop : -1.51 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 340 HIS 0.013 0.001 HIS G 251 PHE 0.032 0.002 PHE F 489 TYR 0.034 0.002 TYR F 164 ARG 0.006 0.001 ARG H 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 3497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 897 time to evaluate : 3.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 SER cc_start: 0.9279 (t) cc_final: 0.9040 (p) REVERT: A 82 MET cc_start: 0.8848 (mmm) cc_final: 0.8427 (mmm) REVERT: A 107 GLU cc_start: 0.7762 (tp30) cc_final: 0.7476 (tp30) REVERT: A 118 LYS cc_start: 0.7243 (tptt) cc_final: 0.6977 (tptt) REVERT: A 167 GLU cc_start: 0.8103 (tp30) cc_final: 0.7553 (tp30) REVERT: A 191 LYS cc_start: 0.7710 (ttmt) cc_final: 0.7465 (ttpp) REVERT: A 195 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7595 (tm-30) REVERT: A 207 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8077 (mp0) REVERT: A 291 LYS cc_start: 0.8234 (tttt) cc_final: 0.7699 (ttpp) REVERT: A 326 LYS cc_start: 0.8070 (ttpt) cc_final: 0.7837 (tptt) REVERT: A 355 MET cc_start: 0.7864 (mmm) cc_final: 0.7638 (mmm) REVERT: F 239 ASP cc_start: 0.8391 (m-30) cc_final: 0.7790 (t70) REVERT: F 269 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6941 (mm-30) REVERT: F 302 LEU cc_start: 0.7970 (mp) cc_final: 0.7736 (mt) REVERT: F 349 MET cc_start: 0.6026 (mmt) cc_final: 0.5821 (mmt) REVERT: F 433 GLU cc_start: 0.7859 (tt0) cc_final: 0.7164 (tm-30) REVERT: F 435 MET cc_start: 0.8341 (tmm) cc_final: 0.8132 (tmm) REVERT: F 439 MET cc_start: 0.7366 (ttp) cc_final: 0.6953 (tmm) REVERT: F 474 GLU cc_start: 0.7788 (tp30) cc_final: 0.7316 (tp30) REVERT: F 484 LYS cc_start: 0.8432 (tptt) cc_final: 0.7837 (tppt) REVERT: F 537 GLU cc_start: 0.7773 (tp30) cc_final: 0.7232 (tp30) REVERT: F 588 TYR cc_start: 0.8103 (m-80) cc_final: 0.7893 (m-80) REVERT: F 594 LEU cc_start: 0.7512 (mt) cc_final: 0.7167 (mt) REVERT: F 653 GLU cc_start: 0.7831 (tp30) cc_final: 0.7330 (tp30) REVERT: F 776 MET cc_start: 0.4496 (ttm) cc_final: 0.4210 (mtm) REVERT: B 14 SER cc_start: 0.7997 (t) cc_final: 0.7332 (m) REVERT: B 60 SER cc_start: 0.8858 (t) cc_final: 0.8614 (t) REVERT: B 91 TYR cc_start: 0.8477 (m-80) cc_final: 0.8275 (m-80) REVERT: B 184 ASP cc_start: 0.7520 (t0) cc_final: 0.7264 (m-30) REVERT: B 203 THR cc_start: 0.8165 (p) cc_final: 0.7957 (t) REVERT: B 205 GLU cc_start: 0.6920 (mp0) cc_final: 0.6357 (mp0) REVERT: B 217 CYS cc_start: 0.8552 (m) cc_final: 0.8345 (m) REVERT: B 325 MET cc_start: 0.7256 (ttm) cc_final: 0.7043 (mtt) REVERT: G 165 MET cc_start: 0.5690 (tpt) cc_final: 0.4280 (tpt) REVERT: G 345 GLU cc_start: 0.7933 (pp20) cc_final: 0.6942 (tt0) REVERT: G 422 TYR cc_start: 0.7787 (m-80) cc_final: 0.7108 (m-10) REVERT: G 438 TRP cc_start: 0.7750 (t60) cc_final: 0.7514 (t60) REVERT: G 478 ILE cc_start: 0.7219 (mm) cc_final: 0.6430 (mm) REVERT: G 526 LYS cc_start: 0.8265 (tptt) cc_final: 0.8053 (mmtp) REVERT: G 668 HIS cc_start: 0.6325 (m-70) cc_final: 0.5451 (m-70) REVERT: G 690 MET cc_start: 0.7222 (tpt) cc_final: 0.6798 (ptt) REVERT: G 700 GLU cc_start: 0.5918 (tm-30) cc_final: 0.5299 (tm-30) REVERT: G 765 PHE cc_start: 0.6766 (m-80) cc_final: 0.6406 (m-80) REVERT: C 16 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8216 (mp) REVERT: C 57 GLU cc_start: 0.8360 (tt0) cc_final: 0.8010 (pt0) REVERT: C 132 MET cc_start: 0.8384 (ppp) cc_final: 0.7699 (ppp) REVERT: C 190 MET cc_start: 0.8150 (mtp) cc_final: 0.7898 (mtt) REVERT: C 215 LYS cc_start: 0.8846 (mttm) cc_final: 0.8439 (mttp) REVERT: C 325 MET cc_start: 0.8800 (tpp) cc_final: 0.8571 (tpp) REVERT: C 328 LYS cc_start: 0.7798 (tttt) cc_final: 0.7436 (tptt) REVERT: C 336 LYS cc_start: 0.7796 (ttmt) cc_final: 0.7488 (ttmt) REVERT: C 351 THR cc_start: 0.8525 (p) cc_final: 0.8200 (t) REVERT: H 153 HIS cc_start: 0.6309 (t70) cc_final: 0.6068 (t70) REVERT: H 168 ASP cc_start: 0.6933 (t0) cc_final: 0.6650 (m-30) REVERT: H 170 GLU cc_start: 0.7323 (tt0) cc_final: 0.6069 (pt0) REVERT: H 382 ASP cc_start: 0.5952 (m-30) cc_final: 0.5722 (m-30) REVERT: H 484 LYS cc_start: 0.8487 (tptt) cc_final: 0.8263 (tppt) REVERT: H 536 GLU cc_start: 0.8287 (pp20) cc_final: 0.7965 (pp20) REVERT: H 552 LEU cc_start: 0.7315 (mt) cc_final: 0.7045 (mt) REVERT: H 657 LYS cc_start: 0.7390 (tmtm) cc_final: 0.6839 (tptp) REVERT: H 659 MET cc_start: 0.7565 (tpp) cc_final: 0.7048 (tmm) REVERT: H 762 LYS cc_start: 0.7210 (mttt) cc_final: 0.6938 (mttm) REVERT: E 18 LYS cc_start: 0.7932 (ptpt) cc_final: 0.7706 (mtmm) REVERT: E 53 TYR cc_start: 0.7635 (m-80) cc_final: 0.7247 (m-80) REVERT: E 132 MET cc_start: 0.8229 (ppp) cc_final: 0.7918 (ppp) REVERT: E 137 GLN cc_start: 0.8168 (tt0) cc_final: 0.7407 (tp40) REVERT: E 155 SER cc_start: 0.8546 (t) cc_final: 0.7893 (m) REVERT: E 179 ASP cc_start: 0.7420 (m-30) cc_final: 0.7140 (m-30) REVERT: E 215 LYS cc_start: 0.8175 (mmtm) cc_final: 0.7611 (mppt) REVERT: E 259 GLU cc_start: 0.7102 (tp30) cc_final: 0.6634 (tp30) REVERT: E 284 LYS cc_start: 0.8339 (tppp) cc_final: 0.7714 (tppt) REVERT: E 372 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.8011 (ttm-80) REVERT: D 9 VAL cc_start: 0.8920 (t) cc_final: 0.8682 (t) REVERT: D 50 LYS cc_start: 0.8768 (mtmm) cc_final: 0.8492 (mtpt) REVERT: D 118 LYS cc_start: 0.7772 (tptt) cc_final: 0.7279 (mttt) REVERT: D 125 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7745 (mt-10) REVERT: D 157 ASP cc_start: 0.7609 (t0) cc_final: 0.7261 (t0) REVERT: D 167 GLU cc_start: 0.8469 (tp30) cc_final: 0.8055 (tp30) REVERT: D 284 LYS cc_start: 0.8011 (tppp) cc_final: 0.7453 (mtpt) REVERT: D 291 LYS cc_start: 0.8481 (tttt) cc_final: 0.7893 (ttpp) REVERT: D 296 ASN cc_start: 0.8652 (m-40) cc_final: 0.8228 (m-40) REVERT: D 313 MET cc_start: 0.7597 (tpp) cc_final: 0.7218 (tpt) REVERT: D 316 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7705 (mm-30) REVERT: D 326 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7773 (tmtt) REVERT: D 328 LYS cc_start: 0.7577 (tttt) cc_final: 0.6925 (tttt) REVERT: D 360 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8392 (tm-30) REVERT: D 361 GLU cc_start: 0.8028 (tt0) cc_final: 0.7556 (tt0) outliers start: 56 outliers final: 31 residues processed: 928 average time/residue: 0.4986 time to fit residues: 737.8825 Evaluate side-chains 805 residues out of total 3497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 772 time to evaluate : 3.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 614 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain G residue 80 ASN Chi-restraints excluded: chain G residue 435 MET Chi-restraints excluded: chain G residue 471 ASN Chi-restraints excluded: chain G residue 674 ILE Chi-restraints excluded: chain G residue 774 GLU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain H residue 359 PHE Chi-restraints excluded: chain H residue 538 CYS Chi-restraints excluded: chain H residue 761 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 326 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 218 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 327 optimal weight: 5.9990 chunk 267 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 393 optimal weight: 9.9990 chunk 425 optimal weight: 30.0000 chunk 350 optimal weight: 9.9990 chunk 390 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 316 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN A 275 HIS A 353 GLN F 65 HIS ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 ASN ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 HIS F 711 ASN ** F 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS B 353 GLN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 482 ASN ** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 651 HIS ** G 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 ASN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 486 GLN ** H 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 726 ASN E 121 GLN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 34619 Z= 0.472 Angle : 0.840 13.482 46858 Z= 0.421 Chirality : 0.050 0.215 5197 Planarity : 0.006 0.075 6060 Dihedral : 6.737 85.747 4768 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.94 % Favored : 93.03 % Rotamer: Outliers : 3.76 % Allowed : 13.57 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.12), residues: 4052 helix: -1.43 (0.11), residues: 1629 sheet: -2.46 (0.21), residues: 520 loop : -1.53 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP E 340 HIS 0.015 0.002 HIS G 358 PHE 0.034 0.003 PHE B 262 TYR 0.028 0.003 TYR B 337 ARG 0.008 0.001 ARG F 723 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1055 residues out of total 3497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 928 time to evaluate : 3.964 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: A 24 ASP cc_start: 0.8705 (m-30) cc_final: 0.8408 (m-30) REVERT: A 143 TYR cc_start: 0.8718 (m-80) cc_final: 0.8232 (m-80) REVERT: A 167 GLU cc_start: 0.8447 (tp30) cc_final: 0.7848 (tp30) REVERT: A 191 LYS cc_start: 0.7979 (ttmt) cc_final: 0.7591 (ttpp) REVERT: A 195 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7015 (tm-30) REVERT: A 224 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8270 (mm-30) REVERT: A 291 LYS cc_start: 0.8422 (tttt) cc_final: 0.7852 (ttpp) REVERT: A 325 MET cc_start: 0.8644 (tpp) cc_final: 0.8424 (tpp) REVERT: F 6 MET cc_start: 0.4770 (mtm) cc_final: 0.4129 (mtm) REVERT: F 17 ARG cc_start: 0.5792 (tpt170) cc_final: 0.5403 (tpt170) REVERT: F 165 MET cc_start: 0.6876 (tpt) cc_final: 0.6126 (tpt) REVERT: F 388 MET cc_start: 0.7489 (mpp) cc_final: 0.7271 (mpp) REVERT: F 433 GLU cc_start: 0.7871 (tt0) cc_final: 0.7364 (tm-30) REVERT: F 439 MET cc_start: 0.7639 (ttp) cc_final: 0.7077 (tmm) REVERT: F 525 GLU cc_start: 0.8035 (tt0) cc_final: 0.7584 (tt0) REVERT: F 526 LYS cc_start: 0.7311 (mmtt) cc_final: 0.7023 (mmtt) REVERT: F 537 GLU cc_start: 0.8250 (tp30) cc_final: 0.7708 (tp30) REVERT: F 564 GLN cc_start: 0.8311 (mt0) cc_final: 0.8111 (mt0) REVERT: F 597 ASN cc_start: 0.8175 (t0) cc_final: 0.7928 (t0) REVERT: F 700 GLU cc_start: 0.8086 (tp30) cc_final: 0.7631 (tp30) REVERT: F 776 MET cc_start: 0.4610 (ttm) cc_final: 0.4340 (mtm) REVERT: B 14 SER cc_start: 0.8233 (t) cc_final: 0.7658 (m) REVERT: B 82 MET cc_start: 0.7460 (mmm) cc_final: 0.6894 (tmm) REVERT: B 136 ILE cc_start: 0.8765 (mt) cc_final: 0.8562 (tt) REVERT: B 140 