Starting phenix.real_space_refine on Wed Feb 21 15:33:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uaj_20707/02_2024/6uaj_20707_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uaj_20707/02_2024/6uaj_20707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uaj_20707/02_2024/6uaj_20707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uaj_20707/02_2024/6uaj_20707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uaj_20707/02_2024/6uaj_20707_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uaj_20707/02_2024/6uaj_20707_updated.pdb" } resolution = 3.84 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= 0.128 sd= 3.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 96 5.49 5 S 168 5.16 5 C 19240 2.51 5 N 5336 2.21 5 O 6192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 231": "NH1" <-> "NH2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 149": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "D ARG 412": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 149": "NH1" <-> "NH2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "E ARG 182": "NH1" <-> "NH2" Residue "E ARG 203": "NH1" <-> "NH2" Residue "E ARG 231": "NH1" <-> "NH2" Residue "E ARG 356": "NH1" <-> "NH2" Residue "E PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 407": "NH1" <-> "NH2" Residue "E ARG 412": "NH1" <-> "NH2" Residue "E ARG 512": "NH1" <-> "NH2" Residue "F ARG 126": "NH1" <-> "NH2" Residue "F ARG 128": "NH1" <-> "NH2" Residue "F ARG 136": "NH1" <-> "NH2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 149": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 182": "NH1" <-> "NH2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "F ARG 231": "NH1" <-> "NH2" Residue "F ARG 356": "NH1" <-> "NH2" Residue "F PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 407": "NH1" <-> "NH2" Residue "F ARG 412": "NH1" <-> "NH2" Residue "F ARG 512": "NH1" <-> "NH2" Residue "G ARG 126": "NH1" <-> "NH2" Residue "G ARG 128": "NH1" <-> "NH2" Residue "G ARG 136": "NH1" <-> "NH2" Residue "G PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 149": "NH1" <-> "NH2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ARG 182": "NH1" <-> "NH2" Residue "G ARG 203": "NH1" <-> "NH2" Residue "G ARG 231": "NH1" <-> "NH2" Residue "G ARG 356": "NH1" <-> "NH2" Residue "G PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 407": "NH1" <-> "NH2" Residue "G ARG 412": "NH1" <-> "NH2" Residue "G ARG 512": "NH1" <-> "NH2" Residue "H ARG 126": "NH1" <-> "NH2" Residue "H ARG 128": "NH1" <-> "NH2" Residue "H ARG 136": "NH1" <-> "NH2" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 149": "NH1" <-> "NH2" Residue "H ARG 153": "NH1" <-> "NH2" Residue "H ARG 182": "NH1" <-> "NH2" Residue "H ARG 203": "NH1" <-> "NH2" Residue "H ARG 231": "NH1" <-> "NH2" Residue "H ARG 356": "NH1" <-> "NH2" Residue "H PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 407": "NH1" <-> "NH2" Residue "H ARG 412": "NH1" <-> "NH2" Residue "H ARG 512": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31032 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3717 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain breaks: 1 Chain: "B" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3717 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain breaks: 1 Chain: "C" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3717 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain breaks: 1 Chain: "D" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3717 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain breaks: 1 Chain: "E" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3717 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain breaks: 1 Chain: "F" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3717 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain breaks: 1 Chain: "G" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3717 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain breaks: 1 Chain: "H" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3717 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain breaks: 1 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Time building chain proxies: 15.43, per 1000 atoms: 0.50 Number of scatterers: 31032 At special positions: 0 Unit cell: (150.15, 150.15, 116.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 P 96 15.00 O 6192 8.00 N 5336 7.00 C 19240 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.48 Conformation dependent library (CDL) restraints added in 5.5 seconds 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 48 sheets defined 30.9% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.86 Creating SS restraints... Processing helix chain 'A' and resid 20 through 24 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 77 through 84 Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 127 through 135 removed outlier: 3.869A pdb=" N PHE A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 202 Processing helix chain 'A' and resid 225 through 232 Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.643A pdb=" N ASP A 261 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'A' and resid 333 through 336 No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 343 through 357 removed outlier: 3.762A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE A 357 " --> pdb=" O TYR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 379 Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 453 through 471 removed outlier: 5.408A pdb=" N VAL A 457 " --> pdb=" O HIS A 454 " (cutoff:3.500A) Proline residue: A 458 - end of helix removed outlier: 3.544A pdb=" N ALA A 462 " --> pdb=" O TYR A 459 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS A 466 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 497 through 501 Processing helix chain 'B' and resid 20 through 24 Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 127 through 135 removed outlier: 3.870A pdb=" N PHE B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 202 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.642A pdb=" N ASP B 261 " --> pdb=" O TYR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 307 through 314 Processing helix chain 'B' and resid 333 through 336 No H-bonds generated for 'chain 'B' and resid 333 through 336' Processing helix chain 'B' and resid 343 through 357 removed outlier: 3.763A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 453 through 471 removed outlier: 5.406A pdb=" N VAL B 457 " --> pdb=" O HIS B 454 " (cutoff:3.500A) Proline residue: B 458 - end of helix removed outlier: 3.543A pdb=" N ALA B 462 " --> pdb=" O TYR B 459 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS B 466 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 485 Processing helix chain 'B' and resid 497 through 501 Processing helix chain 'C' and resid 20 through 24 Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 77 through 84 Processing helix chain 'C' and resid 97 through 108 Processing helix chain 'C' and resid 127 through 135 removed outlier: 3.869A pdb=" N PHE C 131 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 202 Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 254 through 266 removed outlier: 3.641A pdb=" N ASP C 261 " --> pdb=" O TYR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 307 through 314 Processing helix chain 'C' and resid 333 through 336 No H-bonds generated for 'chain 'C' and resid 333 through 336' Processing helix chain 'C' and resid 343 through 357 removed outlier: 3.762A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 379 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 453 through 471 removed outlier: 5.407A pdb=" N VAL C 457 " --> pdb=" O HIS C 454 " (cutoff:3.500A) Proline residue: C 458 - end of helix removed outlier: 3.543A pdb=" N ALA C 462 " --> pdb=" O TYR C 459 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS C 466 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 485 Processing helix chain 'C' and resid 497 through 501 Processing helix chain 'D' and resid 20 through 24 Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 77 through 84 Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 127 through 135 removed outlier: 3.871A pdb=" N PHE D 131 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU D 132 " --> pdb=" O ARG D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 202 Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.643A pdb=" N ASP D 261 " --> pdb=" O TYR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 291 Processing helix chain 'D' and resid 307 through 314 Processing helix chain 'D' and resid 333 through 336 No H-bonds generated for 'chain 'D' and resid 333 through 336' Processing helix chain 'D' and resid 343 through 357 removed outlier: 3.762A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE D 357 " --> pdb=" O TYR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 379 Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 453 through 471 removed outlier: 5.408A pdb=" N VAL D 457 " --> pdb=" O HIS D 454 " (cutoff:3.500A) Proline residue: D 458 - end of helix removed outlier: 3.544A pdb=" N ALA D 462 " --> pdb=" O TYR D 459 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS D 466 " --> pdb=" O GLY D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 485 Processing helix chain 'D' and resid 497 through 501 Processing helix chain 'E' and resid 20 through 24 Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 77 through 84 Processing helix chain 'E' and resid 97 through 108 Processing helix chain 'E' and resid 127 through 135 removed outlier: 3.870A pdb=" N PHE E 131 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 202 Processing helix chain 'E' and resid 225 through 232 Processing helix chain 'E' and resid 254 through 266 removed outlier: 3.642A pdb=" N ASP E 261 " --> pdb=" O TYR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 291 Processing helix chain 'E' and resid 307 through 314 Processing helix chain 'E' and resid 333 through 336 No H-bonds generated for 'chain 'E' and resid 333 through 336' Processing helix chain 'E' and resid 343 through 357 removed outlier: 3.763A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE E 357 " --> pdb=" O TYR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 379 Processing helix chain 'E' and resid 417 through 419 No H-bonds generated for 'chain 'E' and resid 417 through 419' Processing helix chain 'E' and resid 453 through 471 removed outlier: 5.407A pdb=" N VAL E 457 " --> pdb=" O HIS E 454 " (cutoff:3.500A) Proline residue: E 458 - end of helix removed outlier: 3.543A pdb=" N ALA E 462 " --> pdb=" O TYR E 459 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS E 466 " --> pdb=" O GLY E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 485 Processing helix chain 'E' and resid 497 through 501 Processing helix chain 'F' and resid 20 through 24 Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 77 through 84 Processing helix chain 'F' and resid 97 through 108 Processing helix chain 'F' and resid 127 through 135 removed outlier: 3.870A pdb=" N PHE F 131 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU F 132 " --> pdb=" O ARG F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 202 Processing helix chain 'F' and resid 225 through 232 Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.643A pdb=" N ASP F 261 " --> pdb=" O TYR F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 291 Processing helix chain 'F' and resid 307 through 314 Processing helix chain 'F' and resid 333 through 336 No H-bonds generated for 'chain 'F' and resid 333 through 336' Processing helix chain 'F' and resid 343 through 357 removed outlier: 3.762A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 379 Processing helix chain 'F' and resid 417 through 419 No H-bonds generated for 'chain 'F' and resid 417 through 419' Processing helix chain 'F' and resid 453 through 471 removed outlier: 5.407A pdb=" N VAL F 457 " --> pdb=" O HIS F 454 " (cutoff:3.500A) Proline residue: F 458 - end of helix removed outlier: 3.544A pdb=" N ALA F 462 " --> pdb=" O TYR F 459 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS F 466 " --> pdb=" O GLY F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 485 Processing helix chain 'F' and resid 497 through 501 Processing helix chain 'G' and resid 20 through 24 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 77 through 84 Processing helix chain 'G' and resid 97 through 108 Processing helix chain 'G' and resid 127 through 135 removed outlier: 3.870A pdb=" N PHE G 131 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 202 Processing helix chain 'G' and resid 225 through 232 Processing helix chain 'G' and resid 254 through 266 removed outlier: 3.642A pdb=" N ASP G 261 " --> pdb=" O TYR G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 291 Processing helix chain 'G' and resid 307 through 314 Processing helix chain 'G' and resid 333 through 336 No H-bonds generated for 'chain 'G' and resid 333 through 336' Processing helix chain 'G' and resid 343 through 357 removed outlier: 3.763A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE G 357 " --> pdb=" O TYR G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 371 through 379 Processing helix chain 'G' and resid 417 through 419 No H-bonds generated for 'chain 'G' and resid 417 through 419' Processing helix chain 'G' and resid 453 through 471 removed outlier: 5.407A pdb=" N VAL G 457 " --> pdb=" O HIS G 454 " (cutoff:3.500A) Proline residue: G 458 - end of helix removed outlier: 3.544A pdb=" N ALA G 462 " --> pdb=" O TYR G 459 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS G 466 " --> pdb=" O GLY G 463 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 485 Processing helix chain 'G' and resid 497 through 501 Processing helix chain 'H' and resid 20 through 24 Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 77 through 84 Processing helix chain 'H' and resid 97 through 108 Processing helix chain 'H' and resid 127 through 135 removed outlier: 3.869A pdb=" N PHE H 131 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU H 132 " --> pdb=" O ARG H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 202 Processing helix chain 'H' and resid 225 through 232 Processing helix chain 'H' and resid 254 through 266 removed outlier: 3.643A pdb=" N ASP H 261 " --> pdb=" O TYR H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 291 Processing helix chain 'H' and resid 307 through 314 Processing helix chain 'H' and resid 333 through 336 No H-bonds generated for 'chain 'H' and resid 333 through 336' Processing helix chain 'H' and resid 343 through 357 removed outlier: 3.763A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE H 357 " --> pdb=" O TYR H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 371 through 379 Processing helix chain 'H' and resid 417 through 419 No H-bonds generated for 'chain 'H' and resid 417 through 419' Processing helix chain 'H' and resid 453 through 471 removed outlier: 5.407A pdb=" N VAL H 457 " --> pdb=" O HIS H 454 " (cutoff:3.500A) Proline residue: H 458 - end of helix removed outlier: 3.544A pdb=" N ALA H 462 " --> pdb=" O TYR H 459 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS H 466 " --> pdb=" O GLY H 463 " (cutoff:3.500A) Processing helix chain 'H' and resid 476 through 485 Processing helix chain 'H' and resid 497 through 501 Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.734A pdb=" N ILE A 142 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 248 through 250 removed outlier: 7.085A pdb=" N GLN A 298 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 320 through 323 removed outlier: 7.290A pdb=" N VAL A 323 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE A 362 " --> pdb=" O VAL A 323 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 401 through 403 Processing sheet with id= F, first strand: chain 'A' and resid 209 through 212 Processing sheet with id= G, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= H, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.734A pdb=" N ILE B 142 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 248 through 250 removed outlier: 7.084A pdb=" N GLN B 298 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 320 through 323 removed outlier: 7.290A pdb=" N VAL B 323 " --> pdb=" O PRO B 360 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE B 362 " --> pdb=" O VAL B 323 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 401 through 403 Processing sheet with id= L, first strand: chain 'B' and resid 209 through 212 Processing sheet with id= M, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= N, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.734A pdb=" N ILE C 142 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 248 through 250 removed outlier: 7.084A pdb=" N GLN C 298 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 320 through 323 removed outlier: 7.290A pdb=" N VAL C 323 " --> pdb=" O PRO C 360 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE C 362 " --> pdb=" O VAL C 323 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 401 through 403 Processing sheet with id= R, first strand: chain 'C' and resid 209 through 212 Processing sheet with id= S, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= T, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.734A pdb=" N ILE D 142 " --> pdb=" O ILE D 158 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 248 through 250 removed outlier: 7.084A pdb=" N GLN D 298 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 320 through 323 removed outlier: 7.289A pdb=" N VAL D 323 " --> pdb=" O PRO D 360 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE D 362 " --> pdb=" O VAL D 323 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'D' and resid 401 through 403 Processing sheet with id= X, first strand: chain 'D' and resid 209 through 212 Processing sheet with id= Y, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= Z, first strand: chain 'E' and resid 120 through 122 removed outlier: 3.734A pdb=" N ILE E 142 " --> pdb=" O ILE E 158 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 248 through 250 removed outlier: 7.085A pdb=" N GLN E 298 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 320 through 323 removed outlier: 7.290A pdb=" N VAL E 323 " --> pdb=" O PRO E 360 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE E 362 " --> pdb=" O VAL E 323 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'E' and resid 401 through 403 Processing sheet with id= AD, first strand: chain 'E' and resid 209 through 212 Processing sheet with id= AE, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= AF, first strand: chain 'F' and resid 120 through 122 removed outlier: 3.734A pdb=" N ILE F 142 " --> pdb=" O ILE F 158 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 248 through 250 removed outlier: 7.084A pdb=" N GLN F 298 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 320 through 323 removed outlier: 7.290A pdb=" N VAL F 323 " --> pdb=" O PRO F 360 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE F 362 " --> pdb=" O VAL F 323 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'F' and resid 401 through 403 Processing sheet with id= AJ, first strand: chain 'F' and resid 209 through 212 Processing sheet with id= AK, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AL, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.733A pdb=" N ILE G 142 " --> pdb=" O ILE G 158 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 248 through 250 removed outlier: 7.085A pdb=" N GLN G 298 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'G' and resid 320 through 323 removed outlier: 7.290A pdb=" N VAL G 323 " --> pdb=" O PRO G 360 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE G 362 " --> pdb=" O VAL G 323 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'G' and resid 401 through 403 Processing sheet with id= AP, first strand: chain 'G' and resid 209 through 212 Processing sheet with id= AQ, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AR, first strand: chain 'H' and resid 120 through 122 removed outlier: 3.735A pdb=" N ILE H 142 " --> pdb=" O ILE H 158 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'H' and resid 248 through 250 removed outlier: 7.085A pdb=" N GLN H 298 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'H' and resid 320 through 323 removed outlier: 7.289A pdb=" N VAL H 323 " --> pdb=" O PRO H 360 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE H 362 " --> pdb=" O VAL H 323 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'H' and resid 401 through 403 Processing sheet with id= AV, first strand: chain 'H' and resid 209 through 212 728 hydrogen bonds defined for protein. 1632 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: 9.62 Time building geometry restraints manager: 13.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 5210 1.30 - 1.43: 7481 1.43 - 1.55: 18337 1.55 - 1.68: 268 1.68 - 1.80: 280 Bond restraints: 31576 Sorted by residual: bond pdb=" C2' ATP F 603 " pdb=" C3' ATP F 603 " ideal model delta sigma weight residual 1.531 1.252 0.279 1.20e-02 6.94e+03 5.40e+02 bond pdb=" C2' ATP A 603 " pdb=" C3' ATP A 603 " ideal model delta sigma weight residual 1.531 1.252 0.279 1.20e-02 6.94e+03 5.39e+02 bond pdb=" C2' ATP B 603 " pdb=" C3' ATP B 603 " ideal model delta sigma weight residual 1.531 1.253 0.278 1.20e-02 6.94e+03 5.37e+02 bond pdb=" C2' ATP D 603 " pdb=" C3' ATP D 603 " ideal model delta sigma weight residual 1.531 1.253 0.278 1.20e-02 6.94e+03 5.36e+02 bond pdb=" C2' ATP C 603 " pdb=" C3' ATP C 603 " ideal model delta sigma weight residual 1.531 1.253 0.278 1.20e-02 6.94e+03 5.36e+02 ... (remaining 31571 not shown) Histogram of bond angle deviations from ideal: 93.69 - 103.35: 362 103.35 - 113.00: 17232 113.00 - 122.65: 21696 122.65 - 132.31: 3486 132.31 - 141.96: 112 Bond angle restraints: 42888 Sorted by residual: angle pdb=" PB ATP D 603 " pdb=" O3B ATP D 603 " pdb=" PG ATP D 603 " ideal model delta sigma weight residual 139.87 121.11 18.76 1.00e+00 1.00e+00 3.52e+02 angle pdb=" PB ATP A 603 " pdb=" O3B ATP A 603 " pdb=" PG ATP A 603 " ideal model delta sigma weight residual 139.87 121.13 18.74 1.00e+00 1.00e+00 3.51e+02 angle pdb=" PB ATP E 603 " pdb=" O3B ATP E 603 " pdb=" PG ATP E 603 " ideal model delta sigma weight residual 139.87 121.14 18.73 1.00e+00 1.00e+00 3.51e+02 angle pdb=" PB ATP H 603 " pdb=" O3B ATP H 603 " pdb=" PG ATP H 603 " ideal model delta sigma weight residual 139.87 121.15 18.72 1.00e+00 1.00e+00 3.50e+02 angle pdb=" PB ATP F 603 " pdb=" O3B ATP F 603 " pdb=" PG ATP F 603 " ideal model delta sigma weight residual 139.87 121.16 18.71 1.00e+00 1.00e+00 3.50e+02 ... (remaining 42883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 18284 34.54 - 69.09: 920 69.09 - 103.63: 124 103.63 - 138.18: 8 138.18 - 172.72: 32 Dihedral angle restraints: 19368 sinusoidal: 8248 harmonic: 11120 Sorted by residual: dihedral pdb=" C1' IMP C 604 " pdb=" C2' IMP C 604 " pdb=" C3' IMP C 604 " pdb=" C4' IMP C 604 " ideal model delta sinusoidal sigma weight residual -35.00 17.35 -52.35 1 8.00e+00 1.56e-02 5.84e+01 dihedral pdb=" C1' IMP D 604 " pdb=" C2' IMP D 604 " pdb=" C3' IMP D 604 " pdb=" C4' IMP D 604 " ideal model delta sinusoidal sigma weight residual -35.00 17.30 -52.30 1 8.00e+00 1.56e-02 5.83e+01 dihedral pdb=" C1' IMP H 604 " pdb=" C2' IMP H 604 " pdb=" C3' IMP H 604 " pdb=" C4' IMP H 604 " ideal model delta sinusoidal sigma weight residual -35.00 17.28 -52.28 1 8.00e+00 1.56e-02 5.82e+01 ... (remaining 19365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 4436 0.130 - 0.260: 388 0.260 - 0.390: 48 0.390 - 0.520: 8 0.520 - 0.650: 8 Chirality restraints: 4888 Sorted by residual: chirality pdb=" CB ILE C 115 " pdb=" CA ILE C 115 " pdb=" CG1 ILE C 115 " pdb=" CG2 ILE C 115 " both_signs ideal model delta sigma weight residual False 2.64 1.99 0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CB ILE E 115 " pdb=" CA ILE E 115 " pdb=" CG1 ILE E 115 " pdb=" CG2 ILE E 115 " both_signs ideal model delta sigma weight residual False 2.64 2.00 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CB ILE D 115 " pdb=" CA ILE D 115 " pdb=" CG1 ILE D 115 " pdb=" CG2 ILE D 115 " both_signs ideal model delta sigma weight residual False 2.64 2.00 0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 4885 not shown) Planarity restraints: 5328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE G 115 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.26e+01 pdb=" C ILE G 115 " 0.061 2.00e-02 2.50e+03 pdb=" O ILE G 115 " -0.024 2.00e-02 2.50e+03 pdb=" N THR G 116 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 115 " 0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ILE A 115 " -0.061 2.00e-02 2.50e+03 pdb=" O ILE A 115 " 0.023 2.00e-02 2.50e+03 pdb=" N THR A 116 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 115 " -0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C ILE F 115 " 0.061 2.00e-02 2.50e+03 pdb=" O ILE F 115 " -0.023 2.00e-02 2.50e+03 pdb=" N THR F 116 " -0.020 2.00e-02 2.50e+03 ... (remaining 5325 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 9328 2.80 - 3.33: 31302 3.33 - 3.85: 55635 3.85 - 4.38: 63758 4.38 - 4.90: 102520 Nonbonded interactions: 262543 Sorted by model distance: nonbonded pdb=" N GLU E 487 " pdb=" OE1 GLU E 487 " model vdw 2.275 2.520 nonbonded pdb=" N GLU G 487 " pdb=" OE1 GLU G 487 " model vdw 2.275 2.520 nonbonded pdb=" N GLU A 487 " pdb=" OE1 GLU A 487 " model vdw 2.275 2.520 nonbonded pdb=" N GLU F 487 " pdb=" OE1 GLU F 487 " model vdw 2.275 2.520 nonbonded pdb=" N GLU C 487 " pdb=" OE1 GLU C 487 " model vdw 2.276 2.520 ... (remaining 262538 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=1.00 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.190 Check model and map are aligned: 0.430 Set scattering table: 0.250 Process input model: 77.170 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.230 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 : 0.018 0.288 31576 Z= 1.104 Angle : 1.861 20.561 42888 Z= 1.024 Chirality : 0.086 0.650 4888 Planarity : 0.008 0.068 5328 Dihedral : 20.747 172.723 12264 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 12.03 % Allowed : 14.54 % Favored : 73.43 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -4.34 (0.11), residues: 3880 helix: -3.42 (0.10), residues: 1200 sheet: -3.60 (0.18), residues: 376 loop : -2.49 (0.11), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.003 HIS E 171 PHE 0.024 0.004 PHE H 456 TYR 0.015 0.003 TYR C 233 ARG 0.010 0.002 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1779 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 384 poor density : 1395 time to evaluate : 3.659 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: 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 18 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8689 (tm) REVERT: A 19 THR cc_start: 0.8678 (p) cc_final: 0.8254 (t) REVERT: A 32 TYR cc_start: 0.8723 (m-80) cc_final: 0.8416 (m-10) REVERT: A 95 CYS cc_start: 0.8545 (p) cc_final: 0.8320 (p) REVERT: A 128 ARG cc_start: 0.8980 (mmt90) cc_final: 0.8744 (mmm-85) REVERT: A 144 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9039 (pp) REVERT: A 202 GLN cc_start: 0.9418 (mt0) cc_final: 0.8363 (mt0) REVERT: A 205 LYS cc_start: 0.9366 (mppt) cc_final: 0.9127 (mttt) REVERT: A 208 LYS cc_start: 0.8512 (mtpp) cc_final: 0.8052 (mtpt) REVERT: A 214 GLU cc_start: 0.9436 (mm-30) cc_final: 0.9212 (mp0) REVERT: A 250 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7924 (pp) REVERT: A 285 ASN cc_start: 0.9435 (m110) cc_final: 0.9057 (m-40) REVERT: A 311 LYS cc_start: 0.8935 (tmtt) cc_final: 0.8365 (tptt) REVERT: A 351 SER cc_start: 0.8952 (OUTLIER) cc_final: 0.8669 (t) REVERT: A 379 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9157 (tm) REVERT: A 386 MET cc_start: 0.8983 (ppp) cc_final: 0.8258 (ppp) REVERT: A 407 ARG cc_start: 0.7336 (ttt180) cc_final: 0.6635 (ttt180) REVERT: A 482 MET cc_start: 0.8448 (tpt) cc_final: 0.8154 (tpt) REVERT: A 489 LYS cc_start: 0.8479 (ttmm) cc_final: 0.8213 (tptm) REVERT: A 490 PHE cc_start: 0.8119 (m-80) cc_final: 0.7872 (m-80) REVERT: A 509 TYR cc_start: 0.7708 (p90) cc_final: 0.7117 (p90) REVERT: A 514 PHE cc_start: 0.7356 (p90) cc_final: 0.6847 (p90) REVERT: B 128 ARG cc_start: 0.8987 (mmt90) cc_final: 0.8760 (mmm-85) REVERT: B 194 LEU cc_start: 0.9502 (tp) cc_final: 0.9246 (tp) REVERT: B 202 GLN cc_start: 0.9419 (mt0) cc_final: 0.8266 (mt0) REVERT: B 208 LYS cc_start: 0.8354 (mtpp) cc_final: 0.8114 (ttmm) REVERT: B 214 GLU cc_start: 0.9387 (mm-30) cc_final: 0.9167 (mp0) REVERT: B 216 ASP cc_start: 0.9021 (t70) cc_final: 0.8745 (t0) REVERT: B 284 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9217 (mp) REVERT: B 285 ASN cc_start: 0.9309 (m110) cc_final: 0.8931 (m110) REVERT: B 311 LYS cc_start: 0.9102 (tmtt) cc_final: 0.8542 (tptt) REVERT: B 353 TYR cc_start: 0.8303 (t80) cc_final: 0.8066 (t80) REVERT: B 357 PHE cc_start: 0.8807 (m-80) cc_final: 0.8243 (m-10) REVERT: B 386 MET cc_start: 0.8901 (ppp) cc_final: 0.8285 (ppp) REVERT: B 401 PHE cc_start: 0.8317 (p90) cc_final: 0.8077 (p90) REVERT: B 407 ARG cc_start: 0.7387 (ttt180) cc_final: 0.6746 (ttt180) REVERT: B 420 MET cc_start: 0.6106 (tpp) cc_final: 0.5868 (mmm) REVERT: B 470 ASP cc_start: 0.8732 (m-30) cc_final: 0.8522 (m-30) REVERT: B 482 MET cc_start: 0.8497 (tpt) cc_final: 0.8181 (tpt) REVERT: B 490 PHE cc_start: 0.8142 (m-80) cc_final: 0.7789 (m-80) REVERT: B 509 TYR cc_start: 0.7760 (p90) cc_final: 0.7112 (p90) REVERT: B 514 PHE cc_start: 0.7283 (p90) cc_final: 0.6919 (p90) REVERT: C 18 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8723 (tm) REVERT: C 19 THR cc_start: 0.8618 (p) cc_final: 0.8245 (t) REVERT: C 32 TYR cc_start: 0.8743 (m-80) cc_final: 0.8490 (m-10) REVERT: C 128 ARG cc_start: 0.9000 (mmt90) cc_final: 0.8777 (mmm-85) REVERT: C 144 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.9070 (pp) REVERT: C 199 GLU cc_start: 0.9392 (tp30) cc_final: 0.8858 (tp30) REVERT: C 202 GLN cc_start: 0.9461 (mt0) cc_final: 0.8530 (mt0) REVERT: C 203 ARG cc_start: 0.9084 (ptp-110) cc_final: 0.8841 (ptp-110) REVERT: C 205 LYS cc_start: 0.9361 (mppt) cc_final: 0.9124 (mttt) REVERT: C 208 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8007 (mtpt) REVERT: C 214 GLU cc_start: 0.9417 (mm-30) cc_final: 0.9179 (mp0) REVERT: C 216 ASP cc_start: 0.9109 (t70) cc_final: 0.8838 (t0) REVERT: C 250 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7625 (pp) REVERT: C 284 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9229 (mp) REVERT: C 285 ASN cc_start: 0.9396 (m110) cc_final: 0.9015 (m-40) REVERT: C 311 LYS cc_start: 0.9023 (tmtt) cc_final: 0.8483 (tptt) REVERT: C 379 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9166 (tm) REVERT: C 386 MET cc_start: 0.8950 (ppp) cc_final: 0.8339 (ppp) REVERT: C 407 ARG cc_start: 0.7343 (ttt180) cc_final: 0.6700 (ttt180) REVERT: C 482 MET cc_start: 0.8543 (tpt) cc_final: 0.8240 (tpt) REVERT: C 489 LYS cc_start: 0.8346 (ttmm) cc_final: 0.8124 (tptm) REVERT: C 490 PHE cc_start: 0.8065 (m-80) cc_final: 0.7796 (m-80) REVERT: C 509 TYR cc_start: 0.7646 (p90) cc_final: 0.7022 (p90) REVERT: C 514 PHE cc_start: 0.7356 (p90) cc_final: 0.6944 (p90) REVERT: D 91 ILE cc_start: 0.9103 (mm) cc_final: 0.8878 (mm) REVERT: D 128 ARG cc_start: 0.9040 (mmt90) cc_final: 0.8797 (mmm-85) REVERT: D 199 GLU cc_start: 0.9362 (tp30) cc_final: 0.8998 (tp30) REVERT: D 202 GLN cc_start: 0.9415 (mt0) cc_final: 0.8663 (mt0) REVERT: D 214 GLU cc_start: 0.9444 (mm-30) cc_final: 0.9205 (mp0) REVERT: D 216 ASP cc_start: 0.9054 (t70) cc_final: 0.8764 (t0) REVERT: D 284 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.9150 (mp) REVERT: D 285 ASN cc_start: 0.9320 (m110) cc_final: 0.8946 (m110) REVERT: D 311 LYS cc_start: 0.9078 (tmtt) cc_final: 0.8534 (tptt) REVERT: D 351 SER cc_start: 0.8939 (OUTLIER) cc_final: 0.8660 (t) REVERT: D 386 MET cc_start: 0.8845 (ppp) cc_final: 0.8204 (ppp) REVERT: D 407 ARG cc_start: 0.7443 (ttt180) cc_final: 0.6810 (ttt180) REVERT: D 420 MET cc_start: 0.6190 (tpp) cc_final: 0.5896 (mmm) REVERT: D 470 ASP cc_start: 0.8691 (m-30) cc_final: 0.8474 (m-30) REVERT: D 482 MET cc_start: 0.8579 (tpt) cc_final: 0.8243 (tpt) REVERT: D 490 PHE cc_start: 0.8246 (m-80) cc_final: 0.7880 (m-80) REVERT: D 509 TYR cc_start: 0.7723 (p90) cc_final: 0.7098 (p90) REVERT: D 514 PHE cc_start: 0.7419 (p90) cc_final: 0.7016 (p90) REVERT: E 52 THR cc_start: 0.9792 (m) cc_final: 0.9590 (t) REVERT: E 95 CYS cc_start: 0.8572 (p) cc_final: 0.8364 (p) REVERT: E 128 ARG cc_start: 0.8968 (mmt90) cc_final: 0.8702 (mmm-85) REVERT: E 199 GLU cc_start: 0.9406 (tp30) cc_final: 0.9072 (tp30) REVERT: E 206 LYS cc_start: 0.8076 (tppt) cc_final: 0.7633 (tppt) REVERT: E 214 GLU cc_start: 0.9401 (mm-30) cc_final: 0.9165 (mp0) REVERT: E 216 ASP cc_start: 0.9106 (t70) cc_final: 0.8847 (t0) REVERT: E 250 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7670 (pp) REVERT: E 285 ASN cc_start: 0.9391 (m110) cc_final: 0.9009 (m-40) REVERT: E 311 LYS cc_start: 0.9063 (tmtt) cc_final: 0.8563 (tptt) REVERT: E 386 MET cc_start: 0.8929 (ppp) cc_final: 0.8248 (ppp) REVERT: E 470 ASP cc_start: 0.8749 (m-30) cc_final: 0.8536 (m-30) REVERT: E 482 MET cc_start: 0.8560 (tpt) cc_final: 0.8273 (tpt) REVERT: E 490 PHE cc_start: 0.8215 (m-80) cc_final: 0.7916 (m-80) REVERT: E 509 TYR cc_start: 0.7810 (p90) cc_final: 0.7160 (p90) REVERT: F 91 ILE cc_start: 0.9027 (mm) cc_final: 0.8804 (mm) REVERT: F 109 LYS cc_start: 0.8830 (mmtm) cc_final: 0.8606 (mmtm) REVERT: F 128 ARG cc_start: 0.9007 (mmt90) cc_final: 0.8748 (mmm-85) REVERT: F 199 GLU cc_start: 0.9385 (tp30) cc_final: 0.9029 (tp30) REVERT: F 216 ASP cc_start: 0.9053 (t70) cc_final: 0.8772 (t0) REVERT: F 284 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9248 (mp) REVERT: F 285 ASN cc_start: 0.9316 (m110) cc_final: 0.8936 (m110) REVERT: F 311 LYS cc_start: 0.9063 (tmtt) cc_final: 0.8536 (tptt) REVERT: F 386 MET cc_start: 0.8857 (ppp) cc_final: 0.8293 (ppp) REVERT: F 401 PHE cc_start: 0.8300 (p90) cc_final: 