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8750 (mt) REVERT: B 202 THR cc_start: 0.8433 (m) cc_final: 0.7853 (p) REVERT: B 205 GLU cc_start: 0.7076 (mp0) cc_final: 0.5706 (mp0) REVERT: B 221 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8238 (tt) REVERT: B 360 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7923 (tm-30) REVERT: G 117 TYR cc_start: 0.5792 (m-80) cc_final: 0.5507 (m-80) REVERT: G 280 GLU cc_start: 0.5164 (mt-10) cc_final: 0.4920 (tt0) REVERT: G 357 MET cc_start: 0.6279 (mmm) cc_final: 0.5337 (mmm) REVERT: G 429 LYS cc_start: 0.7687 (mtmt) cc_final: 0.7309 (mtmm) REVERT: G 489 PHE cc_start: 0.5517 (t80) cc_final: 0.5109 (t80) REVERT: G 539 MET cc_start: 0.8264 (mmm) cc_final: 0.8032 (mmp) REVERT: G 568 ASN cc_start: 0.7454 (OUTLIER) cc_final: 0.7083 (m-40) REVERT: G 666 HIS cc_start: 0.7112 (t70) cc_final: 0.6885 (t70) REVERT: G 700 GLU cc_start: 0.6601 (tm-30) cc_final: 0.5912 (tm-30) REVERT: G 765 PHE cc_start: 0.6772 (m-80) cc_final: 0.6503 (m-80) REVERT: C 80 ASP cc_start: 0.7878 (t70) cc_final: 0.6295 (t0) REVERT: C 82 MET cc_start: 0.8865 (tpt) cc_final: 0.8650 (mmm) REVERT: C 84 LYS cc_start: 0.7938 (mttt) cc_final: 0.7533 (mtmm) REVERT: C 87 HIS cc_start: 0.7464 (t70) cc_final: 0.7138 (t-90) REVERT: C 100 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7631 (tp30) REVERT: C 118 LYS cc_start: 0.7212 (tptt) cc_final: 0.6929 (tptt) REVERT: C 125 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8464 (mp0) REVERT: C 133 TYR cc_start: 0.8308 (t80) cc_final: 0.8032 (t80) REVERT: C 143 TYR cc_start: 0.8584 (m-80) cc_final: 0.7764 (m-80) REVERT: C 161 HIS cc_start: 0.8752 (p90) cc_final: 0.8392 (p90) REVERT: C 167 GLU cc_start: 0.9154 (tp30) cc_final: 0.8628 (tp30) REVERT: C 191 LYS cc_start: 0.8212 (ttmm) cc_final: 0.7752 (ttmt) REVERT: C 215 LYS cc_start: 0.9117 (mttm) cc_final: 0.8839 (mttp) REVERT: C 237 GLU cc_start: 0.8935 (tt0) cc_final: 0.8719 (tt0) REVERT: C 296 ASN cc_start: 0.8920 (m-40) cc_final: 0.8671 (m-40) REVERT: C 325 MET cc_start: 0.8780 (tpp) cc_final: 0.7970 (tpp) REVERT: C 328 LYS cc_start: 0.7792 (tttt) cc_final: 0.7293 (tptt) REVERT: C 351 THR cc_start: 0.8779 (p) cc_final: 0.8452 (t) REVERT: H 163 GLN cc_start: 0.6558 (tp40) cc_final: 0.6336 (tp40) REVERT: H 268 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8191 (tt) REVERT: H 281 ARG cc_start: 0.5814 (mtp-110) cc_final: 0.5041 (mtp180) REVERT: H 339 LEU cc_start: 0.6400 (tp) cc_final: 0.5341 (tp) REVERT: H 410 TYR cc_start: 0.7844 (m-80) cc_final: 0.7512 (m-80) REVERT: H 422 TYR cc_start: 0.8289 (m-80) cc_final: 0.7360 (m-80) REVERT: H 436 PHE cc_start: 0.7794 (t80) cc_final: 0.7454 (t80) REVERT: H 451 GLN cc_start: 0.7323 (mp-120) cc_final: 0.6993 (mp10) REVERT: H 483 GLU cc_start: 0.7622 (tp30) cc_final: 0.7134 (tp30) REVERT: H 486 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8077 (tp40) REVERT: H 553 TYR cc_start: 0.8264 (m-80) cc_final: 0.7996 (m-80) REVERT: H 656 ASN cc_start: 0.8168 (m-40) cc_final: 0.7589 (m-40) REVERT: H 659 MET cc_start: 0.7799 (tpp) cc_final: 0.6421 (mmm) REVERT: H 666 HIS cc_start: 0.6374 (t70) cc_final: 0.6037 (t-90) REVERT: E 52 SER cc_start: 0.9173 (t) cc_final: 0.8906 (p) REVERT: E 57 GLU cc_start: 0.8129 (pt0) cc_final: 0.7923 (pt0) REVERT: E 61 LYS cc_start: 0.8469 (mptm) cc_final: 0.8236 (mptt) REVERT: E 113 LYS cc_start: 0.8059 (ttmt) cc_final: 0.7038 (ttmt) REVERT: E 117 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7515 (mt-10) REVERT: E 130 PRO cc_start: 0.8813 (Cg_endo) cc_final: 0.8579 (Cg_exo) REVERT: E 167 GLU cc_start: 0.8543 (tp30) cc_final: 0.7478 (tp30) REVERT: E 191 LYS cc_start: 0.8029 (ttmt) cc_final: 0.7646 (mmtp) REVERT: E 195 GLU cc_start: 0.8293 (tt0) cc_final: 0.7961 (tp30) REVERT: E 211 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7960 (m-30) REVERT: E 246 GLN cc_start: 0.9113 (pm20) cc_final: 0.8803 (pm20) REVERT: E 284 LYS cc_start: 0.8524 (tppp) cc_final: 0.8288 (tppt) REVERT: E 291 LYS cc_start: 0.8173 (tttt) cc_final: 0.7652 (ttpt) REVERT: E 296 ASN cc_start: 0.8504 (m-40) cc_final: 0.8027 (m-40) REVERT: E 325 MET cc_start: 0.8578 (tpp) cc_final: 0.8260 (tpp) REVERT: E 372 ARG cc_start: 0.8360 (ttm-80) cc_final: 0.8087 (ttm-80) REVERT: D 50 LYS cc_start: 0.8857 (mtmm) cc_final: 0.8514 (mtpt) REVERT: D 82 MET cc_start: 0.8564 (mmm) cc_final: 0.8296 (mmm) REVERT: D 118 LYS cc_start: 0.7930 (tptt) cc_final: 0.7500 (tppt) REVERT: D 128 ASN cc_start: 0.8651 (t0) cc_final: 0.8205 (t0) REVERT: D 167 GLU cc_start: 0.8571 (tp30) cc_final: 0.8313 (tp30) REVERT: D 291 LYS cc_start: 0.8560 (tttt) cc_final: 0.7973 (ttpp) REVERT: D 296 ASN cc_start: 0.8704 (m-40) cc_final: 0.8234 (m-40) REVERT: D 313 MET cc_start: 0.7851 (tpp) cc_final: 0.7560 (tpt) REVERT: D 316 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7786 (mm-30) REVERT: D 325 MET cc_start: 0.8967 (tpp) cc_final: 0.8766 (tpp) REVERT: D 355 MET cc_start: 0.9280 (mmm) cc_final: 0.9035 (mmm) REVERT: D 360 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8323 (tm-30) REVERT: D 361 GLU cc_start: 0.7974 (tt0) cc_final: 0.7498 (tp30) outliers start: 127 outliers final: 62 residues processed: 994 average time/residue: 0.4628 time to fit residues: 736.4784 Evaluate side-chains 885 residues out of total 3497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 817 time to evaluate : 3.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 568 ASN Chi-restraints excluded: chain F residue 614 LEU Chi-restraints excluded: chain F residue 676 ASN Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 353 THR Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 568 ASN Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 267 LEU Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 486 GLN Chi-restraints excluded: chain H residue 538 CYS Chi-restraints excluded: chain H residue 557 LEU Chi-restraints excluded: chain H residue 601 LEU Chi-restraints excluded: chain H residue 615 LYS Chi-restraints excluded: chain H residue 674 ILE Chi-restraints excluded: chain H residue 702 ILE Chi-restraints excluded: chain H residue 761 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 335 ARG Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 389 optimal weight: 8.9990 chunk 296 optimal weight: 6.9990 chunk 204 optimal weight: 4.9990 chunk 43 optimal weight: 30.0000 chunk 187 optimal weight: 9.9990 chunk 264 optimal weight: 20.0000 chunk 395 optimal weight: 0.6980 chunk 418 optimal weight: 30.0000 chunk 206 optimal weight: 8.9990 chunk 374 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS F 78 GLN ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 490 ASN ** F 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 711 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 ASN H 135 ASN H 219 GLN H 222 GLN ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 661 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 34619 Z= 0.378 Angle : 0.732 12.237 46858 Z= 0.364 Chirality : 0.047 0.236 5197 Planarity : 0.005 0.060 6060 Dihedral : 6.428 83.446 4766 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 4.13 % Allowed : 16.48 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.13), residues: 4052 helix: -1.19 (0.12), residues: 1656 sheet: -2.37 (0.21), residues: 533 loop : -1.42 (0.15), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP E 340 HIS 0.018 0.002 HIS D 161 PHE 0.027 0.002 PHE H 465 TYR 0.026 0.002 TYR F 164 ARG 0.007 0.001 ARG G 671 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 3497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 840 time to evaluate : 4.050 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: A 24 ASP cc_start: 0.8589 (m-30) cc_final: 0.8278 (m-30) REVERT: A 52 SER cc_start: 0.9480 (t) cc_final: 0.9092 (p) REVERT: A 118 LYS cc_start: 0.7933 (tppt) cc_final: 0.7729 (tptt) REVERT: A 143 TYR cc_start: 0.8576 (m-80) cc_final: 0.8244 (m-80) REVERT: A 167 GLU cc_start: 0.8414 (tp30) cc_final: 0.7787 (tm-30) REVERT: A 191 LYS cc_start: 0.7994 (ttmt) cc_final: 0.7671 (ttpp) REVERT: A 244 ASP cc_start: 0.8160 (p0) cc_final: 0.7870 (p0) REVERT: A 246 GLN cc_start: 0.9164 (pm20) cc_final: 0.8674 (pm20) REVERT: A 291 LYS cc_start: 0.8442 (tttt) cc_final: 0.7817 (ttpp) REVERT: F 99 PRO cc_start: 0.6309 (Cg_endo) cc_final: 0.6105 (Cg_exo) REVERT: F 113 MET cc_start: 0.6306 (mmm) cc_final: 0.6030 (mmm) REVERT: F 433 GLU cc_start: 0.7914 (tt0) cc_final: 0.7309 (tm-30) REVERT: F 439 MET cc_start: 0.7576 (ttp) cc_final: 0.6951 (tmm) REVERT: F 484 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8189 (tppt) REVERT: F 526 LYS cc_start: 0.7294 (mmtt) cc_final: 0.6994 (mmtt) REVERT: F 537 GLU cc_start: 0.8105 (tp30) cc_final: 0.7710 (tp30) REVERT: F 776 MET cc_start: 0.4729 (ttm) cc_final: 0.4439 (ptp) REVERT: B 61 LYS cc_start: 0.7977 (mttt) cc_final: 0.7720 (mtmt) REVERT: B 82 MET cc_start: 0.7113 (mmm) cc_final: 0.6637 (tmm) REVERT: B 136 ILE cc_start: 0.8892 (mt) cc_final: 0.8286 (tt) REVERT: B 140 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8682 (mm) REVERT: B 202 THR cc_start: 0.8489 (m) cc_final: 0.7936 (p) REVERT: B 205 GLU cc_start: 0.6624 (mp0) cc_final: 0.5230 (mp0) REVERT: B 317 ILE cc_start: 0.8355 (tp) cc_final: 0.7939 (tt) REVERT: B 355 MET cc_start: 0.9060 (mmm) cc_final: 0.8683 (mmt) REVERT: B 360 GLN cc_start: 0.8261 (tm-30) cc_final: 0.8060 (tm-30) REVERT: G 109 TYR cc_start: 0.4754 (t80) cc_final: 0.4441 (t80) REVERT: G 117 TYR cc_start: 0.5933 (m-80) cc_final: 0.5446 (m-80) REVERT: G 280 GLU cc_start: 0.5112 (mt-10) cc_final: 0.4778 (tt0) REVERT: G 313 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7337 (mm) REVERT: G 357 MET cc_start: 0.6242 (mmm) cc_final: 0.5334 (mmm) REVERT: G 489 PHE cc_start: 0.5511 (t80) cc_final: 0.5223 (t80) REVERT: G 546 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7350 (mtp) REVERT: C 80 ASP cc_start: 0.7911 (t70) cc_final: 0.7387 (t0) REVERT: C 118 LYS cc_start: 0.7298 (tptt) cc_final: 0.7047 (tptt) REVERT: C 132 MET cc_start: 0.8968 (ppp) cc_final: 0.8161 (ppp) REVERT: C 143 TYR cc_start: 0.8499 (m-80) cc_final: 0.7852 (m-80) REVERT: C 161 HIS cc_start: 0.8747 (p90) cc_final: 0.8234 (p90) REVERT: C 167 GLU cc_start: 0.9125 (tp30) cc_final: 0.8415 (tp30) REVERT: C 291 LYS cc_start: 0.8014 (tptt) cc_final: 0.7456 (mtpt) REVERT: C 296 ASN cc_start: 0.8869 (m-40) cc_final: 0.8603 (m-40) REVERT: C 328 LYS cc_start: 0.7911 (tttt) cc_final: 0.7415 (tptt) REVERT: C 351 THR cc_start: 0.8790 (p) cc_final: 0.8459 (t) REVERT: H 163 GLN cc_start: 0.6445 (tp40) cc_final: 0.6216 (tp40) REVERT: H 170 GLU cc_start: 0.7625 (tt0) cc_final: 0.6795 (pt0) REVERT: H 172 GLN cc_start: 0.7363 (mm-40) cc_final: 0.7040 (mm-40) REVERT: H 222 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6825 (tt0) REVERT: H 268 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8104 (tt) REVERT: H 281 ARG cc_start: 0.6100 (mtp-110) cc_final: 0.5454 (mtp180) REVERT: H 357 MET cc_start: 0.7641 (mmm) cc_final: 0.7072 (mtt) REVERT: H 434 LYS cc_start: 0.7242 (mttp) cc_final: 0.6851 (mmtm) REVERT: H 436 PHE cc_start: 0.7899 (t80) cc_final: 0.7416 (t80) REVERT: H 473 PHE cc_start: 0.7760 (t80) cc_final: 0.7554 (t80) REVERT: H 553 TYR cc_start: 0.8275 (m-80) cc_final: 0.7878 (m-80) REVERT: H 595 GLN cc_start: 0.8686 (tp40) cc_final: 0.8367 (tp40) REVERT: H 656 ASN cc_start: 0.8223 (m-40) cc_final: 0.7657 (m-40) REVERT: H 659 MET cc_start: 0.7791 (tpp) cc_final: 0.7437 (mmm) REVERT: E 52 SER cc_start: 0.9180 (t) cc_final: 0.8893 (p) REVERT: E 57 GLU cc_start: 0.8042 (pt0) cc_final: 0.7700 (pt0) REVERT: E 61 LYS cc_start: 0.8473 (mptm) cc_final: 0.8243 (mptt) REVERT: E 195 GLU cc_start: 0.8308 (tt0) cc_final: 0.7915 (tp30) REVERT: E 211 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7893 (t0) REVERT: E 284 LYS cc_start: 0.8647 (tppp) cc_final: 0.8435 (tppt) REVERT: E 291 LYS cc_start: 0.7955 (tttt) cc_final: 0.7733 (tttt) REVERT: E 296 ASN cc_start: 0.8677 (m-40) cc_final: 0.8305 (m-40) REVERT: E 325 MET cc_start: 0.8537 (tpp) cc_final: 0.8012 (tpp) REVERT: E 361 GLU cc_start: 0.8929 (tp30) cc_final: 0.8505 (tp30) REVERT: E 372 ARG cc_start: 0.8353 (ttm-80) cc_final: 0.8064 (ttm-80) REVERT: D 50 LYS cc_start: 0.8812 (mtmm) cc_final: 0.8382 (mtpt) REVERT: D 82 MET cc_start: 0.8438 (mmm) cc_final: 0.8191 (mmm) REVERT: D 118 LYS cc_start: 0.7906 (tptt) cc_final: 0.7402 (mttp) REVERT: D 167 GLU cc_start: 0.8528 (tp30) cc_final: 0.8054 (tp30) REVERT: D 205 GLU cc_start: 0.6575 (mp0) cc_final: 0.6282 (mp0) REVERT: D 291 LYS cc_start: 0.8634 (tttt) cc_final: 0.8000 (ttpp) REVERT: D 296 ASN cc_start: 0.8663 (m-40) cc_final: 0.8213 (m-40) REVERT: D 313 MET cc_start: 0.7834 (tpp) cc_final: 0.7544 (tpt) REVERT: D 316 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7811 (mm-30) REVERT: D 346 LEU cc_start: 0.8703 (tp) cc_final: 0.8478 (mp) REVERT: D 355 MET cc_start: 0.9257 (mmm) cc_final: 0.8993 (mmm) REVERT: D 360 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8339 (tm-30) REVERT: D 361 GLU cc_start: 0.8019 (tt0) cc_final: 0.7473 (tp30) outliers start: 140 outliers final: 79 residues processed: 913 average time/residue: 0.4598 time to fit residues: 674.2867 Evaluate side-chains 873 residues out of total 3497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 787 time to evaluate : 3.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 614 LEU Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 353 THR Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 408 ASN Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 537 GLU Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 547 THR Chi-restraints excluded: chain G residue 651 HIS Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 674 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain H residue 239 ASP Chi-restraints excluded: chain H residue 267 LEU Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 538 CYS Chi-restraints excluded: chain H residue 557 LEU Chi-restraints excluded: chain H residue 601 LEU Chi-restraints excluded: chain H residue 674 ILE Chi-restraints excluded: chain H residue 702 ILE Chi-restraints excluded: chain H residue 761 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 137 GLN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 348 optimal weight: 8.9990 chunk 237 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 311 optimal weight: 0.8980 chunk 172 optimal weight: 9.9990 chunk 357 optimal weight: 6.9990 chunk 289 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 213 optimal weight: 8.9990 chunk 375 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 GLN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS ** F 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 219 GLN ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 475 GLN ** F 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 645 GLN F 666 HIS ** F 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN G 75 GLN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 645 GLN G 711 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 401 HIS H 661 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN D 41 GLN D 49 GLN D 87 HIS ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34619 Z= 0.238 Angle : 0.662 9.927 46858 Z= 0.324 Chirality : 0.044 0.209 5197 Planarity : 0.004 0.046 6060 Dihedral : 6.092 82.065 4766 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.74 % Allowed : 18.05 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.13), residues: 4052 helix: -0.81 (0.12), residues: 1654 sheet: -2.12 (0.21), residues: 563 loop : -1.19 (0.15), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP E 340 HIS 0.019 0.002 HIS D 87 PHE 0.025 0.002 PHE H 465 TYR 0.032 0.002 TYR F 164 ARG 0.009 0.001 ARG H 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 3497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 817 time to evaluate : 3.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8496 (m-30) cc_final: 0.8060 (m-30) REVERT: A 52 SER cc_start: 0.9458 (t) cc_final: 0.9097 (p) REVERT: A 111 ASN cc_start: 0.8719 (m-40) cc_final: 0.8263 (m-40) REVERT: A 118 LYS cc_start: 0.7836 (tppt) cc_final: 0.7618 (tppt) REVERT: A 143 TYR cc_start: 0.8535 (m-80) cc_final: 0.8307 (m-80) REVERT: A 157 ASP cc_start: 0.8268 (t0) cc_final: 0.8061 (t0) REVERT: A 167 GLU cc_start: 0.8382 (tp30) cc_final: 0.7724 (tm-30) REVERT: A 191 LYS cc_start: 0.8040 (ttmt) cc_final: 0.7622 (ttpp) REVERT: A 198 TYR cc_start: 0.8570 (m-80) cc_final: 0.7932 (m-80) REVERT: A 283 MET cc_start: 0.8194 (mmm) cc_final: 0.7936 (mmp) REVERT: A 291 LYS cc_start: 0.8395 (tttt) cc_final: 0.7830 (ttpp) REVERT: F 17 ARG cc_start: 0.5501 (tpt170) cc_final: 0.5117 (tpt170) REVERT: F 99 PRO cc_start: 0.5821 (Cg_endo) cc_final: 0.5518 (Cg_exo) REVERT: F 272 ARG cc_start: 0.7615 (tpp-160) cc_final: 0.7328 (mmt-90) REVERT: F 280 GLU cc_start: 0.7633 (mt-10) cc_final: 0.6776 (mt-10) REVERT: F 330 MET cc_start: 0.7161 (ttm) cc_final: 0.6888 (ttm) REVERT: F 388 MET cc_start: 0.7356 (mpp) cc_final: 0.6565 (pmm) REVERT: F 433 GLU cc_start: 0.7859 (tt0) cc_final: 0.7297 (tm-30) REVERT: F 439 MET cc_start: 0.7397 (ttp) cc_final: 0.6979 (tmm) REVERT: F 484 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8164 (tttt) REVERT: F 526 LYS cc_start: 0.7333 (mmtt) cc_final: 0.7099 (mmtt) REVERT: F 537 GLU cc_start: 0.7907 (tp30) cc_final: 0.7490 (tp30) REVERT: F 709 PHE cc_start: 0.6205 (m-10) cc_final: 0.5801 (m-80) REVERT: F 774 GLU cc_start: 0.5926 (tm-30) cc_final: 0.5694 (tm-30) REVERT: B 61 LYS cc_start: 0.7846 (mttt) cc_final: 0.7645 (mtmt) REVERT: B 82 MET cc_start: 0.7070 (mmm) cc_final: 0.6650 (tmm) REVERT: B 136 ILE cc_start: 0.8853 (mt) cc_final: 0.8622 (mt) REVERT: B 202 THR cc_start: 0.8540 (m) cc_final: 0.8100 (p) REVERT: B 205 GLU cc_start: 0.6634 (mp0) cc_final: 0.5360 (mp0) REVERT: B 217 CYS cc_start: 0.8154 (m) cc_final: 0.7796 (m) REVERT: B 305 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8332 (tpp) REVERT: B 317 ILE cc_start: 0.8257 (tp) cc_final: 0.7843 (tt) REVERT: B 355 MET cc_start: 0.9031 (mmm) cc_final: 0.8689 (mmt) REVERT: B 374 CYS cc_start: 0.7203 (p) cc_final: 0.6834 (m) REVERT: G 280 GLU cc_start: 0.5159 (mt-10) cc_final: 0.4735 (tt0) REVERT: G 357 MET cc_start: 0.6257 (mmm) cc_final: 0.5388 (mmm) REVERT: G 408 ASN cc_start: 0.7849 (OUTLIER) cc_final: 0.7595 (m-40) REVERT: G 489 PHE cc_start: 0.5525 (t80) cc_final: 0.5196 (t80) REVERT: G 528 MET cc_start: 0.8467 (mmm) cc_final: 0.8066 (tpp) REVERT: G 778 ASP cc_start: 0.6473 (m-30) cc_final: 0.6098 (m-30) REVERT: C 80 ASP cc_start: 0.8103 (t70) cc_final: 0.7581 (t0) REVERT: C 91 TYR cc_start: 0.8858 (m-80) cc_final: 0.8508 (m-10) REVERT: C 118 LYS cc_start: 0.7337 (tptt) cc_final: 0.7065 (tptt) REVERT: C 132 MET cc_start: 0.8965 (ppp) cc_final: 0.8159 (ppp) REVERT: C 143 TYR cc_start: 0.8382 (m-80) cc_final: 0.7963 (m-80) REVERT: C 167 GLU cc_start: 0.9091 (tp30) cc_final: 0.8392 (tp30) REVERT: C 244 ASP cc_start: 0.8978 (p0) cc_final: 0.8442 (p0) REVERT: C 296 ASN cc_start: 0.8830 (m-40) cc_final: 0.8529 (m-40) REVERT: C 328 LYS cc_start: 0.7965 (tttt) cc_final: 0.7434 (tptt) REVERT: H 92 MET cc_start: 0.4182 (OUTLIER) cc_final: 0.3823 (tpt) REVERT: H 172 GLN cc_start: 0.7376 (mm-40) cc_final: 0.6719 (mm-40) REVERT: H 281 ARG cc_start: 0.5853 (mtp-110) cc_final: 0.4695 (mtp180) REVERT: H 357 MET cc_start: 0.7601 (mmm) cc_final: 0.7024 (mtt) REVERT: H 359 PHE cc_start: 0.6556 (OUTLIER) cc_final: 0.6248 (m-10) REVERT: H 434 LYS cc_start: 0.7309 (mttp) cc_final: 0.6834 (mmtm) REVERT: H 451 GLN cc_start: 0.7538 (mp-120) cc_final: 0.7161 (mp10) REVERT: H 486 GLN cc_start: 0.7973 (tp40) cc_final: 0.7693 (tp-100) REVERT: H 553 TYR cc_start: 0.8130 (m-80) cc_final: 0.7778 (m-80) REVERT: H 565 LYS cc_start: 0.8672 (mmmt) cc_final: 0.8185 (mmmt) REVERT: H 666 HIS cc_start: 0.6806 (t70) cc_final: 0.6534 (t-170) REVERT: E 52 SER cc_start: 0.9158 (t) cc_final: 0.8900 (p) REVERT: E 143 TYR cc_start: 0.8041 (m-80) cc_final: 0.7574 (m-80) REVERT: E 195 GLU cc_start: 0.8328 (tt0) cc_final: 0.8059 (tp30) REVERT: E 284 LYS cc_start: 0.8560 (tppp) cc_final: 0.8156 (tppt) REVERT: E 291 LYS cc_start: 0.7895 (tttt) cc_final: 0.7688 (tttt) REVERT: E 296 ASN cc_start: 0.8566 (m-40) cc_final: 0.8289 (m-40) REVERT: E 325 MET cc_start: 0.8335 (tpp) cc_final: 0.7897 (tpp) REVERT: E 361 GLU cc_start: 0.8688 (tp30) cc_final: 0.8282 (tp30) REVERT: E 372 ARG cc_start: 0.8305 (ttm-80) cc_final: 0.8028 (ttm-80) REVERT: D 50 LYS cc_start: 0.8712 (mtmm) cc_final: 0.8291 (mtpt) REVERT: D 99 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8130 (mt-10) REVERT: D 118 LYS cc_start: 0.7820 (tptt) cc_final: 0.7271 (mttp) REVERT: D 167 GLU cc_start: 0.8525 (tp30) cc_final: 0.8002 (tp30) REVERT: D 205 GLU cc_start: 0.6602 (mp0) cc_final: 0.6389 (mp0) REVERT: D 207 GLU cc_start: 0.8647 (mp0) cc_final: 0.8417 (mp0) REVERT: D 253 GLU cc_start: 0.8072 (mp0) cc_final: 0.7851 (mp0) REVERT: D 291 LYS cc_start: 0.8576 (tttt) cc_final: 0.7929 (ttpp) REVERT: D 296 ASN cc_start: 0.8589 (m-40) cc_final: 0.8133 (m-40) REVERT: D 313 MET cc_start: 0.7717 (tpp) cc_final: 0.7428 (tpt) REVERT: D 316 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7764 (mm-30) REVERT: D 355 MET cc_start: 0.9267 (mmm) cc_final: 0.8976 (mmm) REVERT: D 360 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8201 (tm-30) REVERT: D 361 GLU cc_start: 0.8124 (tt0) cc_final: 0.7550 (tp30) outliers start: 126 outliers final: 80 residues processed: 879 average time/residue: 0.4522 time to fit residues: 641.5592 Evaluate side-chains 841 residues out of total 3497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 756 time to evaluate : 3.