0.8046 (p90) REVERT: F 407 ARG cc_start: 0.7430 (ttt180) cc_final: 0.7162 (ttt90) REVERT: F 470 ASP cc_start: 0.8733 (m-30) cc_final: 0.8503 (m-30) REVERT: F 482 MET cc_start: 0.8602 (tpt) cc_final: 0.8275 (tpt) REVERT: F 490 PHE cc_start: 0.8233 (m-80) cc_final: 0.7849 (m-80) REVERT: F 509 TYR cc_start: 0.7861 (p90) cc_final: 0.7259 (p90) REVERT: F 514 PHE cc_start: 0.7391 (p90) cc_final: 0.7038 (p90) REVERT: G 32 TYR cc_start: 0.8706 (m-80) cc_final: 0.8486 (m-10) REVERT: G 98 GLU cc_start: 0.8858 (mp0) cc_final: 0.8652 (mp0) REVERT: G 128 ARG cc_start: 0.9032 (mmt90) cc_final: 0.8758 (mmm-85) REVERT: G 199 GLU cc_start: 0.9388 (tp30) cc_final: 0.9037 (tp30) REVERT: G 214 GLU cc_start: 0.9443 (mm-30) cc_final: 0.9204 (mp0) REVERT: G 250 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7845 (pp) REVERT: G 285 ASN cc_start: 0.9409 (m110) cc_final: 0.9042 (m-40) REVERT: G 311 LYS cc_start: 0.9071 (tmtt) cc_final: 0.8577 (tptt) REVERT: G 379 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9167 (tm) REVERT: G 386 MET cc_start: 0.8995 (ppp) cc_final: 0.8233 (ppp) REVERT: G 482 MET cc_start: 0.8617 (tpt) cc_final: 0.8303 (tpt) REVERT: G 490 PHE cc_start: 0.8282 (m-80) cc_final: 0.7998 (m-80) REVERT: G 509 TYR cc_start: 0.7860 (p90) cc_final: 0.7254 (p90) REVERT: H 18 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8664 (tm) REVERT: H 19 THR cc_start: 0.8725 (p) cc_final: 0.8246 (t) REVERT: H 91 ILE cc_start: 0.8996 (mm) cc_final: 0.8767 (mm) REVERT: H 128 ARG cc_start: 0.9049 (mmt90) cc_final: 0.8829 (mmm-85) REVERT: H 199 GLU cc_start: 0.9365 (tp30) cc_final: 0.9039 (tp30) REVERT: H 205 LYS cc_start: 0.9386 (mppt) cc_final: 0.9132 (mmtt) REVERT: H 216 ASP cc_start: 0.8981 (t70) cc_final: 0.8728 (t0) REVERT: H 284 ILE cc_start: 0.9484 (OUTLIER) cc_final: 0.9245 (mp) REVERT: H 285 ASN cc_start: 0.9389 (m110) cc_final: 0.8979 (m-40) REVERT: H 311 LYS cc_start: 0.8974 (tmtt) cc_final: 0.8412 (tptt) REVERT: H 351 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8667 (t) REVERT: H 386 MET cc_start: 0.8863 (ppp) cc_final: 0.8294 (ppp) REVERT: H 407 ARG cc_start: 0.7402 (ttt180) cc_final: 0.7096 (ttt90) REVERT: H 482 MET cc_start: 0.8478 (tpt) cc_final: 0.8160 (tpt) REVERT: H 489 LYS cc_start: 0.8418 (ttmm) cc_final: 0.8136 (tptm) REVERT: H 509 TYR cc_start: 0.7950 (p90) cc_final: 0.7370 (p90) outliers start: 384 outliers final: 166 residues processed: 1505 average time/residue: 0.4366 time to fit residues: 1022.5090 Evaluate side-chains 1221 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1035 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 487 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 487 GLU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 487 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 449 ASP Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 487 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 284 ILE Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 487 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 0.8980 chunk 291 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 300 optimal weight: 0.0020 chunk 116 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 224 optimal weight: 0.9980 chunk 348 optimal weight: 8.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN ** F 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN ** H 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31576 Z= 0.253 Angle : 0.809 9.918 42888 Z= 0.404 Chirality : 0.048 0.171 4888 Planarity : 0.005 0.041 5328 Dihedral : 21.303 161.999 5600 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 9.30 % Allowed : 23.25 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -3.19 (0.12), residues: 3880 helix: -2.38 (0.12), residues: 1192 sheet: -2.56 (0.19), residues: 512 loop : -1.82 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 253 PHE 0.020 0.002 PHE F 456 TYR 0.024 0.002 TYR H 484 ARG 0.008 0.001 ARG H 149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1369 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 1072 time to evaluate : 3.308 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: 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 32 TYR cc_start: 0.8602 (m-80) cc_final: 0.8344 (m-10) REVERT: A 73 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.6934 (t) REVERT: A 78 MET cc_start: 0.8371 (ttm) cc_final: 0.8061 (ttt) REVERT: A 128 ARG cc_start: 0.8832 (mmt90) cc_final: 0.8369 (mmt90) REVERT: A 165 PHE cc_start: 0.8336 (p90) cc_final: 0.8110 (p90) REVERT: A 202 GLN cc_start: 0.9437 (mt0) cc_final: 0.9042 (mt0) REVERT: A 206 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8018 (ttpt) REVERT: A 208 LYS cc_start: 0.8445 (mtpp) cc_final: 0.8055 (ttmm) REVERT: A 216 ASP cc_start: 0.9080 (t70) cc_final: 0.8773 (t0) REVERT: A 285 ASN cc_start: 0.9466 (m110) cc_final: 0.9164 (m110) REVERT: A 289 TYR cc_start: 0.9054 (t80) cc_final: 0.8741 (t80) REVERT: A 297 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8748 (tm) REVERT: A 311 LYS cc_start: 0.8872 (tmtt) cc_final: 0.8371 (tptt) REVERT: A 348 TYR cc_start: 0.9226 (t80) cc_final: 0.9000 (t80) REVERT: A 379 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9062 (tm) REVERT: A 386 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8267 (ppp) REVERT: A 407 ARG cc_start: 0.7357 (ttt180) cc_final: 0.7080 (ttt180) REVERT: A 420 MET cc_start: 0.6516 (mmm) cc_final: 0.5998 (mmm) REVERT: A 466 HIS cc_start: 0.8696 (OUTLIER) cc_final: 0.7999 (t-90) REVERT: A 469 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8047 (pt0) REVERT: A 470 ASP cc_start: 0.8512 (m-30) cc_final: 0.8229 (m-30) REVERT: A 482 MET cc_start: 0.8585 (tpt) cc_final: 0.8130 (tpt) REVERT: A 487 GLU cc_start: 0.8521 (pm20) cc_final: 0.7942 (pm20) REVERT: A 490 PHE cc_start: 0.8272 (m-80) cc_final: 0.7810 (m-80) REVERT: A 509 TYR cc_start: 0.7849 (p90) cc_final: 0.7608 (p90) REVERT: A 510 GLU cc_start: 0.6602 (mm-30) cc_final: 0.6351 (mm-30) REVERT: A 514 PHE cc_start: 0.7209 (p90) cc_final: 0.6572 (p90) REVERT: B 62 LYS cc_start: 0.9196 (mmtp) cc_final: 0.8964 (mttp) REVERT: B 73 VAL cc_start: 0.8077 (OUTLIER) cc_final: 0.6515 (t) REVERT: B 78 MET cc_start: 0.8184 (ttm) cc_final: 0.7856 (ttt) REVERT: B 161 ARG cc_start: 0.9431 (mpp-170) cc_final: 0.9011 (mtt90) REVERT: B 165 PHE cc_start: 0.8069 (p90) cc_final: 0.7785 (p90) REVERT: B 180 THR cc_start: 0.8194 (p) cc_final: 0.7828 (t) REVERT: B 206 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8155 (ttpt) REVERT: B 208 LYS cc_start: 0.8350 (mtpp) cc_final: 0.7985 (ttmm) REVERT: B 214 GLU cc_start: 0.9399 (mm-30) cc_final: 0.9169 (mp0) REVERT: B 216 ASP cc_start: 0.9086 (t70) cc_final: 0.8779 (t0) REVERT: B 235 LEU cc_start: 0.9145 (mt) cc_final: 0.8306 (mt) REVERT: B 250 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8262 (pp) REVERT: B 258 TYR cc_start: 0.8451 (t80) cc_final: 0.8131 (t80) REVERT: B 297 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8696 (tm) REVERT: B 311 LYS cc_start: 0.8989 (tmtt) cc_final: 0.8394 (tptt) REVERT: B 386 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8350 (pmm) REVERT: B 390 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8912 (tt) REVERT: B 399 GLU cc_start: 0.7297 (pp20) cc_final: 0.7071 (pp20) REVERT: B 401 PHE cc_start: 0.8284 (p90) cc_final: 0.7968 (p90) REVERT: B 407 ARG cc_start: 0.7493 (ttt180) cc_final: 0.6697 (ttt90) REVERT: B 466 HIS cc_start: 0.8674 (OUTLIER) cc_final: 0.7938 (t-90) REVERT: B 469 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8039 (pt0) REVERT: B 482 MET cc_start: 0.8571 (tpt) cc_final: 0.8118 (tpt) REVERT: B 487 GLU cc_start: 0.8596 (pm20) cc_final: 0.8090 (pm20) REVERT: B 490 PHE cc_start: 0.8319 (m-80) cc_final: 0.7855 (m-80) REVERT: B 514 PHE cc_start: 0.7238 (p90) cc_final: 0.6977 (p90) REVERT: C 32 TYR cc_start: 0.8620 (m-80) cc_final: 0.8378 (m-10) REVERT: C 70 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8253 (mtm) REVERT: C 73 VAL cc_start: 0.8364 (OUTLIER) cc_final: 0.6913 (t) REVERT: C 78 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8049 (ttm) REVERT: C 199 GLU cc_start: 0.9359 (tp30) cc_final: 0.9105 (tp30) REVERT: C 202 GLN cc_start: 0.9418 (mt0) cc_final: 0.9037 (mt0) REVERT: C 206 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8072 (ttpt) REVERT: C 208 LYS cc_start: 0.8428 (mtpp) cc_final: 0.8056 (ttmm) REVERT: C 214 GLU cc_start: 0.9446 (mm-30) cc_final: 0.9158 (mp0) REVERT: C 216 ASP cc_start: 0.9138 (t70) cc_final: 0.8794 (t0) REVERT: C 250 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8320 (pp) REVERT: C 258 TYR cc_start: 0.8627 (t80) cc_final: 0.8350 (t80) REVERT: C 285 ASN cc_start: 0.9418 (m110) cc_final: 0.9107 (m110) REVERT: C 297 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8695 (tm) REVERT: C 311 LYS cc_start: 0.8897 (tmtt) cc_final: 0.8371 (tptt) REVERT: C 352 GLU cc_start: 0.8591 (tp30) cc_final: 0.8046 (tp30) REVERT: C 379 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9122 (tm) REVERT: C 386 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8363 (ppp) REVERT: C 420 MET cc_start: 0.6384 (mmm) cc_final: 0.5930 (mmm) REVERT: C 466 HIS cc_start: 0.8688 (OUTLIER) cc_final: 0.7906 (t-90) REVERT: C 469 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8045 (pt0) REVERT: C 470 ASP cc_start: 0.8491 (m-30) cc_final: 0.8209 (m-30) REVERT: C 482 MET cc_start: 0.8597 (tpt) cc_final: 0.8168 (tpt) REVERT: C 487 GLU cc_start: 0.8645 (pm20) cc_final: 0.8124 (pm20) REVERT: C 490 PHE cc_start: 0.8329 (m-80) cc_final: 0.7898 (m-80) REVERT: C 510 GLU cc_start: 0.6501 (mm-30) cc_final: 0.6268 (mm-30) REVERT: C 514 PHE cc_start: 0.7363 (p90) cc_final: 0.7133 (p90) REVERT: D 32 TYR cc_start: 0.8540 (m-10) cc_final: 0.8316 (m-10) REVERT: D 73 VAL cc_start: 0.8224 (OUTLIER) cc_final: 0.6410 (t) REVERT: D 78 MET cc_start: 0.8314 (ttm) cc_final: 0.7912 (ttp) REVERT: D 161 ARG cc_start: 0.9438 (mpp-170) cc_final: 0.8913 (mtt90) REVERT: D 165 PHE cc_start: 0.8092 (p90) cc_final: 0.7810 (p90) REVERT: D 180 THR cc_start: 0.8220 (p) cc_final: 0.7782 (t) REVERT: D 199 GLU cc_start: 0.9566 (tp30) cc_final: 0.9209 (tp30) REVERT: D 206 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7974 (ttpt) REVERT: D 216 ASP cc_start: 0.9141 (t70) cc_final: 0.8856 (t0) REVERT: D 250 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8376 (pp) REVERT: D 258 TYR cc_start: 0.8446 (t80) cc_final: 0.8158 (t80) REVERT: D 297 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8725 (tm) REVERT: D 311 LYS cc_start: 0.8964 (tmtt) cc_final: 0.8399 (tptt) REVERT: D 379 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9001 (tm) REVERT: D 385 MET cc_start: 0.8685 (ttp) cc_final: 0.8476 (ttp) REVERT: D 386 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8303 (pmm) REVERT: D 399 GLU cc_start: 0.7310 (pp20) cc_final: 0.7101 (pp20) REVERT: D 400 TYR cc_start: 0.7795 (m-80) cc_final: 0.7200 (m-80) REVERT: D 407 ARG cc_start: 0.7411 (ttt180) cc_final: 0.7157 (ttt90) REVERT: D 420 MET cc_start: 0.5986 (tpp) cc_final: 0.5723 (mmm) REVERT: D 466 HIS cc_start: 0.8726 (OUTLIER) cc_final: 0.7999 (t-90) REVERT: D 469 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8144 (pt0) REVERT: D 482 MET cc_start: 0.8684 (tpt) cc_final: 0.8233 (tpt) REVERT: D 487 GLU cc_start: 0.8606 (pm20) cc_final: 0.8092 (pm20) REVERT: D 490 PHE cc_start: 0.8357 (m-80) cc_final: 0.7897 (m-80) REVERT: D 510 GLU cc_start: 0.6555 (mm-30) cc_final: 0.6161 (mm-30) REVERT: D 514 PHE cc_start: 0.7380 (p90) cc_final: 0.7076 (p90) REVERT: E 78 MET cc_start: 0.8553 (ttm) cc_final: 0.8224 (ttt) REVERT: E 128 ARG cc_start: 0.8843 (mmt90) cc_final: 0.8631 (mmm-85) REVERT: E 165 PHE cc_start: 0.8360 (p90) cc_final: 0.8134 (p90) REVERT: E 180 THR cc_start: 0.8377 (p) cc_final: 0.8031 (t) REVERT: E 185 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7501 (mt) REVERT: E 199 GLU cc_start: 0.9584 (tp30) cc_final: 0.9366 (tp30) REVERT: E 206 LYS cc_start: 0.8012 (tppt) cc_final: 0.7661 (tppt) REVERT: E 216 ASP cc_start: 0.9132 (t70) cc_final: 0.8799 (t0) REVERT: E 235 LEU cc_start: 0.9136 (mt) cc_final: 0.8308 (mt) REVERT: E 250 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8352 (pp) REVERT: E 258 TYR cc_start: 0.8724 (t80) cc_final: 0.8431 (t80) REVERT: E 285 ASN cc_start: 0.9300 (m110) cc_final: 0.8996 (m110) REVERT: E 297 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8757 (tm) REVERT: E 311 LYS cc_start: 0.8923 (tmtt) cc_final: 0.8458 (tptt) REVERT: E 379 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9094 (tm) REVERT: E 386 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8287 (pmm) REVERT: E 390 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8825 (tt) REVERT: E 420 MET cc_start: 0.6429 (mmm) cc_final: 0.6027 (mmm) REVERT: E 466 HIS cc_start: 0.8802 (OUTLIER) cc_final: 0.8023 (t-90) REVERT: E 469 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8072 (pt0) REVERT: E 482 MET cc_start: 0.8635 (tpt) cc_final: 0.8152 (tpt) REVERT: E 487 GLU cc_start: 0.8665 (pm20) cc_final: 0.8160 (pm20) REVERT: E 490 PHE cc_start: 0.8333 (m-80) cc_final: 0.7925 (m-80) REVERT: E 509 TYR cc_start: 0.7929 (p90) cc_final: 0.7727 (p90) REVERT: F 62 LYS cc_start: 0.9194 (mmtp) cc_final: 0.8971 (mttp) REVERT: F 78 MET cc_start: 0.8544 (ttm) cc_final: 0.8235 (ttt) REVERT: F 109 LYS cc_start: 0.8759 (mmtm) cc_final: 0.8468 (mptt) REVERT: F 165 PHE cc_start: 0.8248 (p90) cc_final: 0.7724 (p90) REVERT: F 180 THR cc_start: 0.8245 (p) cc_final: 0.7916 (t) REVERT: F 185 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7768 (mt) REVERT: F 199 GLU cc_start: 0.9564 (tp30) cc_final: 0.9222 (tp30) REVERT: F 206 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8101 (ttpt) REVERT: F 208 LYS cc_start: 0.8184 (ttmm) cc_final: 0.7908 (ttmm) REVERT: F 216 ASP cc_start: 0.9133 (t70) cc_final: 0.8833 (t0) REVERT: F 235 LEU cc_start: 0.9113 (mt) cc_final: 0.8266 (mt) REVERT: F 250 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8195 (pp) REVERT: F 258 TYR cc_start: 0.8500 (t80) cc_final: 0.8202 (t80) REVERT: F 297 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8710 (tm) REVERT: F 311 LYS cc_start: 0.8919 (tmtt) cc_final: 0.8468 (tptt) REVERT: F 379 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9080 (tm) REVERT: F 386 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8262 (pmm) REVERT: F 390 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8904 (tt) REVERT: F 400 TYR cc_start: 0.7891 (m-80) cc_final: 0.7098 (m-80) REVERT: F 407 ARG cc_start: 0.7633 (ttt180) cc_final: 0.7134 (ttt90) REVERT: F 466 HIS cc_start: 0.8729 (OUTLIER) cc_final: 0.7961 (t-90) REVERT: F 469 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8077 (pt0) REVERT: F 482 MET cc_start: 0.8645 (tpt) cc_final: 0.8174 (tpt) REVERT: F 487 GLU cc_start: 0.8708 (pm20) cc_final: 0.8197 (pm20) REVERT: F 490 PHE cc_start: 0.8374 (m-80) cc_final: 0.7873 (m-80) REVERT: F 510 GLU cc_start: 0.6450 (mm-30) cc_final: 0.6064 (mm-30) REVERT: F 514 PHE cc_start: 0.7392 (p90) cc_final: 0.7135 (p90) REVERT: G 32 TYR cc_start: 0.8622 (m-80) cc_final: 0.8391 (m-10) REVERT: G 73 VAL cc_start: 0.8439 (OUTLIER) cc_final: 0.6766 (t) REVERT: G 78 MET cc_start: 0.8393 (ttm) cc_final: 0.7967 (ttp) REVERT: G 165 PHE cc_start: 0.8153 (p90) cc_final: 0.7825 (p90) REVERT: G 199 GLU cc_start: 0.9581 (tp30) cc_final: 0.9337 (tp30) REVERT: G 206 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7988 (ttpt) REVERT: G 250 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8471 (pp) REVERT: G 258 TYR cc_start: 0.8683 (t80) cc_final: 0.8467 (t80) REVERT: G 285 ASN cc_start: 0.9366 (m110) cc_final: 0.9044 (m110) REVERT: G 297 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8769 (tm) REVERT: G 311 LYS cc_start: 0.8950 (tmtt) cc_final: 0.8517 (tptt) REVERT: G 348 TYR cc_start: 0.9270 (t80) cc_final: 0.8887 (t80) REVERT: G 379 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9138 (tm) REVERT: G 386 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8259 (pmm) REVERT: G 420 MET cc_start: 0.6462 (mmm) cc_final: 0.6083 (mmm) REVERT: G 466 HIS cc_start: 0.8776 (OUTLIER) cc_final: 0.8033 (t-90) REVERT: G 469 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8129 (pt0) REVERT: G 470 ASP cc_start: 0.8459 (m-30) cc_final: 0.8258 (m-30) REVERT: G 482 MET cc_start: 0.8657 (tpt) cc_final: 0.8432 (tpt) REVERT: G 490 PHE cc_start: 0.8364 (m-80) cc_final: 0.7964 (m-80) REVERT: G 509 TYR cc_start: 0.7946 (p90) cc_final: 0.7719 (p90) REVERT: G 510 GLU cc_start: 0.6692 (mm-30) cc_final: 0.6419 (mm-30) REVERT: H 32 TYR cc_start: 0.8520 (m-10) cc_final: 0.8295 (m-10) REVERT: H 73 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.6540 (t) REVERT: H 78 MET cc_start: 0.8409 (ttm) cc_final: 0.8107 (ttp) REVERT: H 165 PHE cc_start: 0.8190 (p90) cc_final: 0.7686 (p90) REVERT: H 185 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7722 (mt) REVERT: H 199 GLU cc_start: 0.9551 (tp30) cc_final: 0.9084 (tp30) REVERT: H 203 ARG cc_start: 0.9444 (ptp-110) cc_final: 0.9014 (ptp-110) REVERT: H 216 ASP cc_start: 0.9027 (t70) cc_final: 0.8717 (t0) REVERT: H 250 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8429 (pp) REVERT: H 258 TYR cc_start: 0.8626 (t80) cc_final: 0.8317 (t80) REVERT: H 297 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8625 (tm) REVERT: H 311 LYS cc_start: 0.8881 (tmtt) cc_final: 0.8358 (tptt) REVERT: H 379 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9004 (tm) REVERT: H 386 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8229 (pmm) REVERT: H 401 PHE cc_start: 0.8376 (p90) cc_final: 0.8043 (p90) REVERT: H 407 ARG cc_start: 0.7491 (ttt180) cc_final: 0.7153 (ttt90) REVERT: H 466 HIS cc_start: 0.8689 (OUTLIER) cc_final: 0.8063 (t-90) REVERT: H 482 MET cc_start: 0.8592 (tpt) cc_final: 0.8135 (tpt) REVERT: H 487 GLU cc_start: 0.8677 (pm20) cc_final: 0.8125 (pm20) REVERT: H 490 PHE cc_start: 0.8291 (m-80) cc_final: 0.7856 (m-80) REVERT: H 514 PHE cc_start: 0.7413 (p90) cc_final: 0.7146 (p90) outliers start: 297 outliers final: 139 residues processed: 1193 average time/residue: 0.4288 time to fit residues: 825.3582 Evaluate side-chains 1128 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 924 time to evaluate : 3.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 466 HIS Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 466 HIS Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 466 HIS Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 466 HIS Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 466 HIS Chi-restraints excluded: chain H residue 469 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 290 optimal weight: 0.8980 chunk 237 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 349 optimal weight: 1.9990 chunk 377 optimal weight: 0.9990 chunk 311 optimal weight: 0.6980 chunk 346 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 280 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 GLN D 171 HIS ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS E 243 GLN E 283 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN ** F 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 HIS ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 HIS ** H 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 GLN ** H 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31576 Z= 0.200 Angle : 0.771 14.779 42888 Z= 0.368 Chirality : 0.047 0.149 4888 Planarity : 0.005 0.052 5328 Dihedral : 19.698 165.539 5402 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 7.77 % Allowed : 26.38 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -2.88 (0.12), residues: 3880 helix: -2.20 (0.12), residues: 1304 sheet: -2.53 (0.20), residues: 464 loop : -1.49 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 93 PHE 0.017 0.001 PHE H 90 TYR 0.027 0.002 TYR H 233 ARG 0.007 0.001 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1310 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1062 time to evaluate : 3.362 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: 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 32 TYR cc_start: 0.8569 (m-80) cc_final: 0.8300 (m-10) REVERT: A 33 ASN cc_start: 0.8947 (p0) cc_final: 0.8673 (p0) REVERT: A 73 VAL cc_start: 0.8025 (OUTLIER) cc_final: 0.6393 (t) REVERT: A 78 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7681 (ttt) REVERT: A 128 ARG cc_start: 0.8809 (mmt90) cc_final: 0.8513 (ttm-80) REVERT: A 165 PHE cc_start: 0.8209 (p90) cc_final: 0.7936 (p90) REVERT: A 202 GLN cc_start: 0.9311 (mt0) cc_final: 0.8682 (pp30) REVERT: A 216 ASP cc_start: 0.9085 (t70) cc_final: 0.8714 (t0) REVERT: A 233 TYR cc_start: 0.8585 (m-80) cc_final: 0.8373 (m-80) REVERT: A 285 ASN cc_start: 0.9428 (m110) cc_final: 0.9122 (m110) REVERT: A 297 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8798 (tm) REVERT: A 311 LYS cc_start: 0.8905 (tmtt) cc_final: 0.8424 (tptt) REVERT: A 352 GLU cc_start: 0.8593 (tp30) cc_final: 0.8103 (tp30) REVERT: A 379 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9059 (tm) REVERT: A 386 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8309 (ppp) REVERT: A 407 ARG cc_start: 0.7430 (ttt180) cc_final: 0.7149 (ttt90) REVERT: A 420 MET cc_start: 0.6285 (mmm) cc_final: 0.5776 (mmm) REVERT: A 466 HIS cc_start: 0.8645 (OUTLIER) cc_final: 0.7943 (t-90) REVERT: A 469 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8057 (pt0) REVERT: A 470 ASP cc_start: 0.8622 (m-30) cc_final: 0.8211 (m-30) REVERT: A 482 MET cc_start: 0.8666 (tpt) cc_final: 0.8330 (tpt) REVERT: A 487 GLU cc_start: 0.8512 (pm20) cc_final: 0.7889 (pm20) REVERT: A 488 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8082 (tm) REVERT: A 489 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7914 (ttmt) REVERT: A 490 PHE cc_start: 0.8205 (m-80) cc_final: 0.7840 (m-80) REVERT: A 510 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6659 (mm-30) REVERT: B 78 MET cc_start: 0.8098 (ttm) cc_final: 0.7748 (ttp) REVERT: B 128 ARG cc_start: 0.9155 (mmm-85) cc_final: 0.8814 (mmt90) REVERT: B 161 ARG cc_start: 0.9388 (mpp-170) cc_final: 0.8945 (mtt90) REVERT: B 165 PHE cc_start: 0.8007 (p90) cc_final: 0.7729 (p90) REVERT: B 176 GLU cc_start: 0.9237 (mp0) cc_final: 0.8782 (mp0) REVERT: B 202 GLN cc_start: 0.9356 (mt0) cc_final: 0.8467 (mm-40) REVERT: B 203 ARG cc_start: 0.9090 (mpt180) cc_final: 0.8849 (mmp-170) REVERT: B 206 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8023 (ttpt) REVERT: B 214 GLU cc_start: 0.9375 (mm-30) cc_final: 0.9137 (mp0) REVERT: B 216 ASP cc_start: 0.9108 (t70) cc_final: 0.8762 (t0) REVERT: B 297 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8827 (tm) REVERT: B 311 LYS cc_start: 0.8996 (tmtt) cc_final: 0.8459 (tptt) REVERT: B 352 GLU cc_start: 0.8742 (tp30) cc_final: 0.8384 (tp30) REVERT: B 357 PHE cc_start: 0.8810 (m-80) cc_final: 0.8407 (m-10) REVERT: B 386 MET cc_start: 0.8768 (ppp) cc_final: 0.8238 (ppp) REVERT: B 420 MET cc_start: 0.6553 (mmm) cc_final: 0.6151 (mmm) REVERT: B 466 HIS cc_start: 0.8499 (OUTLIER) cc_final: 0.7800 (t-90) REVERT: B 469 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8013 (pt0) REVERT: B 482 MET cc_start: 0.8658 (tpt) cc_final: 0.8316 (tpt) REVERT: B 484 TYR cc_start: 0.8899 (m-10) cc_final: 0.8195 (m-10) REVERT: B 487 GLU cc_start: 0.8616 (pm20) cc_final: 0.8060 (pm20) REVERT: B 490 PHE cc_start: 0.8354 (m-80) cc_final: 0.7811 (m-80) REVERT: B 509 TYR cc_start: 0.7726 (p90) cc_final: 0.7353 (p90) REVERT: B 514 PHE cc_start: 0.7041 (p90) cc_final: 0.6819 (p90) REVERT: C 32 TYR cc_start: 0.8601 (m-80) cc_final: 0.8331 (m-10) REVERT: C 33 ASN cc_start: 0.8934 (p0) cc_final: 0.8607 (p0) REVERT: C 73 VAL cc_start: 0.8227 (OUTLIER) cc_final: 0.6372 (t) REVERT: C 165 PHE cc_start: 0.8042 (p90) cc_final: 0.7807 (p90) REVERT: C 199 GLU cc_start: 0.9563 (tp30) cc_final: 0.9111 (tp30) REVERT: C 203 ARG cc_start: 0.9451 (ptp-110) cc_final: 0.9060 (ptp-110) REVERT: C 206 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7832 (ttpt) REVERT: C 208 LYS cc_start: 0.8524 (mtpp) cc_final: 0.7780 (mtpp) REVERT: C 216 ASP cc_start: 0.9173 (t70) cc_final: 0.8794 (t0) REVERT: C 285 ASN cc_start: 0.9397 (m110) cc_final: 0.9100 (m110) REVERT: C 297 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8732 (tm) REVERT: C 311 LYS cc_start: 0.8950 (tmtt) cc_final: 0.8419 (tptt) REVERT: C 348 TYR cc_start: 0.9252 (t80) cc_final: 0.9042 (t80) REVERT: C 379 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9074 (tm) REVERT: C 386 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8233 (ppp) REVERT: C 420 MET cc_start: 0.6366 (mmm) cc_final: 0.5972 (mmm) REVERT: C 466 HIS cc_start: 0.8630 (OUTLIER) cc_final: 0.8062 (t-90) REVERT: C 470 ASP cc_start: 0.8572 (m-30) cc_final: 0.8164 (m-30) REVERT: C 482 MET cc_start: 0.8707 (tpt) cc_final: 0.8365 (tpt) REVERT: C 487 GLU cc_start: 0.8668 (pm20) cc_final: 0.8131 (pm20) REVERT: C 490 PHE cc_start: 0.8332 (m-80) cc_final: 0.7794 (m-80) REVERT: C 509 TYR cc_start: 0.7626 (p90) cc_final: 0.7070 (p90) REVERT: C 510 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6474 (mm-30) REVERT: C 514 PHE cc_start: 0.7207 (p90) cc_final: 0.7000 (p90) REVERT: D 33 ASN cc_start: 0.8898 (p0) cc_final: 0.8658 (p0) REVERT: D 62 LYS cc_start: 0.9131 (mttm) cc_final: 0.8917 (ttpt) REVERT: D 73 VAL cc_start: 0.7879 (OUTLIER) cc_final: 0.6213 (t) REVERT: D 78 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7747 (ttt) REVERT: D 161 ARG cc_start: 0.9404 (mpp-170) cc_final: 0.9118 (mtt90) REVERT: D 165 PHE cc_start: 0.7974 (p90) cc_final: 0.7697 (p90) REVERT: D 176 GLU cc_start: 0.9264 (mp0) cc_final: 0.8840 (mp0) REVERT: D 199 GLU cc_start: 0.9562 (tp30) cc_final: 0.9361 (tp30) REVERT: D 206 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7911 (ttpt) REVERT: D 216 ASP cc_start: 0.9160 (t70) cc_final: 0.8836 (t0) REVERT: D 250 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8353 (pp) REVERT: D 258 TYR cc_start: 0.8452 (t80) cc_final: 0.8232 (t80) REVERT: D 297 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8820 (tm) REVERT: D 311 LYS cc_start: 0.8955 (tmtt) cc_final: 0.8382 (tptt) REVERT: D 352 GLU cc_start: 0.8609 (tp30) cc_final: 0.8257 (tp30) REVERT: D 386 MET cc_start: 0.8806 (ppp) cc_final: 0.8250 (ppp) REVERT: D 390 LEU cc_start: 0.9082 (tt) cc_final: 0.8855 (tt) REVERT: D 407 ARG cc_start: 0.7440 (ttt180) cc_final: 0.7169 (ttt180) REVERT: D 466 HIS cc_start: 0.8612 (OUTLIER) cc_final: 0.8141 (t-90) REVERT: D 482 MET cc_start: 0.8749 (tpt) cc_final: 0.8386 (tpt) REVERT: D 487 GLU cc_start: 0.8611 (pm20) cc_final: 0.8036 (pm20) REVERT: D 490 PHE cc_start: 0.8365 (m-80) cc_final: 0.7849 (m-80) REVERT: D 509 TYR cc_start: 0.7690 (p90) cc_final: 0.7366 (p90) REVERT: E 33 ASN cc_start: 0.8923 (p0) cc_final: 0.8580 (p0) REVERT: E 62 LYS cc_start: 0.9173 (mmtp) cc_final: 0.8899 (mttm) REVERT: E 78 MET cc_start: 0.8469 (ttm) cc_final: 0.8222 (ttm) REVERT: E 128 ARG cc_start: 0.8824 (mmt90) cc_final: 0.8538 (mmt90) REVERT: E 165 PHE cc_start: 0.8341 (p90) cc_final: 0.7272 (p90) REVERT: E 216 ASP cc_start: 0.9154 (t70) cc_final: 0.8802 (t0) REVERT: E 235 LEU cc_start: 0.9092 (mt) cc_final: 0.8581 (mt) REVERT: E 258 TYR cc_start: 0.8686 (t80) cc_final: 0.8467 (t80) REVERT: E 285 ASN cc_start: 0.9368 (m110) cc_final: 0.9046 (m110) REVERT: E 297 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8755 (tm) REVERT: E 311 LYS cc_start: 0.8951 (tmtt) cc_final: 0.8478 (tptt) REVERT: E 348 TYR cc_start: 0.9248 (t80) cc_final: 0.8969 (t80) REVERT: E 379 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9035 (tm) REVERT: E 386 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8357 (ppp) REVERT: E 420 MET cc_start: 0.6250 (mmm) cc_final: 0.5855 (mmm) REVERT: E 466 HIS cc_start: 0.8642 (OUTLIER) cc_final: 0.7924 (t-90) REVERT: E 469 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8057 (pt0) REVERT: E 470 ASP cc_start: 0.8623 (m-30) cc_final: 0.8341 (m-30) REVERT: E 482 MET cc_start: 0.8692 (tpt) cc_final: 0.8372 (tpt) REVERT: E 484 TYR cc_start: 0.8939 (m-10) cc_final: 0.8709 (m-10) REVERT: E 487 GLU cc_start: 0.8678 (pm20) cc_final: 0.8123 (pm20) REVERT: E 488 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7452 (tp) REVERT: E 490 PHE cc_start: 0.8397 (m-80) cc_final: 0.8005 (m-80) REVERT: F 33 ASN cc_start: 0.8932 (p0) cc_final: 0.8639 (p0) REVERT: F 62 LYS cc_start: 0.9126 (mmtp) cc_final: 0.8889 (mmmt) REVERT: F 78 MET cc_start: 0.8504 (ttm) cc_final: 0.8211 (ttt) REVERT: F 109 LYS cc_start: 0.8735 (mmtm) cc_final: 0.8407 (mmtm) REVERT: F 132 GLU cc_start: 0.9466 (mp0) cc_final: 0.9223 (pm20) REVERT: F 161 ARG cc_start: 0.9387 (mpp-170) cc_final: 0.8605 (mtt90) REVERT: F 165 PHE cc_start: 0.8262 (p90) cc_final: 0.7964 (p90) REVERT: F 185 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7695 (mt) REVERT: F 199 GLU cc_start: 0.9546 (tp30) cc_final: 0.9238 (tp30) REVERT: F 203 ARG cc_start: 0.9490 (ptp-110) cc_final: 0.9283 (ptp-110) REVERT: F 216 ASP cc_start: 0.9147 (t70) cc_final: 0.8831 (t0) REVERT: F 235 LEU cc_start: 0.9093 (mt) cc_final: 0.8608 (mt) REVERT: F 258 TYR cc_start: 0.8462 (t80) cc_final: 0.8214 (t80) REVERT: F 297 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8817 (tm) REVERT: F 311 LYS cc_start: 0.8957 (tmtt) cc_final: 0.8469 (tptt) REVERT: F 352 GLU cc_start: 0.8763 (tp30) cc_final: 0.8528 (tp30) REVERT: F 386 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8295 (pmm) REVERT: F 466 HIS cc_start: 0.8613 (OUTLIER) cc_final: 0.8116 (t-90) REVERT: F 470 ASP cc_start: 0.8614 (m-30) cc_final: 0.8273 (m-30) REVERT: F 482 MET cc_start: 0.8738 (tpt) cc_final: 0.8327 (tpt) REVERT: F 487 GLU cc_start: 0.8731 (pm20) cc_final: 0.8278 (pm20) REVERT: F 490 PHE cc_start: 0.8397 (m-80) cc_final: 0.7824 (m-80) REVERT: F 509 TYR cc_start: 0.7778 (p90) cc_final: 0.7446 (p90) REVERT: F 514 PHE cc_start: 0.7216 (p90) cc_final: 0.7000 (p90) REVERT: G 32 TYR cc_start: 0.8605 (m-80) cc_final: 0.8356 (m-10) REVERT: G 33 ASN cc_start: 0.8878 (p0) cc_final: 0.8571 (p0) REVERT: G 73 VAL cc_start: 0.8037 (OUTLIER) cc_final: 0.6473 (t) REVERT: G 78 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7725 (ttt) REVERT: G 128 ARG cc_start: 0.8879 (mmt90) cc_final: 0.8441 (mmt90) REVERT: G 165 PHE cc_start: 0.8134 (p90) cc_final: 0.7778 (p90) REVERT: G 206 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7825 (ttpt) REVERT: G 285 ASN cc_start: 0.9371 (m110) cc_final: 0.9048 (m110) REVERT: G 297 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8805 (tm) REVERT: G 311 LYS cc_start: 0.8950 (tmtt) cc_final: 0.8484 (tptt) REVERT: G 348 TYR cc_start: 0.9238 (t80) cc_final: 0.8959 (t80) REVERT: G 379 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9092 (tm) REVERT: G 386 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8238 (ppp) REVERT: G 390 LEU cc_start: 0.8952 (tt) cc_final: 0.8697 (tt) REVERT: G 466 HIS cc_start: 0.8723 (OUTLIER) cc_final: 0.8018 (t-90) REVERT: G 469 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8195 (pt0) REVERT: G 470 ASP cc_start: 0.8629 (m-30) cc_final: 0.8213 (m-30) REVERT: G 482 MET cc_start: 0.8740 (tpt) cc_final: 0.8396 (tpt) REVERT: G 484 TYR cc_start: 0.8989 (m-10) cc_final: 0.8699 (m-10) REVERT: G 487 GLU cc_start: 0.8718 (pm20) cc_final: 0.8164 (pm20) REVERT: G 490 PHE cc_start: 0.8463 (m-80) cc_final: 0.7913 (m-80) REVERT: H 33 ASN cc_start: 0.9013 (p0) cc_final: 0.8809 (p0) REVERT: H 161 ARG cc_start: 0.9451 (mpp-170) cc_final: 0.8738 (mtt90) REVERT: H 165 PHE cc_start: 0.8076 (p90) cc_final: 0.7739 (p90) REVERT: H 199 GLU cc_start: 0.9532 (tp30) cc_final: 0.9244 (tp30) REVERT: H 206 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7887 (tttm) REVERT: H 216 ASP cc_start: 0.9072 (t70) cc_final: 0.8748 (t0) REVERT: H 297 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8768 (tm) REVERT: H 311 LYS cc_start: 0.8854 (tmtt) cc_final: 0.8323 (tptt) REVERT: H 379 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9021 (tm) REVERT: H 386 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8215 (pmm) REVERT: H 390 LEU cc_start: 0.9049 (tt) cc_final: 0.8622 (tt) REVERT: H 401 PHE cc_start: 0.8314 (p90) cc_final: 0.7972 (p90) REVERT: H 466 HIS cc_start: 0.8596 (OUTLIER) cc_final: 0.8088 (t-90) REVERT: H 470 ASP cc_start: 0.8614 (m-30) cc_final: 0.8279 (m-30) REVERT: H 482 MET cc_start: 0.8669 (tpt) cc_final: 0.8291 (tpt) REVERT: H 487 GLU cc_start: 0.8655 (pm20) cc_final: 0.8076 (pm20) REVERT: H 490 PHE cc_start: 0.8301 (m-80) cc_final: 0.7746 (m-80) REVERT: H 509 TYR cc_start: 0.7964 (p90) cc_final: 0.7558 (p90) outliers start: 248 outliers final: 155 residues processed: 1174 average time/residue: 0.4083 time to fit residues: 765.5053 Evaluate side-chains 1124 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 921 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 489 LYS Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 466 HIS Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 466 HIS Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 466 HIS Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 466 HIS Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 466 HIS Chi-restraints excluded: chain H residue 469 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 5.9990 chunk 262 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 166 optimal weight: 9.9990 chunk 234 optimal weight: 3.9990 chunk 350 optimal weight: 3.9990 chunk 371 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 332 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 303 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN D 303 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN E 303 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** F 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 31576 Z= 0.375 Angle : 0.829 12.097 42888 Z= 0.409 Chirality : 0.049 0.212 4888 Planarity : 0.006 0.068 5328 Dihedral : 17.843 146.921 5370 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 26.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 10.87 % Allowed : 25.94 % Favored : 63.