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 416 ASN Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 538 CYS Chi-restraints excluded: chain F residue 545 ASP Chi-restraints excluded: chain F residue 568 ASN Chi-restraints excluded: chain F residue 614 LEU Chi-restraints excluded: chain F residue 684 ILE Chi-restraints excluded: chain F residue 691 HIS Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain G residue 276 GLN Chi-restraints excluded: chain G residue 391 ASN Chi-restraints excluded: chain G residue 408 ASN Chi-restraints excluded: chain G residue 446 THR Chi-restraints excluded: chain G residue 462 ILE Chi-restraints excluded: chain G residue 471 ASN Chi-restraints excluded: chain G residue 645 GLN Chi-restraints excluded: chain G residue 651 HIS Chi-restraints excluded: chain G residue 673 ILE Chi-restraints excluded: chain G residue 674 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 220 ILE Chi-restraints excluded: chain H residue 267 LEU Chi-restraints excluded: chain H residue 353 THR Chi-restraints excluded: chain H residue 359 PHE Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 457 ILE Chi-restraints excluded: chain H residue 538 CYS Chi-restraints excluded: chain H residue 601 LEU Chi-restraints excluded: chain H residue 674 ILE Chi-restraints excluded: chain H residue 702 ILE Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 137 GLN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 335 ARG Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 140 optimal weight: 9.9990 chunk 376 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 245 optimal weight: 3.9990 chunk 103 optimal weight: 0.1980 chunk 418 optimal weight: 30.0000 chunk 347 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS ** F 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 475 GLN ** F 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 691 HIS H 126 ASN ** H 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 222 GLN ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 49 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34619 Z= 0.272 Angle : 0.675 12.716 46858 Z= 0.329 Chirality : 0.044 0.196 5197 Planarity : 0.004 0.044 6060 Dihedral : 6.030 81.831 4766 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.11 % Allowed : 18.73 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.13), residues: 4052 helix: -0.66 (0.12), residues: 1666 sheet: -2.03 (0.21), residues: 563 loop : -1.21 (0.15), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP E 340 HIS 0.026 0.002 HIS A 275 PHE 0.024 0.002 PHE F 489 TYR 0.032 0.002 TYR F 164 ARG 0.009 0.001 ARG F 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 3497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 802 time to evaluate : 4.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8430 (m-30) cc_final: 0.8085 (m-30) REVERT: A 52 SER cc_start: 0.9443 (t) cc_final: 0.9058 (p) REVERT: A 107 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7259 (tm-30) REVERT: A 111 ASN cc_start: 0.8544 (m-40) cc_final: 0.8239 (m-40) REVERT: A 118 LYS cc_start: 0.7974 (tppt) cc_final: 0.7634 (tppt) REVERT: A 143 TYR cc_start: 0.8555 (m-80) cc_final: 0.8327 (m-80) REVERT: A 167 GLU cc_start: 0.8422 (tp30) cc_final: 0.7763 (tm-30) REVERT: A 191 LYS cc_start: 0.8116 (ttmt) cc_final: 0.7592 (ttpp) REVERT: A 198 TYR cc_start: 0.8566 (m-80) cc_final: 0.7912 (m-80) REVERT: A 291 LYS cc_start: 0.8407 (tttt) cc_final: 0.7853 (ttpp) REVERT: F 99 PRO cc_start: 0.6194 (Cg_endo) cc_final: 0.5795 (Cg_exo) REVERT: F 330 MET cc_start: 0.7201 (ttm) cc_final: 0.6941 (ttm) REVERT: F 362 MET cc_start: 0.7091 (tpt) cc_final: 0.6487 (mtt) REVERT: F 388 MET cc_start: 0.7328 (mpp) cc_final: 0.6559 (pmm) REVERT: F 433 GLU cc_start: 0.7889 (tt0) cc_final: 0.7334 (tm-30) REVERT: F 439 MET cc_start: 0.7649 (ttp) cc_final: 0.7126 (tmm) REVERT: F 470 PHE cc_start: 0.7318 (t80) cc_final: 0.6922 (t80) REVERT: F 484 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8188 (tttt) REVERT: F 526 LYS cc_start: 0.7328 (mmtt) cc_final: 0.7112 (mmtt) REVERT: F 537 GLU cc_start: 0.7973 (tp30) cc_final: 0.7435 (tp30) REVERT: F 597 ASN cc_start: 0.8034 (t0) cc_final: 0.7805 (t0) REVERT: F 709 PHE cc_start: 0.6546 (m-10) cc_final: 0.6341 (m-10) REVERT: B 61 LYS cc_start: 0.7840 (mttt) cc_final: 0.7589 (mtmt) REVERT: B 64 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8099 (tp) REVERT: B 82 MET cc_start: 0.7165 (mmm) cc_final: 0.6745 (tmm) REVERT: B 202 THR cc_start: 0.8596 (m) cc_final: 0.8124 (p) REVERT: B 205 GLU cc_start: 0.6648 (mp0) cc_final: 0.5420 (mp0) REVERT: B 217 CYS cc_start: 0.8116 (m) cc_final: 0.7774 (m) REVERT: B 313 MET cc_start: 0.7666 (ttm) cc_final: 0.7425 (ttm) REVERT: B 317 ILE cc_start: 0.8146 (tp) cc_final: 0.7721 (tt) REVERT: B 374 CYS cc_start: 0.7273 (p) cc_final: 0.6950 (m) REVERT: G 117 TYR cc_start: 0.5816 (m-80) cc_final: 0.5426 (m-80) REVERT: G 280 GLU cc_start: 0.5220 (mt-10) cc_final: 0.4738 (tt0) REVERT: G 357 MET cc_start: 0.6452 (mmm) cc_final: 0.5599 (mmm) REVERT: G 408 ASN cc_start: 0.7800 (OUTLIER) cc_final: 0.7581 (m-40) REVERT: G 429 LYS cc_start: 0.7652 (mtmt) cc_final: 0.7168 (mtmm) REVERT: G 489 PHE cc_start: 0.5535 (t80) cc_final: 0.5271 (t80) REVERT: G 528 MET cc_start: 0.8469 (mmm) cc_final: 0.8215 (tpp) REVERT: G 659 MET cc_start: 0.7065 (mmp) cc_final: 0.6444 (mmp) REVERT: G 721 ARG cc_start: 0.5141 (tpp-160) cc_final: 0.4797 (mmm160) REVERT: G 722 TYR cc_start: 0.4831 (m-80) cc_final: 0.4496 (m-80) REVERT: G 778 ASP cc_start: 0.6256 (m-30) cc_final: 0.6000 (m-30) REVERT: C 80 ASP cc_start: 0.8090 (t70) cc_final: 0.7594 (t0) REVERT: C 91 TYR cc_start: 0.8884 (m-80) cc_final: 0.8549 (m-10) REVERT: C 118 LYS cc_start: 0.7340 (tptt) cc_final: 0.7089 (tptt) REVERT: C 132 MET cc_start: 0.8966 (ppp) cc_final: 0.8170 (ppp) REVERT: C 143 TYR cc_start: 0.8379 (m-80) cc_final: 0.8028 (m-80) REVERT: C 167 GLU cc_start: 0.9111 (tp30) cc_final: 0.8387 (tp30) REVERT: C 191 LYS cc_start: 0.8264 (ttmm) cc_final: 0.8049 (ttpp) REVERT: C 244 ASP cc_start: 0.9001 (p0) cc_final: 0.8476 (p0) REVERT: C 253 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: C 296 ASN cc_start: 0.8831 (m-40) cc_final: 0.8493 (m-40) REVERT: C 328 LYS cc_start: 0.7955 (tttt) cc_final: 0.7439 (tptt) REVERT: H 6 MET cc_start: 0.2918 (tpt) cc_final: 0.2104 (ppp) REVERT: H 92 MET cc_start: 0.4240 (OUTLIER) cc_final: 0.3875 (tpt) REVERT: H 172 GLN cc_start: 0.7375 (mm-40) cc_final: 0.6786 (mm-40) REVERT: H 281 ARG cc_start: 0.5847 (mtp-110) cc_final: 0.4375 (mtp85) REVERT: H 434 LYS cc_start: 0.7422 (mttp) cc_final: 0.6955 (mmtm) REVERT: H 451 GLN cc_start: 0.7608 (mp-120) cc_final: 0.7239 (mp10) REVERT: H 553 TYR cc_start: 0.8106 (m-80) cc_final: 0.7822 (m-80) REVERT: H 659 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.6869 (tmm) REVERT: H 666 HIS cc_start: 0.6898 (t70) cc_final: 0.6571 (t-90) REVERT: E 51 ASP cc_start: 0.8372 (t0) cc_final: 0.7737 (t70) REVERT: E 52 SER cc_start: 0.9126 (t) cc_final: 0.8845 (p) REVERT: E 100 GLU cc_start: 0.9103 (pt0) cc_final: 0.8565 (pm20) REVERT: E 143 TYR cc_start: 0.8054 (m-80) cc_final: 0.7572 (m-80) REVERT: E 195 GLU cc_start: 0.8386 (tt0) cc_final: 0.8009 (mt-10) REVERT: E 276 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7354 (tm-30) REVERT: E 284 LYS cc_start: 0.8796 (tppp) cc_final: 0.8320 (tppt) REVERT: E 296 ASN cc_start: 0.8526 (m-40) cc_final: 0.8262 (m-40) REVERT: E 325 MET cc_start: 0.8476 (tpp) cc_final: 0.7797 (tpp) REVERT: E 328 LYS cc_start: 0.7937 (tttt) cc_final: 0.7268 (ttpp) REVERT: E 361 GLU cc_start: 0.8719 (tp30) cc_final: 0.8327 (tp30) REVERT: E 372 ARG cc_start: 0.8323 (ttm-80) cc_final: 0.8046 (ttm-80) REVERT: D 50 LYS cc_start: 0.8718 (mtmm) cc_final: 0.8314 (mtpt) REVERT: D 100 GLU cc_start: 0.8419 (pm20) cc_final: 0.8178 (pm20) REVERT: D 118 LYS cc_start: 0.7853 (tptt) cc_final: 0.7368 (mttp) REVERT: D 161 HIS cc_start: 0.8793 (p-80) cc_final: 0.8574 (p-80) REVERT: D 167 GLU cc_start: 0.8538 (tp30) cc_final: 0.8026 (tp30) REVERT: D 207 GLU cc_start: 0.8573 (mp0) cc_final: 0.8359 (mp0) REVERT: D 246 GLN cc_start: 0.8557 (pm20) cc_final: 0.8244 (pm20) REVERT: D 253 GLU cc_start: 0.8053 (mp0) cc_final: 0.7821 (mp0) REVERT: D 291 LYS cc_start: 0.8584 (tttt) cc_final: 0.7955 (ttpp) REVERT: D 296 ASN cc_start: 0.8478 (m-40) cc_final: 0.8044 (m-40) REVERT: D 313 MET cc_start: 0.7786 (tpp) cc_final: 0.7491 (tpt) REVERT: D 316 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7689 (mm-30) REVERT: D 355 MET cc_start: 0.9280 (mmm) cc_final: 0.8996 (mmm) REVERT: D 360 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8222 (tm-30) REVERT: D 361 GLU cc_start: 0.8212 (tt0) cc_final: 0.7581 (tp30) outliers start: 139 outliers final: 95 residues processed: 877 average time/residue: 0.4643 time to fit residues: 661.2213 Evaluate side-chains 868 residues out of total 3497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 767 time to evaluate : 3.