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -2.63 (0.13), residues: 3880 helix: -2.13 (0.12), residues: 1280 sheet: -2.90 (0.22), residues: 384 loop : -1.21 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS D 253 PHE 0.012 0.002 PHE H 90 TYR 0.025 0.002 TYR G 233 ARG 0.008 0.001 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1334 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 987 time to evaluate : 3.502 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: 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 32 TYR cc_start: 0.8687 (m-80) cc_final: 0.8408 (m-10) REVERT: A 66 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8834 (p) REVERT: A 73 VAL cc_start: 0.8390 (OUTLIER) cc_final: 0.6847 (t) REVERT: A 78 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7951 (ttt) REVERT: A 100 GLN cc_start: 0.8999 (tt0) cc_final: 0.8710 (tp40) REVERT: A 128 ARG cc_start: 0.8829 (mmt90) cc_final: 0.8532 (mmt90) REVERT: A 165 PHE cc_start: 0.8180 (p90) cc_final: 0.7867 (p90) REVERT: A 202 GLN cc_start: 0.9387 (mt0) cc_final: 0.8597 (pp30) REVERT: A 203 ARG cc_start: 0.9588 (ptp-110) cc_final: 0.9002 (ptp90) REVERT: A 216 ASP cc_start: 0.9107 (t70) cc_final: 0.8737 (t0) REVERT: A 285 ASN cc_start: 0.9477 (m110) cc_final: 0.9190 (m110) REVERT: A 311 LYS cc_start: 0.8872 (tmtt) cc_final: 0.8284 (tptt) REVERT: A 315 ASP cc_start: 0.9049 (p0) cc_final: 0.8815 (p0) REVERT: A 379 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9128 (tm) REVERT: A 386 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.7986 (ppp) REVERT: A 466 HIS cc_start: 0.8754 (OUTLIER) cc_final: 0.7932 (t-90) REVERT: A 469 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8118 (pt0) REVERT: A 470 ASP cc_start: 0.8575 (m-30) cc_final: 0.8143 (m-30) REVERT: A 482 MET cc_start: 0.8785 (tpt) cc_final: 0.8373 (tpt) REVERT: A 487 GLU cc_start: 0.8444 (pm20) cc_final: 0.7986 (pm20) REVERT: A 489 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.8002 (ttmt) REVERT: A 490 PHE cc_start: 0.8339 (m-80) cc_final: 0.7819 (m-80) REVERT: A 509 TYR cc_start: 0.7704 (p90) cc_final: 0.7308 (p90) REVERT: A 510 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6672 (mm-30) REVERT: B 73 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.6671 (t) REVERT: B 78 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7981 (ttp) REVERT: B 165 PHE cc_start: 0.8150 (p90) cc_final: 0.7812 (p90) REVERT: B 206 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7997 (ttpt) REVERT: B 214 GLU cc_start: 0.9371 (mm-30) cc_final: 0.9144 (mp0) REVERT: B 216 ASP cc_start: 0.9111 (t70) cc_final: 0.8758 (t0) REVERT: B 297 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8919 (tm) REVERT: B 311 LYS cc_start: 0.8973 (tmtt) cc_final: 0.8377 (tptt) REVERT: B 315 ASP cc_start: 0.9005 (p0) cc_final: 0.8718 (p0) REVERT: B 379 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9049 (tm) REVERT: B 386 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8100 (ppp) REVERT: B 407 ARG cc_start: 0.7483 (ttt180) cc_final: 0.6959 (ttt-90) REVERT: B 420 MET cc_start: 0.6770 (mmm) cc_final: 0.6349 (mmm) REVERT: B 466 HIS cc_start: 0.8773 (OUTLIER) cc_final: 0.8062 (t-90) REVERT: B 469 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8147 (pt0) REVERT: B 482 MET cc_start: 0.8802 (tpt) cc_final: 0.8383 (tpt) REVERT: B 487 GLU cc_start: 0.8507 (pm20) cc_final: 0.8019 (pm20) REVERT: B 489 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7937 (ttmt) REVERT: B 490 PHE cc_start: 0.8376 (m-80) cc_final: 0.7814 (m-80) REVERT: C 32 TYR cc_start: 0.8706 (m-80) cc_final: 0.8454 (m-10) REVERT: C 62 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8703 (mtmm) REVERT: C 78 MET cc_start: 0.8084 (ttt) cc_final: 0.7858 (ttt) REVERT: C 165 PHE cc_start: 0.8246 (p90) cc_final: 0.7959 (p90) REVERT: C 199 GLU cc_start: 0.9566 (tp30) cc_final: 0.9297 (tp30) REVERT: C 208 LYS cc_start: 0.8611 (mtpp) cc_final: 0.8151 (mtpp) REVERT: C 214 GLU cc_start: 0.9421 (mm-30) cc_final: 0.9146 (mp0) REVERT: C 216 ASP cc_start: 0.9164 (t70) cc_final: 0.8788 (t0) REVERT: C 235 LEU cc_start: 0.8953 (mt) cc_final: 0.8655 (pp) REVERT: C 285 ASN cc_start: 0.9455 (m110) cc_final: 0.9185 (m110) REVERT: C 311 LYS cc_start: 0.8902 (tmtt) cc_final: 0.8353 (tptt) REVERT: C 348 TYR cc_start: 0.9301 (t80) cc_final: 0.9044 (t80) REVERT: C 379 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9168 (tm) REVERT: C 386 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8091 (ppp) REVERT: C 420 MET cc_start: 0.6673 (mmm) cc_final: 0.6212 (mmm) REVERT: C 466 HIS cc_start: 0.8761 (OUTLIER) cc_final: 0.8040 (t-90) REVERT: C 470 ASP cc_start: 0.8523 (m-30) cc_final: 0.8133 (m-30) REVERT: C 482 MET cc_start: 0.8816 (tpt) cc_final: 0.8412 (tpt) REVERT: C 487 GLU cc_start: 0.8541 (pm20) cc_final: 0.7947 (pm20) REVERT: C 490 PHE cc_start: 0.8260 (m-80) cc_final: 0.7809 (m-80) REVERT: C 510 GLU cc_start: 0.6818 (mm-30) cc_final: 0.6424 (mm-30) REVERT: C 514 PHE cc_start: 0.7729 (p90) cc_final: 0.7385 (p90) REVERT: D 73 VAL cc_start: 0.8334 (OUTLIER) cc_final: 0.6739 (t) REVERT: D 78 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7995 (ttt) REVERT: D 165 PHE cc_start: 0.8092 (p90) cc_final: 0.7760 (p90) REVERT: D 202 GLN cc_start: 0.9462 (mt0) cc_final: 0.9227 (mt0) REVERT: D 206 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7859 (ttpt) REVERT: D 208 LYS cc_start: 0.8494 (mtpp) cc_final: 0.8177 (ttmm) REVERT: D 216 ASP cc_start: 0.9221 (t70) cc_final: 0.8902 (t0) REVERT: D 297 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8944 (tm) REVERT: D 311 LYS cc_start: 0.8909 (tmtt) cc_final: 0.8351 (tptt) REVERT: D 352 GLU cc_start: 0.8689 (tp30) cc_final: 0.8355 (tp30) REVERT: D 390 LEU cc_start: 0.9119 (tt) cc_final: 0.8683 (tt) REVERT: D 420 MET cc_start: 0.7074 (mmm) cc_final: 0.6656 (mmm) REVERT: D 466 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8308 (t-90) REVERT: D 482 MET cc_start: 0.8861 (tpt) cc_final: 0.8423 (tpt) REVERT: D 487 GLU cc_start: 0.8570 (pm20) cc_final: 0.7987 (pm20) REVERT: D 488 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7871 (tp) REVERT: D 490 PHE cc_start: 0.8312 (m-80) cc_final: 0.7940 (m-80) REVERT: D 514 PHE cc_start: 0.7744 (p90) cc_final: 0.7323 (p90) REVERT: E 32 TYR cc_start: 0.8697 (m-10) cc_final: 0.8374 (m-10) REVERT: E 62 LYS cc_start: 0.9270 (mmtp) cc_final: 0.8858 (mttm) REVERT: E 78 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8193 (ttm) REVERT: E 128 ARG cc_start: 0.8812 (mmt90) cc_final: 0.8598 (mmm-85) REVERT: E 206 LYS cc_start: 0.8294 (mtmt) cc_final: 0.7941 (ttpt) REVERT: E 208 LYS cc_start: 0.8142 (ttmm) cc_final: 0.7695 (ttmm) REVERT: E 214 GLU cc_start: 0.9392 (mm-30) cc_final: 0.9159 (mp0) REVERT: E 216 ASP cc_start: 0.9194 (t70) cc_final: 0.8851 (t0) REVERT: E 235 LEU cc_start: 0.9067 (mt) cc_final: 0.8517 (mt) REVERT: E 297 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8871 (tm) REVERT: E 311 LYS cc_start: 0.8939 (tmtt) cc_final: 0.8429 (tptt) REVERT: E 348 TYR cc_start: 0.9335 (t80) cc_final: 0.9075 (t80) REVERT: E 379 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9136 (tm) REVERT: E 386 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8037 (ppp) REVERT: E 407 ARG cc_start: 0.7698 (ttt180) cc_final: 0.7497 (ttt180) REVERT: E 408 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8653 (mp) REVERT: E 420 MET cc_start: 0.6731 (mmm) cc_final: 0.6330 (mmm) REVERT: E 466 HIS cc_start: 0.8759 (OUTLIER) cc_final: 0.8049 (t-90) REVERT: E 470 ASP cc_start: 0.8666 (m-30) cc_final: 0.8218 (m-30) REVERT: E 482 MET cc_start: 0.8837 (tpt) cc_final: 0.8425 (tpt) REVERT: E 487 GLU cc_start: 0.8654 (pm20) cc_final: 0.8178 (pm20) REVERT: E 489 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7911 (tttm) REVERT: E 490 PHE cc_start: 0.8299 (m-80) cc_final: 0.7888 (m-80) REVERT: E 509 TYR cc_start: 0.7828 (p90) cc_final: 0.7549 (p90) REVERT: E 510 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6415 (mm-30) REVERT: F 32 TYR cc_start: 0.8666 (m-10) cc_final: 0.8463 (m-10) REVERT: F 62 LYS cc_start: 0.9223 (mmtp) cc_final: 0.8956 (mttp) REVERT: F 109 LYS cc_start: 0.8853 (mmtm) cc_final: 0.8516 (mptt) REVERT: F 165 PHE cc_start: 0.8344 (p90) cc_final: 0.7854 (p90) REVERT: F 185 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7749 (mt) REVERT: F 216 ASP cc_start: 0.9227 (t70) cc_final: 0.8886 (t0) REVERT: F 235 LEU cc_start: 0.9129 (mt) cc_final: 0.8380 (mt) REVERT: F 311 LYS cc_start: 0.8956 (tmtt) cc_final: 0.8355 (tptt) REVERT: F 315 ASP cc_start: 0.8999 (p0) cc_final: 0.8735 (p0) REVERT: F 352 GLU cc_start: 0.8801 (tp30) cc_final: 0.8541 (tp30) REVERT: F 379 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9126 (tm) REVERT: F 386 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8601 (pmm) REVERT: F 466 HIS cc_start: 0.8747 (OUTLIER) cc_final: 0.8127 (t-90) REVERT: F 470 ASP cc_start: 0.8605 (m-30) cc_final: 0.8255 (m-30) REVERT: F 482 MET cc_start: 0.8895 (tpt) cc_final: 0.8505 (tpt) REVERT: F 487 GLU cc_start: 0.8640 (pm20) cc_final: 0.8168 (pm20) REVERT: F 490 PHE cc_start: 0.8368 (m-80) cc_final: 0.7814 (m-80) REVERT: F 510 GLU cc_start: 0.6676 (mm-30) cc_final: 0.6289 (mm-30) REVERT: F 514 PHE cc_start: 0.7694 (p90) cc_final: 0.7312 (p90) REVERT: G 32 TYR cc_start: 0.8706 (m-80) cc_final: 0.8435 (m-10) REVERT: G 66 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8723 (p) REVERT: G 68 SER cc_start: 0.8856 (t) cc_final: 0.8491 (t) REVERT: G 73 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.7063 (t) REVERT: G 78 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8125 (ttt) REVERT: G 165 PHE cc_start: 0.8176 (p90) cc_final: 0.7724 (p90) REVERT: G 214 GLU cc_start: 0.9409 (mm-30) cc_final: 0.9159 (mp0) REVERT: G 216 ASP cc_start: 0.9204 (t70) cc_final: 0.8889 (t0) REVERT: G 311 LYS cc_start: 0.8958 (tmtt) cc_final: 0.8432 (tptt) REVERT: G 348 TYR cc_start: 0.9305 (t80) cc_final: 0.9097 (t80) REVERT: G 379 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9150 (tm) REVERT: G 386 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8125 (ppp) REVERT: G 407 ARG cc_start: 0.7691 (ttt180) cc_final: 0.7180 (ttt90) REVERT: G 408 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8580 (mp) REVERT: G 420 MET cc_start: 0.6701 (mmm) cc_final: 0.6305 (mmm) REVERT: G 466 HIS cc_start: 0.8846 (OUTLIER) cc_final: 0.8130 (t-90) REVERT: G 470 ASP cc_start: 0.8587 (m-30) cc_final: 0.8260 (m-30) REVERT: G 482 MET cc_start: 0.8850 (tpt) cc_final: 0.8410 (tpt) REVERT: G 487 GLU cc_start: 0.8637 (pm20) cc_final: 0.8134 (pm20) REVERT: G 489 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7921 (tttm) REVERT: G 490 PHE cc_start: 0.8368 (m-80) cc_final: 0.7945 (m-80) REVERT: G 509 TYR cc_start: 0.7788 (p90) cc_final: 0.7490 (p90) REVERT: G 510 GLU cc_start: 0.6846 (mm-30) cc_final: 0.6479 (mm-30) REVERT: H 66 VAL cc_start: 0.9144 (OUTLIER) cc_final: 0.8801 (p) REVERT: H 73 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.7166 (t) REVERT: H 165 PHE cc_start: 0.8136 (p90) cc_final: 0.7805 (p90) REVERT: H 206 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7938 (ttpt) REVERT: H 216 ASP cc_start: 0.9150 (t70) cc_final: 0.8823 (t0) REVERT: H 235 LEU cc_start: 0.8798 (mm) cc_final: 0.8023 (mm) REVERT: H 311 LYS cc_start: 0.8834 (tmtt) cc_final: 0.8289 (tptt) REVERT: H 379 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9054 (tm) REVERT: H 386 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8573 (pmm) REVERT: H 466 HIS cc_start: 0.8743 (OUTLIER) cc_final: 0.8085 (t-90) REVERT: H 470 ASP cc_start: 0.8665 (m-30) cc_final: 0.8302 (m-30) REVERT: H 482 MET cc_start: 0.8810 (tpt) cc_final: 0.8366 (tpt) REVERT: H 487 GLU cc_start: 0.8596 (pm20) cc_final: 0.8003 (pm20) REVERT: H 489 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7914 (ttmt) REVERT: H 490 PHE cc_start: 0.8389 (m-80) cc_final: 0.7812 (m-80) REVERT: H 510 GLU cc_start: 0.6733 (mm-30) cc_final: 0.6465 (mm-30) REVERT: H 514 PHE cc_start: 0.7747 (p90) cc_final: 0.7315 (p90) outliers start: 347 outliers final: 229 residues processed: 1141 average time/residue: 0.4133 time to fit residues: 753.2033 Evaluate side-chains 1210 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 928 time to evaluate : 3.