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 410 TYR Chi-restraints excluded: chain F residue 416 ASN Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 545 ASP Chi-restraints excluded: chain F residue 568 ASN Chi-restraints excluded: chain F residue 614 LEU Chi-restraints excluded: chain F residue 676 ASN Chi-restraints excluded: chain F residue 684 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 276 GLN Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 408 ASN Chi-restraints excluded: chain G residue 435 MET Chi-restraints excluded: chain G residue 446 THR Chi-restraints excluded: chain G residue 462 ILE Chi-restraints excluded: chain G residue 537 GLU Chi-restraints excluded: chain G residue 540 PHE Chi-restraints excluded: chain G residue 568 ASN Chi-restraints excluded: chain G residue 651 HIS Chi-restraints excluded: chain G residue 674 ILE Chi-restraints excluded: chain G residue 695 CYS Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 267 LEU Chi-restraints excluded: chain H residue 353 THR Chi-restraints excluded: chain H residue 382 ASP Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 457 ILE Chi-restraints excluded: chain H residue 538 CYS Chi-restraints excluded: chain H residue 557 LEU Chi-restraints excluded: chain H residue 601 LEU Chi-restraints excluded: chain H residue 659 MET Chi-restraints excluded: chain H residue 674 ILE Chi-restraints excluded: chain H residue 702 ILE Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 335 ARG Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 403 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 chunk 305 optimal weight: 6.9990 chunk 237 optimal weight: 8.9990 chunk 352 optimal weight: 10.0000 chunk 233 optimal weight: 9.9990 chunk 417 optimal weight: 30.0000 chunk 261 optimal weight: 3.9990 chunk 254 optimal weight: 0.6980 chunk 192 optimal weight: 20.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 GLN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS ** F 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 GLN ** H 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 ASN ** H 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 486 GLN H 661 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS D 314 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.6482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 34619 Z= 0.298 Angle : 0.692 11.837 46858 Z= 0.337 Chirality : 0.045 0.204 5197 Planarity : 0.004 0.057 6060 Dihedral : 6.050 80.562 4766 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.08 % Allowed : 19.30 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.13), residues: 4052 helix: -0.60 (0.12), residues: 1675 sheet: -1.88 (0.22), residues: 530 loop : -1.26 (0.15), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP E 340 HIS 0.024 0.002 HIS A 275 PHE 0.027 0.002 PHE F 489 TYR 0.029 0.002 TYR F 164 ARG 0.008 0.001 ARG F 17 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 3497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 786 time to evaluate : 3.520 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: A 52 SER cc_start: 0.9434 (t) cc_final: 0.9055 (p) REVERT: A 107 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7265 (tm-30) REVERT: A 111 ASN cc_start: 0.8554 (m-40) cc_final: 0.8200 (m-40) REVERT: A 118 LYS cc_start: 0.7862 (tppt) cc_final: 0.7552 (tppt) REVERT: A 143 TYR cc_start: 0.8547 (m-80) cc_final: 0.8328 (m-80) REVERT: A 167 GLU cc_start: 0.8440 (tp30) cc_final: 0.7775 (tm-30) REVERT: A 191 LYS cc_start: 0.8122 (ttmt) cc_final: 0.7575 (ttpp) REVERT: A 198 TYR cc_start: 0.8501 (m-80) cc_final: 0.7884 (m-80) REVERT: A 283 MET cc_start: 0.8051 (mmm) cc_final: 0.7842 (mmp) REVERT: A 291 LYS cc_start: 0.8359 (tttt) cc_final: 0.7860 (ttpp) REVERT: F 99 PRO cc_start: 0.6072 (Cg_endo) cc_final: 0.5618 (Cg_exo) REVERT: F 312 PHE cc_start: 0.6174 (m-80) cc_final: 0.5569 (m-80) REVERT: F 330 MET cc_start: 0.7196 (ttm) cc_final: 0.6966 (ttm) REVERT: F 388 MET cc_start: 0.7512 (mpp) cc_final: 0.6698 (pmm) REVERT: F 410 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.7783 (m-10) REVERT: F 433 GLU cc_start: 0.7898 (tt0) cc_final: 0.7343 (tm-30) REVERT: F 439 MET cc_start: 0.7677 (ttp) cc_final: 0.7171 (tmm) REVERT: F 470 PHE cc_start: 0.7316 (t80) cc_final: 0.6915 (t80) REVERT: F 484 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8197 (tttt) REVERT: F 526 LYS cc_start: 0.7255 (mmtt) cc_final: 0.7048 (mmtt) REVERT: F 537 GLU cc_start: 0.8018 (tp30) cc_final: 0.7758 (tp30) REVERT: F 597 ASN cc_start: 0.7973 (t0) cc_final: 0.7749 (t0) REVERT: F 688 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7535 (mp) REVERT: F 709 PHE cc_start: 0.6527 (m-10) cc_final: 0.6269 (m-10) REVERT: F 722 TYR cc_start: 0.6335 (m-80) cc_final: 0.6012 (m-80) REVERT: F 765 PHE cc_start: 0.6251 (m-80) cc_final: 0.5928 (m-80) REVERT: F 776 MET cc_start: 0.3932 (ptp) cc_final: 0.3729 (pmm) REVERT: B 61 LYS cc_start: 0.7801 (mttt) cc_final: 0.7473 (mtmt) REVERT: B 64 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8147 (tp) REVERT: B 82 MET cc_start: 0.7236 (mmm) cc_final: 0.6786 (tmm) REVERT: B 169 TYR cc_start: 0.8999 (m-80) cc_final: 0.8772 (m-10) REVERT: B 217 CYS cc_start: 0.8111 (m) cc_final: 0.7750 (m) REVERT: B 313 MET cc_start: 0.7716 (ttm) cc_final: 0.7502 (ttm) REVERT: B 317 ILE cc_start: 0.8180 (tp) cc_final: 0.7736 (tt) REVERT: B 374 CYS cc_start: 0.7168 (p) cc_final: 0.6890 (m) REVERT: G 117 TYR cc_start: 0.5938 (m-80) cc_final: 0.5187 (m-80) REVERT: G 174 ILE cc_start: 0.8525 (mt) cc_final: 0.8308 (mm) REVERT: G 280 GLU cc_start: 0.5322 (mt-10) cc_final: 0.4795 (tt0) REVERT: G 357 MET cc_start: 0.6536 (mmm) cc_final: 0.5710 (mmm) REVERT: G 365 LYS cc_start: 0.8086 (ttpm) cc_final: 0.7763 (ptpp) REVERT: G 372 GLN cc_start: 0.6444 (mp-120) cc_final: 0.5711 (mp10) REVERT: G 408 ASN cc_start: 0.7818 (OUTLIER) cc_final: 0.7613 (m-40) REVERT: G 429 LYS cc_start: 0.7664 (mtmt) cc_final: 0.7102 (mtmm) REVERT: G 489 PHE cc_start: 0.5505 (t80) cc_final: 0.5289 (t80) REVERT: G 528 MET cc_start: 0.8493 (mmm) cc_final: 0.8253 (tpp) REVERT: G 620 LEU cc_start: 0.5753 (OUTLIER) cc_final: 0.5385 (mp) REVERT: G 659 MET cc_start: 0.7197 (mmp) cc_final: 0.6963 (mmp) REVERT: G 722 TYR cc_start: 0.4779 (m-80) cc_final: 0.4493 (m-80) REVERT: C 80 ASP cc_start: 0.8138 (t70) cc_final: 0.7641 (t0) REVERT: C 118 LYS cc_start: 0.7299 (tptt) cc_final: 0.7073 (tptt) REVERT: C 132 MET cc_start: 0.8942 (ppp) cc_final: 0.8199 (ppp) REVERT: C 143 TYR cc_start: 0.8431 (m-80) cc_final: 0.8100 (m-80) REVERT: C 167 GLU cc_start: 0.9100 (tp30) cc_final: 0.8344 (tp30) REVERT: C 191 LYS cc_start: 0.8325 (ttmm) cc_final: 0.8124 (ttpp) REVERT: C 244 ASP cc_start: 0.9061 (p0) cc_final: 0.8493 (p0) REVERT: C 253 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: C 296 ASN cc_start: 0.8818 (m-40) cc_final: 0.8516 (m-40) REVERT: C 328 LYS cc_start: 0.7989 (tttt) cc_final: 0.7451 (tptt) REVERT: H 6 MET cc_start: 0.3010 (tpt) cc_final: 0.2435 (ppp) REVERT: H 92 MET cc_start: 0.4461 (OUTLIER) cc_final: 0.3989 (tpt) REVERT: H 172 GLN cc_start: 0.7457 (mm-40) cc_final: 0.6881 (mm-40) REVERT: H 281 ARG cc_start: 0.5838 (mtp-110) cc_final: 0.4317 (mtp85) REVERT: H 434 LYS cc_start: 0.7464 (mttp) cc_final: 0.7117 (mmtm) REVERT: H 451 GLN cc_start: 0.7732 (mp-120) cc_final: 0.7319 (mp10) REVERT: H 553 TYR cc_start: 0.8097 (m-80) cc_final: 0.7761 (m-80) REVERT: H 659 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.6716 (tmm) REVERT: H 702 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.7355 (mm) REVERT: E 51 ASP cc_start: 0.8486 (t0) cc_final: 0.7953 (t70) REVERT: E 52 SER cc_start: 0.9124 (t) cc_final: 0.8875 (p) REVERT: E 100 GLU cc_start: 0.9140 (pt0) cc_final: 0.8616 (pm20) REVERT: E 143 TYR cc_start: 0.8045 (m-80) cc_final: 0.7563 (m-80) REVERT: E 195 GLU cc_start: 0.8361 (tt0) cc_final: 0.7957 (mt-10) REVERT: E 276 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7332 (tm-30) REVERT: E 284 LYS cc_start: 0.8783 (tppp) cc_final: 0.8237 (tppt) REVERT: E 291 LYS cc_start: 0.8241 (tttt) cc_final: 0.7646 (mtmt) REVERT: E 296 ASN cc_start: 0.8438 (m-40) cc_final: 0.8136 (m-40) REVERT: E 328 LYS cc_start: 0.7959 (tttt) cc_final: 0.7172 (ttpp) REVERT: E 361 GLU cc_start: 0.8651 (tp30) cc_final: 0.8294 (tp30) REVERT: E 372 ARG cc_start: 0.8350 (ttm-80) cc_final: 0.8080 (ttm-80) REVERT: D 50 LYS cc_start: 0.8702 (mtmm) cc_final: 0.8337 (mtpt) REVERT: D 99 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8042 (mt-10) REVERT: D 100 GLU cc_start: 0.8408 (pm20) cc_final: 0.8126 (pm20) REVERT: D 118 LYS cc_start: 0.7916 (tptt) cc_final: 0.7478 (mttp) REVERT: D 161 HIS cc_start: 0.8831 (p-80) cc_final: 0.8594 (p-80) REVERT: D 167 GLU cc_start: 0.8570 (tp30) cc_final: 0.8043 (tp30) REVERT: D 246 GLN cc_start: 0.8662 (pm20) cc_final: 0.8413 (pm20) REVERT: D 253 GLU cc_start: 0.8060 (mp0) cc_final: 0.7605 (mp0) REVERT: D 291 LYS cc_start: 0.8578 (tttt) cc_final: 0.7958 (ttpp) REVERT: D 296 ASN cc_start: 0.8444 (m-40) cc_final: 0.8038 (m-40) REVERT: D 313 MET cc_start: 0.7809 (tpp) cc_final: 0.7516 (tpt) REVERT: D 316 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7624 (mm-30) REVERT: D 355 MET cc_start: 0.9296 (mmm) cc_final: 0.9027 (mmm) REVERT: D 361 GLU cc_start: 0.8168 (tt0) cc_final: 0.7849 (tp30) outliers start: 138 outliers final: 108 residues processed: 865 average time/residue: 0.4468 time to fit residues: 624.0132 Evaluate side-chains 884 residues out of total 3497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 766 time to evaluate : 3.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 410 TYR Chi-restraints excluded: chain F residue 416 ASN Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 545 ASP Chi-restraints excluded: chain F residue 568 ASN Chi-restraints excluded: chain F residue 614 LEU Chi-restraints excluded: chain F residue 676 ASN Chi-restraints excluded: chain F residue 684 ILE Chi-restraints excluded: chain F residue 688 LEU Chi-restraints excluded: chain F residue 691 HIS Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 276 GLN Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 408 ASN Chi-restraints excluded: chain G residue 435 MET Chi-restraints excluded: chain G residue 446 THR Chi-restraints excluded: chain G residue 462 ILE Chi-restraints excluded: chain G residue 471 ASN Chi-restraints excluded: chain G residue 485 LEU Chi-restraints excluded: chain G residue 537 GLU Chi-restraints excluded: chain G residue 540 PHE Chi-restraints excluded: chain G residue 547 THR Chi-restraints excluded: chain G residue 568 ASN Chi-restraints excluded: chain G residue 620 LEU Chi-restraints excluded: chain G residue 651 HIS Chi-restraints excluded: chain G residue 660 THR Chi-restraints excluded: chain G residue 674 ILE Chi-restraints excluded: chain G residue 695 CYS Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain H residue 267 LEU Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 353 THR Chi-restraints excluded: chain H residue 382 ASP Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 538 CYS Chi-restraints excluded: chain H residue 557 LEU Chi-restraints excluded: chain H residue 601 LEU Chi-restraints excluded: chain H residue 659 MET Chi-restraints excluded: chain H residue 674 ILE Chi-restraints excluded: chain H residue 702 ILE Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 335 ARG Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 258 optimal weight: 0.3980 chunk 166 optimal weight: 30.0000 chunk 249 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 265 optimal weight: 6.9990 chunk 284 optimal weight: 20.0000 chunk 206 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 chunk 328 optimal weight: 20.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS F 104 ASN ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN ** G 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 691 HIS H 126 ASN ** H 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.6637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34619 Z= 0.256 Angle : 0.667 10.730 46858 Z= 0.326 Chirality : 0.044 0.222 5197 Planarity : 0.004 0.045 6060 Dihedral : 5.922 80.289 4766 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.96 % Allowed : 20.05 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.13), residues: 4052 helix: -0.51 (0.13), residues: 1633 sheet: -1.88 (0.22), residues: 548 loop : -1.15 (0.15), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 340 HIS 0.024 0.002 HIS A 275 PHE 0.029 0.002 PHE F 155 TYR 0.031 0.002 TYR F 164 ARG 0.007 0.001 ARG F 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 3497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 784 time to evaluate : 3.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 SER cc_start: 0.9458 (t) cc_final: 0.9068 (p) REVERT: A 107 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7271 (tm-30) REVERT: A 111 ASN cc_start: 0.8507 (m-40) cc_final: 0.8145 (m-40) REVERT: A 118 LYS cc_start: 0.7801 (tppt) cc_final: 0.7413 (tptt) REVERT: A 167 GLU cc_start: 0.8439 (tp30) cc_final: 0.7861 (tm-30) REVERT: A 191 LYS cc_start: 0.8120 (ttmt) cc_final: 0.7555 (ttpp) REVERT: A 198 TYR cc_start: 0.8423 (m-80) cc_final: 0.7820 (m-80) REVERT: A 283 MET cc_start: 0.7990 (mmm) cc_final: 0.7781 (mmp) REVERT: A 291 LYS cc_start: 0.8332 (tttt) cc_final: 0.7832 (ttpp) REVERT: A 361 GLU cc_start: 0.8717 (tt0) cc_final: 0.8034 (tp30) REVERT: F 99 PRO cc_start: 0.6216 (Cg_endo) cc_final: 0.5692 (Cg_exo) REVERT: F 357 MET cc_start: 0.7637 (mmp) cc_final: 0.7417 (mmt) REVERT: F 362 MET cc_start: 0.7296 (tpt) cc_final: 0.6464 (mtt) REVERT: F 388 MET cc_start: 0.7305 (mpp) cc_final: 0.6693 (pmm) REVERT: F 410 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.7781 (m-10) REVERT: F 433 GLU cc_start: 0.7982 (tt0) cc_final: 0.7388 (tm-30) REVERT: F 439 MET cc_start: 0.7630 (ttp) cc_final: 0.7031 (tmm) REVERT: F 470 PHE cc_start: 0.7246 (t80) cc_final: 0.6883 (t80) REVERT: F 484 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8233 (tttt) REVERT: F 526 LYS cc_start: 0.7277 (mmtt) cc_final: 0.7047 (mmtt) REVERT: F 537 GLU cc_start: 0.8021 (tp30) cc_final: 0.7801 (tp30) REVERT: F 598 LYS cc_start: 0.7480 (mtmt) cc_final: 0.7232 (mtmt) REVERT: F 688 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7538 (mp) REVERT: F 709 PHE cc_start: 0.6702 (m-10) cc_final: 0.6424 (m-10) REVERT: F 765 PHE cc_start: 0.6455 (m-80) cc_final: 0.6195 (m-80) REVERT: B 61 LYS cc_start: 0.7753 (mttt) cc_final: 0.7487 (mtmt) REVERT: B 64 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8108 (tp) REVERT: B 82 MET cc_start: 0.7220 (mmm) cc_final: 0.6778 (tmm) REVERT: B 128 ASN cc_start: 0.8793 (t0) cc_final: 0.8364 (t0) REVERT: B 217 CYS cc_start: 0.8098 (m) cc_final: 0.7747 (m) REVERT: B 305 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8364 (tpp) REVERT: B 313 MET cc_start: 0.7691 (ttm) cc_final: 0.7483 (ttm) REVERT: B 317 ILE cc_start: 0.8142 (tp) cc_final: 0.7702 (tt) REVERT: B 374 CYS cc_start: 0.7179 (p) cc_final: 0.6881 (m) REVERT: G 117 TYR cc_start: 0.5714 (m-80) cc_final: 0.5140 (m-80) REVERT: G 174 ILE cc_start: 0.8607 (mt) cc_final: 0.8384 (mm) REVERT: G 280 GLU cc_start: 0.5278 (mt-10) cc_final: 0.4747 (tt0) REVERT: G 357 MET cc_start: 0.6457 (mmm) cc_final: 0.5544 (mmm) REVERT: G 365 LYS cc_start: 0.8094 (ttpm) cc_final: 0.7830 (ptpp) REVERT: G 372 GLN cc_start: 0.6434 (mp-120) cc_final: 0.5755 (mp10) REVERT: G 429 LYS cc_start: 0.7638 (mtmt) cc_final: 0.7071 (mtmm) REVERT: G 489 PHE cc_start: 0.5611 (t80) cc_final: 0.5360 (t80) REVERT: G 528 MET cc_start: 0.8504 (mmm) cc_final: 0.8303 (tpp) REVERT: G 620 LEU cc_start: 0.5749 (OUTLIER) cc_final: 0.5389 (mp) REVERT: G 721 ARG cc_start: 0.6132 (mmm160) cc_final: 0.5538 (mmm160) REVERT: G 722 TYR cc_start: 0.4877 (m-80) cc_final: 0.4462 (m-80) REVERT: C 80 ASP cc_start: 0.8144 (t70) cc_final: 0.7655 (t0) REVERT: C 91 TYR cc_start: 0.8848 (m-80) cc_final: 0.8515 (m-10) REVERT: C 118 LYS cc_start: 0.7307 (tptt) cc_final: 0.7073 (tptt) REVERT: C 132 MET cc_start: 0.8904 (ppp) cc_final: 0.8185 (ppp) REVERT: C 143 TYR cc_start: 0.8402 (m-80) cc_final: 0.8062 (m-80) REVERT: C 167 GLU cc_start: 0.9084 (tp30) cc_final: 0.8424 (tp30) REVERT: C 191 LYS cc_start: 0.8300 (ttmm) cc_final: 0.8093 (ttpp) REVERT: C 244 ASP cc_start: 0.9020 (p0) cc_final: 0.8463 (p0) REVERT: C 296 ASN cc_start: 0.8787 (m-40) cc_final: 0.8483 (m-40) REVERT: C 328 LYS cc_start: 0.8006 (tttt) cc_final: 0.7558 (tptt) REVERT: C 361 GLU cc_start: 0.8540 (tp30) cc_final: 0.8259 (tp30) REVERT: H 6 MET cc_start: 0.3218 (tpt) cc_final: 0.2290 (ppp) REVERT: H 92 MET cc_start: 0.4519 (OUTLIER) cc_final: 0.3981 (tpt) REVERT: H 172 GLN cc_start: 0.7366 (mm-40) cc_final: 0.7136 (mm-40) REVERT: H 281 ARG cc_start: 0.5773 (mtp-110) cc_final: 0.4679 (mtp180) REVERT: H 362 MET cc_start: 0.7022 (mmm) cc_final: 0.6742 (mmm) REVERT: H 434 LYS cc_start: 0.7450 (mttp) cc_final: 0.7164 (mmtm) REVERT: H 451 GLN cc_start: 0.7853 (mp-120) cc_final: 0.7289 (mp10) REVERT: H 553 TYR cc_start: 0.8062 (m-80) cc_final: 0.7860 (m-80) REVERT: H 659 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.6772 (tmm) REVERT: H 702 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7588 (mm) REVERT: H 752 ASP cc_start: 0.0014 (OUTLIER) cc_final: -0.0445 (p0) REVERT: E 51 ASP cc_start: 0.8505 (t0) cc_final: 0.7974 (t70) REVERT: E 52 SER cc_start: 0.9147 (t) cc_final: 0.8913 (p) REVERT: E 100 GLU cc_start: 0.9126 (pt0) cc_final: 0.8637 (pm20) REVERT: E 143 TYR cc_start: 0.8071 (m-80) cc_final: 0.7595 (m-80) REVERT: E 195 GLU cc_start: 0.8283 (tt0) cc_final: 0.7955 (mt-10) REVERT: E 276 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7302 (tm-30) REVERT: E 284 LYS cc_start: 0.8760 (tppp) cc_final: 0.8227 (tppt) REVERT: E 286 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7827 (m-30) REVERT: E 291 LYS cc_start: 0.8161 (tttt) cc_final: 0.7833 (mttp) REVERT: E 296 ASN cc_start: 0.8365 (m-40) cc_final: 0.8119 (m-40) REVERT: E 328 LYS cc_start: 0.7917 (tttt) cc_final: 0.7131 (ttpp) REVERT: E 361 GLU cc_start: 0.8588 (tp30) cc_final: 0.8298 (tp30) REVERT: E 372 ARG cc_start: 0.8342 (ttm-80) cc_final: 0.8083 (ttm-80) REVERT: D 50 LYS cc_start: 0.8695 (mtmm) cc_final: 0.8359 (mtpt) REVERT: D 118 LYS cc_start: 0.7901 (tptt) cc_final: 0.7451 (mttp) REVERT: D 161 HIS cc_start: 0.8779 (p-80) cc_final: 0.8529 (p-80) REVERT: D 167 GLU cc_start: 0.8556 (tp30) cc_final: 0.8013 (tp30) REVERT: D 253 GLU cc_start: 0.8093 (mp0) cc_final: 0.7709 (mp0) REVERT: D 291 LYS cc_start: 0.8541 (tttt) cc_final: 0.7925 (ttpp) REVERT: D 296 ASN cc_start: 0.8385 (m-40) cc_final: 0.7972 (m-40) REVERT: D 313 MET cc_start: 0.7786 (tpp) cc_final: 0.7552 (tpt) REVERT: D 316 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7670 (mm-30) REVERT: D 326 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7803 (tmtt) REVERT: D 355 MET cc_start: 0.9287 (mmm) cc_final: 0.9019 (mmm) REVERT: D 361 GLU cc_start: 0.8206 (tt0) cc_final: 0.7849 (tp30) outliers start: 134 outliers final: 100 residues processed: 859 average time/residue: 0.4442 time to fit residues: 617.2927 Evaluate side-chains 869 residues out of total 3497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 757 time to evaluate : 3.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 410 TYR Chi-restraints excluded: chain F residue 416 ASN Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 545 ASP Chi-restraints excluded: chain F residue 568 ASN Chi-restraints excluded: chain F residue 614 LEU Chi-restraints excluded: chain F residue 676 ASN Chi-restraints excluded: chain F residue 684 ILE Chi-restraints excluded: chain F residue 688 LEU Chi-restraints excluded: chain F residue 691 HIS Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain F residue 770 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 435 MET Chi-restraints excluded: chain G residue 446 THR Chi-restraints excluded: chain G residue 462 ILE Chi-restraints excluded: chain G residue 471 ASN Chi-restraints excluded: chain G residue 484 LYS Chi-restraints excluded: chain G residue 485 LEU Chi-restraints excluded: chain G residue 540 PHE Chi-restraints excluded: chain G residue 620 LEU Chi-restraints excluded: chain G residue 651 HIS Chi-restraints excluded: chain G residue 674 ILE Chi-restraints excluded: chain G residue 695 CYS Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain H residue 267 LEU Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 382 ASP Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 489 PHE Chi-restraints excluded: chain H residue 538 CYS Chi-restraints excluded: chain H residue 557 LEU Chi-restraints excluded: chain H residue 601 LEU Chi-restraints excluded: chain H residue 659 MET Chi-restraints excluded: chain H residue 662 LEU Chi-restraints excluded: chain H residue 674 ILE Chi-restraints excluded: chain H residue 702 ILE Chi-restraints excluded: chain H residue 752 ASP Chi-restraints excluded: chain H residue 761 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 137 GLN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 335 ARG Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 379 optimal weight: 9.9990 chunk 399 optimal weight: 2.9990 chunk 364 optimal weight: 0.2980 chunk 388 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 169 optimal weight: 20.0000 chunk 305 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 351 optimal weight: 5.9990 chunk 367 optimal weight: 1.9990 chunk 387 optimal weight: 8.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN A 121 GLN A 275 HIS F 126 ASN ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN ** G 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 691 HIS H 126 ASN ** H 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 486 GLN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS D 314 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.6775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 34619 Z= 0.237 Angle : 0.667 11.891 46858 Z= 0.325 Chirality : 0.043 0.212 5197 Planarity : 0.004 0.061 6060 Dihedral : 5.821 79.805 4766 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.74 % Allowed : 20.56 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.13), residues: 4052 helix: -0.43 (0.13), residues: 1627 sheet: -1.78 (0.22), residues: 548 loop : -1.12 (0.15), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 340 HIS 0.026 0.002 HIS A 275 PHE 0.028 0.002 PHE G 488 TYR 0.044 0.002 TYR F 103 ARG 0.009 0.001 ARG G 671 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 3497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 774 time to evaluate : 3.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 SER cc_start: 0.9438 (t) cc_final: 0.9039 (p) REVERT: A 107 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7355 (tm-30) REVERT: A 111 ASN cc_start: 0.8556 (m-40) cc_final: 0.8191 (m-40) REVERT: A 118 LYS cc_start: 0.7823 (tppt) cc_final: 0.7459 (tptt) REVERT: A 167 GLU cc_start: 0.8448 (tp30) cc_final: 0.7856 (tm-30) REVERT: A 191 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7545 (ttpp) REVERT: A 246 GLN cc_start: 0.9099 (pm20) cc_final: 0.8742 (pm20) REVERT: A 283 MET cc_start: 0.7967 (mmm) cc_final: 0.7714 (mmp) REVERT: A 291 LYS cc_start: 0.8310 (tttt) cc_final: 0.7812 (ttpp) REVERT: A 361 GLU cc_start: 0.8764 (tt0) cc_final: 0.8128 (tp30) REVERT: F 362 MET cc_start: 0.7213 (tpt) cc_final: 0.6301 (mtt) REVERT: F 388 MET cc_start: 0.7344 (mpp) cc_final: 0.6853 (pmm) REVERT: F 410 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.7897 (m-10) REVERT: F 433 GLU cc_start: 0.7995 (tt0) cc_final: 0.7375 (tm-30) REVERT: F 439 MET cc_start: 0.7581 (ttp) cc_final: 0.7047 (tmm) REVERT: F 470 PHE cc_start: 0.7185 (t80) cc_final: 0.6793 (t80) REVERT: F 484 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8232 (tttt) REVERT: F 526 LYS cc_start: 0.7230 (mmtt) cc_final: 0.7019 (mmtt) REVERT: F 598 LYS cc_start: 0.7257 (mtmt) cc_final: 0.6830 (mtmt) REVERT: F 688 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7533 (mp) REVERT: F 709 PHE cc_start: 0.6686 (m-10) cc_final: 0.6388 (m-10) REVERT: F 765 PHE cc_start: 0.6323 (m-80) cc_final: 0.6090 (m-80) REVERT: B 61 LYS cc_start: 0.7792 (mttt) cc_final: 0.7512 (mtmt) REVERT: B 64 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8107 (tp) REVERT: B 82 MET cc_start: 0.7227 (mmm) cc_final: 0.6776 (tmm) REVERT: B 128 ASN cc_start: 0.8799 (t0) cc_final: 0.8389 (t0) REVERT: B 169 TYR cc_start: 0.9034 (m-10) cc_final: 0.8727 (m-10) REVERT: B 217 CYS cc_start: 0.8064 (m) cc_final: 0.7736 (m) REVERT: B 269 MET cc_start: 0.8158 (mmm) cc_final: 0.7938 (mtp) REVERT: B 283 MET cc_start: 0.7594 (mmm) cc_final: 0.7288 (mmp) REVERT: B 305 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8387 (tpp) REVERT: B 313 MET cc_start: 0.7680 (ttm) cc_final: 0.7469 (ttm) REVERT: B 317 ILE cc_start: 0.8120 (tp) cc_final: 0.7692 (tt) REVERT: G 117 TYR cc_start: 0.5727 (m-80) cc_final: 0.5149 (m-80) REVERT: G 174 ILE cc_start: 0.8637 (mt) cc_final: 0.8411 (mm) REVERT: G 280 GLU cc_start: 0.5258 (mt-10) cc_final: 0.4692 (tt0) REVERT: G 357 MET cc_start: 0.6562 (mmm) cc_final: 0.5608 (mmm) REVERT: G 365 LYS cc_start: 0.8060 (ttpm) cc_final: 0.7838 (ptpp) REVERT: G 372 GLN cc_start: 0.6344 (mp-120) cc_final: 0.5680 (mp10) REVERT: G 429 LYS cc_start: 0.7568 (mtmt) cc_final: 0.7063 (mtmm) REVERT: G 620 LEU cc_start: 0.5857 (OUTLIER) cc_final: 0.5479 (mp) REVERT: G 659 MET cc_start: 0.6654 (mmp) cc_final: 0.5826 (mmp) REVERT: G 721 ARG cc_start: 0.6155 (mmm160) cc_final: 0.5879 (mmm160) REVERT: C 80 ASP cc_start: 0.8175 (t70) cc_final: 0.7670 (t0) REVERT: C 118 LYS cc_start: 0.7299 (tptt) cc_final: 0.7064 (tptt) REVERT: C 132 MET cc_start: 0.8876 (ppp) cc_final: 0.8220 (ppp) REVERT: C 143 TYR cc_start: 0.8383 (m-80) cc_final: 0.8099 (m-80) REVERT: C 167 GLU cc_start: 0.9078 (tp30) cc_final: 0.8429 (tp30) REVERT: C 191 LYS cc_start: 0.8288 (ttmm) cc_final: 0.8070 (ttpp) REVERT: C 244 ASP cc_start: 0.8997 (p0) cc_final: 0.8439 (p0) REVERT: C 296 ASN cc_start: 0.8783 (m-40) cc_final: 0.8404 (m-40) REVERT: C 328 LYS cc_start: 0.7993 (tttt) cc_final: 0.7555 (tptt) REVERT: C 361 GLU cc_start: 0.8506 (tp30) cc_final: 0.8249 (tp30) REVERT: H 6 MET cc_start: 0.3318 (tpt) cc_final: 0.2315 (ppp) REVERT: H 92 MET cc_start: 0.4537 (OUTLIER) cc_final: 0.3987 (tpt) REVERT: H 172 GLN cc_start: 0.7419 (mm-40) cc_final: 0.7125 (mm-40) REVERT: H 362 MET cc_start: 0.6896 (mmm) cc_final: 0.6669 (mmm) REVERT: H 434 LYS cc_start: 0.7442 (mttp) cc_final: 0.7164 (mmtm) REVERT: H 451 GLN cc_start: 0.7915 (mp-120) cc_final: 0.7435 (mp10) REVERT: H 659 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.6559 (tmm) REVERT: H 662 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7529 (tp) REVERT: H 702 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7626 (mm) REVERT: H 752 ASP cc_start: 0.0305 (OUTLIER) cc_final: 0.0087 (p0) REVERT: E 51 ASP cc_start: 0.8500 (t0) cc_final: 0.7980 (t70) REVERT: E 52 SER cc_start: 0.9139 (t) cc_final: 0.8924 (p) REVERT: E 100 GLU cc_start: 0.9093 (pt0) cc_final: 0.8632 (pm20) REVERT: E 143 TYR cc_start: 0.8096 (m-80) cc_final: 0.7712 (m-80) REVERT: E 195 GLU cc_start: 0.8255 (tt0) cc_final: 0.7949 (mt-10) REVERT: E 253 GLU cc_start: 0.7371 (mp0) cc_final: 0.6715 (mp0) REVERT: E 276 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7274 (tm-30) REVERT: E 284 LYS cc_start: 0.8738 (tppp) cc_final: 0.8218 (tppt) REVERT: E 286 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7736 (m-30) REVERT: E 291 LYS cc_start: 0.8053 (tttt) cc_final: 0.7725 (mttp) REVERT: E 296 ASN cc_start: 0.8296 (m-40) cc_final: 0.8074 (m-40) REVERT: E 328 LYS cc_start: 0.7843 (tttt) cc_final: 0.7069 (ttpp) REVERT: E 361 GLU cc_start: 0.8553 (tp30) cc_final: 0.8219 (tp30) REVERT: E 372 ARG cc_start: 0.8344 (ttm-80) cc_final: 0.8087 (ttm-80) REVERT: D 50 LYS cc_start: 0.8694 (mtmm) cc_final: 0.8371 (mtpt) REVERT: D 118 LYS cc_start: 0.7767 (tptt) cc_final: 0.7293 (mttt) REVERT: D 161 HIS cc_start: 0.8769 (p-80) cc_final: 0.8529 (p-80) REVERT: D 167 GLU cc_start: 0.8555 (tp30) cc_final: 0.8005 (tp30) REVERT: D 253 GLU cc_start: 0.8078 (mp0) cc_final: 0.7877 (mp0) REVERT: D 291 LYS cc_start: 0.8531 (tttt) cc_final: 0.7915 (ttpp) REVERT: D 296 ASN cc_start: 0.8375 (m-40) cc_final: 0.7973 (m-40) REVERT: D 313 MET cc_start: 0.7780 (tpp) cc_final: 0.7464 (tpt) REVERT: D 316 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7672 (mm-30) REVERT: D 326 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7816 (tmtt) REVERT: D 361 GLU cc_start: 0.8214 (tt0) cc_final: 0.7842 (tp30) outliers start: 126 outliers final: 98 residues processed: 842 average time/residue: 0.4553 time to fit residues: 619.5554 Evaluate side-chains 869 residues out of total 3497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 758 time to evaluate : 3.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 410 TYR Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 545 ASP Chi-restraints excluded: chain F residue 568 ASN Chi-restraints excluded: chain F residue 614 LEU Chi-restraints excluded: chain F residue 676 ASN Chi-restraints excluded: chain F residue 684 ILE Chi-restraints excluded: chain F residue 688 LEU Chi-restraints excluded: chain F residue 691 HIS Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain F residue 770 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 276 GLN Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 361 ASN Chi-restraints excluded: chain G residue 391 ASN Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 435 MET Chi-restraints excluded: chain G residue 446 THR Chi-restraints excluded: chain G residue 471 ASN Chi-restraints excluded: chain G residue 484 LYS Chi-restraints excluded: chain G residue 485 LEU Chi-restraints excluded: chain G residue 540 PHE Chi-restraints excluded: chain G residue 547 THR Chi-restraints excluded: chain G residue 620 LEU Chi-restraints excluded: chain G residue 674 ILE Chi-restraints excluded: chain G residue 695 CYS Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 382 ASP Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 489 PHE Chi-restraints excluded: chain H residue 538 CYS Chi-restraints excluded: chain H residue 557 LEU Chi-restraints excluded: chain H residue 601 LEU Chi-restraints excluded: chain H residue 659 MET Chi-restraints excluded: chain H residue 662 LEU Chi-restraints excluded: chain H residue 674 ILE Chi-restraints excluded: chain H residue 702 ILE Chi-restraints excluded: chain H residue 752 ASP Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 137 GLN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 335 ARG Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 255 optimal weight: 0.7980 chunk 411 optimal weight: 20.0000 chunk 251 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 chunk 285 optimal weight: 6.9990 chunk 431 optimal weight: 30.0000 chunk 397 optimal weight: 8.9990 chunk 343 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 265 optimal weight: 0.9980 chunk 210 optimal weight: 0.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS F 126 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 361 ASN ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN ** G 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 691 HIS H 126 ASN ** H 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 486 GLN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.6829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34619 Z= 0.219 Angle : 0.669 11.388 46858 Z= 0.325 Chirality : 0.043 0.214 5197 Planarity : 0.004 0.065 6060 Dihedral : 5.790 79.707 4766 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.28 % Allowed : 21.19 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.13), residues: 4052 helix: -0.39 (0.13), residues: 1631 sheet: -1.66 (0.22), residues: 542 loop : -1.11 (0.15), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 340 HIS 0.015 0.001 HIS A 275 PHE 0.026 0.002 PHE F 155 TYR 0.026 0.002 TYR F 164 ARG 0.011 0.001 ARG G 663 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8104 Ramachandran restraints generated. 4052 Oldfield, 0 Emsley, 4052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 3497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 765 time to evaluate : 3.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 SER cc_start: 0.9419 (t) cc_final: 0.9041 (p) REVERT: A 118 LYS cc_start: 0.7864 (tppt) cc_final: 0.7362 (tptt) REVERT: A 132 MET cc_start: 0.8791 (ppp) cc_final: 0.8234 (ppp) REVERT: A 191 LYS cc_start: 0.8098 (ttmt) cc_final: 0.7514 (ttpp) REVERT: A 246 GLN cc_start: 0.9046 (pm20) cc_final: 0.8707 (pm20) REVERT: A 283 MET cc_start: 0.7901 (mmm) cc_final: 0.7648 (mmp) REVERT: A 291 LYS cc_start: 0.8255 (tttt) cc_final: 0.7675 (ttpp) REVERT: F 362 MET cc_start: 0.7201 (tpt) cc_final: 0.6272 (mtt) REVERT: F 388 MET cc_start: 0.7391 (mpp) cc_final: 0.6875 (pmm) REVERT: F 410 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.7848 (m-10) REVERT: F 433 GLU cc_start: 0.7988 (tt0) cc_final: 0.7365 (tm-30) REVERT: F 439 MET cc_start: 0.7582 (ttp) cc_final: 0.7061 (tmm) REVERT: F 470 PHE cc_start: 0.7185 (t80) cc_final: 0.6815 (t80) REVERT: F 484 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8193 (tttt) REVERT: F 526 LYS cc_start: 0.7203 (mmtt) cc_final: 0.7002 (mmtt) REVERT: F 688 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7418 (mp) REVERT: F 709 PHE cc_start: 0.6642 (m-10) cc_final: 0.6339 (m-10) REVERT: F 765 PHE cc_start: 0.6301 (m-80) cc_final: 0.6093 (m-80) REVERT: B 61 LYS cc_start: 0.7797 (mttt) cc_final: 0.7502 (mtmt) REVERT: B 64 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8137 (tp) REVERT: B 82 MET cc_start: 0.7203 (mmm) cc_final: 0.6758 (tmm) REVERT: B 121 GLN cc_start: 0.7990 (tt0) cc_final: 0.7719 (tt0) REVERT: B 128 ASN cc_start: 0.8793 (t0) cc_final: 0.8396 (t0) REVERT: B 169 TYR cc_start: 0.9038 (m-10) cc_final: 0.8683 (m-10) REVERT: B 191 LYS cc_start: 0.8177 (tttt) cc_final: 0.7967 (ttpt) REVERT: B 217 CYS cc_start: 0.8062 (m) cc_final: 0.7732 (m) REVERT: B 269 MET cc_start: 0.8141 (mmm) cc_final: 0.7908 (mtp) REVERT: B 313 MET cc_start: 0.7673 (ttm) cc_final: 0.7463 (ttm) REVERT: B 317 ILE cc_start: 0.8093 (tp) cc_final: 0.7660 (tt) REVERT: G 117 TYR cc_start: 0.5684 (m-80) cc_final: 0.5109 (m-80) REVERT: G 174 ILE cc_start: 0.8643 (mt) cc_final: 0.8415 (mm) REVERT: G 280 GLU cc_start: 0.5228 (mt-10) cc_final: 0.4657 (tt0) REVERT: G 357 MET cc_start: 0.6647 (mmm) cc_final: 0.5679 (mmm) REVERT: G 365 LYS cc_start: 0.8050 (ttpm) cc_final: 0.7843 (ptpp) REVERT: G 372 GLN cc_start: 0.6351 (mp-120) cc_final: 0.5681 (mp10) REVERT: G 429 LYS cc_start: 0.7586 (mtmt) cc_final: 0.7150 (mttm) REVERT: G 620 LEU cc_start: 0.5829 (OUTLIER) cc_final: 0.5448 (mp) REVERT: G 659 MET cc_start: 0.7076 (mmp) cc_final: 0.6864 (mmp) REVERT: G 721 ARG cc_start: 0.6162 (mmm160) cc_final: 0.5940 (mmm160) REVERT: G 774 GLU cc_start: 0.6735 (tp30) cc_final: 0.6259 (tm-30) REVERT: C 80 ASP cc_start: 0.8172 (t70) cc_final: 0.7656 (t0) REVERT: C 118 LYS cc_start: 0.7274 (tptt) cc_final: 0.7033 (tptt) REVERT: C 132 MET cc_start: 0.8885 (ppp) cc_final: 0.8234 (ppp) REVERT: C 143 TYR cc_start: 0.8367 (m-80) cc_final: 0.8117 (m-80) REVERT: C 167 GLU cc_start: 0.9076 (tp30) cc_final: 0.8431 (tp30) REVERT: C 244 ASP cc_start: 0.8971 (p0) cc_final: 0.8415 (p0) REVERT: C 296 ASN cc_start: 0.8763 (m-40) cc_final: 0.8388 (m-40) REVERT: C 325 MET cc_start: 0.8326 (tpt) cc_final: 0.8028 (tpt) REVERT: C 328 LYS cc_start: 0.7998 (tttt) cc_final: 0.7557 (tptt) REVERT: C 361 GLU cc_start: 0.8503 (tp30) cc_final: 0.8221 (tp30) REVERT: H 6 MET cc_start: 0.3364 (tpt) cc_final: 0.2302 (ppp) REVERT: H 92 MET cc_start: 0.4574 (OUTLIER) cc_final: 0.4090 (tpt) REVERT: H 172 GLN cc_start: 0.7479 (mm-40) cc_final: 0.7211 (mm-40) REVERT: H 281 ARG cc_start: 0.5705 (mtp-110) cc_final: 0.4515 (mtp180) REVERT: H 362 MET cc_start: 0.6920 (mmm) cc_final: 0.6690 (mmm) REVERT: H 434 LYS cc_start: 0.7415 (mttp) cc_final: 0.7143 (mmtm) REVERT: H 451 GLN cc_start: 0.7914 (mp-120) cc_final: 0.7440 (mp10) REVERT: H 659 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.6529 (tmm) REVERT: H 662 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7466 (tp) REVERT: H 702 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7589 (mm) REVERT: H 752 ASP cc_start: 0.0372 (OUTLIER) cc_final: 0.0049 (p0) REVERT: E 51 ASP cc_start: 0.8487 (t0) cc_final: 0.8021 (t70) REVERT: E 52 SER cc_start: 0.9133 (t) cc_final: 0.8927 (p) REVERT: E 100 GLU cc_start: 0.9090 (pt0) cc_final: 0.8632 (pm20) REVERT: E 143 TYR cc_start: 0.8102 (m-80) cc_final: 0.7711 (m-80) REVERT: E 195 GLU cc_start: 0.8255 (tt0) cc_final: 0.7954 (mt-10) REVERT: E 253 GLU cc_start: 0.7385 (mp0) cc_final: 0.6712 (mp0) REVERT: E 284 LYS cc_start: 0.8723 (tppp) cc_final: 0.8215 (tppt) REVERT: E 286 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7734 (m-30) REVERT: E 291 LYS cc_start: 0.8118 (tttt) cc_final: 0.7786 (mttp) REVERT: E 296 ASN cc_start: 0.8255 (m-40) cc_final: 0.7941 (m-40) REVERT: E 328 LYS cc_start: 0.7860 (tttt) cc_final: 0.7066 (ttpp) REVERT: E 351 THR cc_start: 0.8795 (m) cc_final: 0.8537 (p) REVERT: E 361 GLU cc_start: 0.8541 (tp30) cc_final: 0.8221 (tp30) REVERT: E 372 ARG cc_start: 0.8318 (ttm-80) cc_final: 0.8050 (ttm-80) REVERT: D 50 LYS cc_start: 0.8691 (mtmm) cc_final: 0.8350 (mtpt) REVERT: D 118 LYS cc_start: 0.7769 (tptt) cc_final: 0.7304 (mttt) REVERT: D 161 HIS cc_start: 0.8764 (p-80) cc_final: 0.8512 (p-80) REVERT: D 167 GLU cc_start: 0.8546 (tp30) cc_final: 0.7993 (tp30) REVERT: D 291 LYS cc_start: 0.8520 (tttt) cc_final: 0.7903 (ttpp) REVERT: D 296 ASN cc_start: 0.8362 (m-40) cc_final: 0.7966 (m-40) REVERT: D 313 MET cc_start: 0.7759 (tpp) cc_final: 0.7448 (tpt) REVERT: D 316 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7641 (mm-30) REVERT: D 326 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7811 (tmtt) REVERT: D 361 GLU cc_start: 0.8297 (tt0) cc_final: 0.7941 (tp30) outliers start: 110 outliers final: 88 residues processed: 825 average time/residue: 0.4467 time to fit residues: 596.7434 Evaluate side-chains 852 residues out of total 3497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 752 time to evaluate : 3.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 410 TYR Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 545 ASP Chi-restraints excluded: chain F residue 568 ASN Chi-restraints excluded: chain F residue 614 LEU Chi-restraints excluded: chain F residue 676 ASN Chi-restraints excluded: chain F residue 684 ILE Chi-restraints excluded: chain F residue 688 LEU Chi-restraints excluded: chain F residue 691 HIS Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain F residue 770 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 276 GLN Chi-restraints excluded: chain G residue 361 ASN Chi-restraints excluded: chain G residue 391 ASN Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 435 MET Chi-restraints excluded: chain G residue 446 THR Chi-restraints excluded: chain G residue 471 ASN Chi-restraints excluded: chain G residue 484 LYS Chi-restraints excluded: chain G residue 485 LEU Chi-restraints excluded: chain G residue 540 PHE Chi-restraints excluded: chain G residue 547 THR Chi-restraints excluded: chain G residue 620 LEU Chi-restraints excluded: chain G residue 674 ILE Chi-restraints excluded: chain G residue 695 CYS Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 382 ASP Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 489 PHE Chi-restraints excluded: chain H residue 538 CYS Chi-restraints excluded: chain H residue 557 LEU Chi-restraints excluded: chain H residue 601 LEU Chi-restraints excluded: chain H residue 659 MET Chi-restraints excluded: chain H residue 662 LEU Chi-restraints excluded: chain H residue 674 ILE Chi-restraints excluded: chain H residue 702 ILE Chi-restraints excluded: chain H residue 752 ASP Chi-restraints excluded: chain H residue 761 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 137 GLN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 326 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 272 optimal weight: 3.9990 chunk 365 optimal weight: 0.6980 chunk 105 optimal weight: 20.0000 chunk 316 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 344 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 353 optimal weight: 3.9990 chunk 43 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN G 80 ASN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 ASN ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 ASN ** H 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 486 GLN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 HIS ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.162674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.145926 restraints weight = 69335.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.140454 restraints weight = 98989.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.138027 restraints weight = 89697.513| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.6970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 34619 Z= 0.340 Angle : 0.728 12.755 46858 Z= 0.355 Chirality : 0.046 0.217 5197 Planarity : 0.005 0.065 6060 Dihedral : 5.998 79.893 4766 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.22 % Allowed : 21.21 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.13), residues: 4052 helix: -0.54 (0.12), residues: 1636 sheet: -1.80 (0.22), residues: 548 loop : -1.16 (0.15), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP E 340 HIS 0.012 0.002 HIS A 161 PHE 0.027 0.002 PHE H 548 TYR 0.021 0.002 TYR F 164 ARG 0.010 0.001 ARG G 671 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10689.21 seconds wall clock time: 191 minutes 29.50 seconds (11489.50 seconds total)