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 489 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 489 LYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 466 HIS Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 466 HIS Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 355 ARG Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 489 LYS Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 466 HIS Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 449 ASP Chi-restraints excluded: chain G residue 466 HIS Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 466 HIS Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 489 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 4.9990 chunk 210 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 276 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 316 optimal weight: 0.0070 chunk 256 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 7.9990 chunk 333 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN D 469 GLN ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN E 309 GLN E 312 ASN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 GLN ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN ** F 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 GLN ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 469 GLN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31576 Z= 0.211 Angle : 0.778 12.948 42888 Z= 0.367 Chirality : 0.048 0.226 4888 Planarity : 0.004 0.055 5328 Dihedral : 17.005 144.629 5354 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 21.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 9.24 % Allowed : 28.26 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -2.60 (0.13), residues: 3880 helix: -2.12 (0.12), residues: 1312 sheet: -2.41 (0.22), residues: 464 loop : -1.19 (0.14), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 504 PHE 0.018 0.001 PHE H 90 TYR 0.033 0.002 TYR H 509 ARG 0.008 0.001 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 1051 time to evaluate : 3.366 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: 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 32 TYR cc_start: 0.8562 (m-10) cc_final: 0.8225 (m-10) REVERT: A 66 VAL cc_start: 0.9010 (OUTLIER) cc_final: 0.8584 (p) REVERT: A 73 VAL cc_start: 0.8012 (OUTLIER) cc_final: 0.6332 (t) REVERT: A 74 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8082 (p) REVERT: A 78 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7714 (ttt) REVERT: A 128 ARG cc_start: 0.8800 (mmt90) cc_final: 0.8498 (mmt90) REVERT: A 165 PHE cc_start: 0.8086 (p90) cc_final: 0.7843 (p90) REVERT: A 202 GLN cc_start: 0.9308 (mt0) cc_final: 0.8520 (pp30) REVERT: A 203 ARG cc_start: 0.9580 (ptp-110) cc_final: 0.8960 (ptp90) REVERT: A 206 LYS cc_start: 0.8174 (mtmt) cc_final: 0.7683 (ttpt) REVERT: A 208 LYS cc_start: 0.8492 (mtpp) cc_final: 0.7652 (mtpp) REVERT: A 216 ASP cc_start: 0.9111 (t70) cc_final: 0.8751 (t0) REVERT: A 285 ASN cc_start: 0.9455 (m110) cc_final: 0.9159 (m110) REVERT: A 297 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8714 (tm) REVERT: A 311 LYS cc_start: 0.8868 (tmtt) cc_final: 0.8317 (tptt) REVERT: A 386 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8130 (pmm) REVERT: A 407 ARG cc_start: 0.7630 (ttt180) cc_final: 0.7194 (ttt90) REVERT: A 420 MET cc_start: 0.6627 (mmm) cc_final: 0.6263 (mmm) REVERT: A 466 HIS cc_start: 0.8650 (OUTLIER) cc_final: 0.7996 (t-90) REVERT: A 469 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8160 (pt0) REVERT: A 470 ASP cc_start: 0.8528 (m-30) cc_final: 0.8147 (m-30) REVERT: A 482 MET cc_start: 0.8820 (tpt) cc_final: 0.8426 (tpt) REVERT: A 487 GLU cc_start: 0.8431 (pm20) cc_final: 0.7870 (pm20) REVERT: A 489 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7905 (tttt) REVERT: A 490 PHE cc_start: 0.8273 (m-80) cc_final: 0.7712 (m-80) REVERT: A 509 TYR cc_start: 0.7729 (p90) cc_final: 0.7299 (p90) REVERT: A 510 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6826 (mm-30) REVERT: B 32 TYR cc_start: 0.8401 (m-10) cc_final: 0.8187 (m-10) REVERT: B 109 LYS cc_start: 0.8714 (mmtm) cc_final: 0.8364 (mptt) REVERT: B 165 PHE cc_start: 0.8031 (p90) cc_final: 0.7087 (p90) REVERT: B 179 MET cc_start: 0.7157 (ttp) cc_final: 0.6822 (tmm) REVERT: B 208 LYS cc_start: 0.8523 (mtpp) cc_final: 0.8310 (mtmt) REVERT: B 214 GLU cc_start: 0.9350 (mm-30) cc_final: 0.9118 (mp0) REVERT: B 216 ASP cc_start: 0.9097 (t70) cc_final: 0.8729 (t0) REVERT: B 235 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8484 (mt) REVERT: B 297 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8795 (tm) REVERT: B 311 LYS cc_start: 0.8920 (tmtt) cc_final: 0.8366 (tptt) REVERT: B 386 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8227 (ppp) REVERT: B 420 MET cc_start: 0.6719 (mmm) cc_final: 0.6348 (mmm) REVERT: B 466 HIS cc_start: 0.8726 (OUTLIER) cc_final: 0.8465 (t-90) REVERT: B 482 MET cc_start: 0.8834 (tpt) cc_final: 0.8466 (tpt) REVERT: B 487 GLU cc_start: 0.8447 (pm20) cc_final: 0.7904 (pm20) REVERT: B 489 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7146 (tptm) REVERT: B 490 PHE cc_start: 0.8197 (m-80) cc_final: 0.7680 (m-80) REVERT: B 509 TYR cc_start: 0.7385 (p90) cc_final: 0.6900 (p90) REVERT: C 32 TYR cc_start: 0.8566 (m-10) cc_final: 0.8259 (m-10) REVERT: C 62 LYS cc_start: 0.9020 (mmtt) cc_final: 0.8807 (mtmm) REVERT: C 78 MET cc_start: 0.7950 (ttt) cc_final: 0.7748 (ttt) REVERT: C 109 LYS cc_start: 0.8780 (mmtm) cc_final: 0.8377 (mptt) REVERT: C 111 GLU cc_start: 0.8580 (mp0) cc_final: 0.8260 (mp0) REVERT: C 128 ARG cc_start: 0.9136 (mmm-85) cc_final: 0.8720 (mmt90) REVERT: C 165 PHE cc_start: 0.8182 (p90) cc_final: 0.7355 (p90) REVERT: C 206 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7715 (ttpt) REVERT: C 214 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9122 (mp0) REVERT: C 216 ASP cc_start: 0.9126 (t70) cc_final: 0.8724 (t0) REVERT: C 285 ASN cc_start: 0.9440 (m110) cc_final: 0.9172 (m110) REVERT: C 311 LYS cc_start: 0.8846 (tmtt) cc_final: 0.8296 (tptt) REVERT: C 386 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8251 (ppp) REVERT: C 420 MET cc_start: 0.6701 (mmm) cc_final: 0.6281 (mmm) REVERT: C 466 HIS cc_start: 0.8715 (OUTLIER) cc_final: 0.8137 (t-90) REVERT: C 470 ASP cc_start: 0.8448 (m-30) cc_final: 0.8123 (m-30) REVERT: C 482 MET cc_start: 0.8827 (tpt) cc_final: 0.8478 (tpt) REVERT: C 487 GLU cc_start: 0.8502 (pm20) cc_final: 0.7913 (pm20) REVERT: C 489 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7788 (ttmt) REVERT: C 490 PHE cc_start: 0.8147 (m-80) cc_final: 0.7734 (m-80) REVERT: C 509 TYR cc_start: 0.7803 (p90) cc_final: 0.7548 (p90) REVERT: C 510 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6660 (mm-30) REVERT: D 32 TYR cc_start: 0.8473 (m-10) cc_final: 0.8199 (m-10) REVERT: D 66 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8217 (p) REVERT: D 78 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7931 (ttt) REVERT: D 109 LYS cc_start: 0.8752 (mmtm) cc_final: 0.8319 (mptt) REVERT: D 165 PHE cc_start: 0.8036 (p90) cc_final: 0.7669 (p90) REVERT: D 166 LEU cc_start: 0.8328 (tp) cc_final: 0.8042 (tp) REVERT: D 206 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7715 (ttpt) REVERT: D 216 ASP cc_start: 0.9187 (t70) cc_final: 0.8843 (t0) REVERT: D 297 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8813 (tm) REVERT: D 311 LYS cc_start: 0.8868 (tmtt) cc_final: 0.8294 (tptt) REVERT: D 352 GLU cc_start: 0.8723 (tp30) cc_final: 0.8405 (tp30) REVERT: D 386 MET cc_start: 0.8512 (pmm) cc_final: 0.8285 (pmm) REVERT: D 390 LEU cc_start: 0.8998 (tt) cc_final: 0.8614 (tt) REVERT: D 420 MET cc_start: 0.7040 (mmm) cc_final: 0.6610 (mmm) REVERT: D 466 HIS cc_start: 0.8786 (OUTLIER) cc_final: 0.8555 (t-90) REVERT: D 482 MET cc_start: 0.8799 (tpt) cc_final: 0.8535 (tpt) REVERT: D 488 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7566 (tp) REVERT: D 490 PHE cc_start: 0.8301 (m-80) cc_final: 0.7815 (m-80) REVERT: D 509 TYR cc_start: 0.7404 (p90) cc_final: 0.6956 (p90) REVERT: D 510 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6867 (mm-30) REVERT: E 32 TYR cc_start: 0.8578 (m-10) cc_final: 0.8317 (m-10) REVERT: E 78 MET cc_start: 0.8663 (ttm) cc_final: 0.8206 (ttm) REVERT: E 128 ARG cc_start: 0.8819 (mmt90) cc_final: 0.8500 (mmt90) REVERT: E 202 GLN cc_start: 0.9353 (mm-40) cc_final: 0.8149 (pp30) REVERT: E 208 LYS cc_start: 0.8229 (ttmm) cc_final: 0.7618 (mtmt) REVERT: E 214 GLU cc_start: 0.9387 (mm-30) cc_final: 0.9147 (mp0) REVERT: E 216 ASP cc_start: 0.9180 (t70) cc_final: 0.8826 (t0) REVERT: E 297 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8774 (tm) REVERT: E 311 LYS cc_start: 0.8907 (tmtt) cc_final: 0.8369 (tptt) REVERT: E 386 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8379 (pmm) REVERT: E 407 ARG cc_start: 0.7708 (ttt180) cc_final: 0.7234 (tpt-90) REVERT: E 408 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8528 (mp) REVERT: E 420 MET cc_start: 0.6750 (mmm) cc_final: 0.6400 (mmm) REVERT: E 466 HIS cc_start: 0.8719 (OUTLIER) cc_final: 0.8163 (t-90) REVERT: E 470 ASP cc_start: 0.8642 (m-30) cc_final: 0.8125 (m-30) REVERT: E 482 MET cc_start: 0.8760 (tpt) cc_final: 0.8400 (tpt) REVERT: E 487 GLU cc_start: 0.8559 (pm20) cc_final: 0.7972 (pm20) REVERT: E 489 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7945 (ttmt) REVERT: E 490 PHE cc_start: 0.8230 (m-80) cc_final: 0.7811 (m-80) REVERT: E 509 TYR cc_start: 0.7874 (p90) cc_final: 0.7574 (p90) REVERT: E 510 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6400 (mm-30) REVERT: F 109 LYS cc_start: 0.8803 (mmtm) cc_final: 0.8389 (mptt) REVERT: F 165 PHE cc_start: 0.8236 (p90) cc_final: 0.7741 (p90) REVERT: F 166 LEU cc_start: 0.8146 (tp) cc_final: 0.7850 (tp) REVERT: F 185 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7677 (mt) REVERT: F 216 ASP cc_start: 0.9210 (t70) cc_final: 0.8856 (t0) REVERT: F 235 LEU cc_start: 0.8997 (mt) cc_final: 0.8295 (mt) REVERT: F 297 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8814 (tm) REVERT: F 311 LYS cc_start: 0.8905 (tmtt) cc_final: 0.8372 (tptt) REVERT: F 352 GLU cc_start: 0.8794 (tp30) cc_final: 0.8177 (tp30) REVERT: F 386 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8427 (pmm) REVERT: F 407 ARG cc_start: 0.7415 (ttt180) cc_final: 0.6829 (ttt-90) REVERT: F 466 HIS cc_start: 0.8712 (OUTLIER) cc_final: 0.8220 (t-90) REVERT: F 470 ASP cc_start: 0.8634 (m-30) cc_final: 0.8323 (m-30) REVERT: F 482 MET cc_start: 0.8883 (tpt) cc_final: 0.8511 (tpt) REVERT: F 484 TYR cc_start: 0.8851 (m-80) cc_final: 0.8455 (m-80) REVERT: F 487 GLU cc_start: 0.8599 (pm20) cc_final: 0.8084 (pm20) REVERT: F 490 PHE cc_start: 0.8280 (m-80) cc_final: 0.7808 (m-80) REVERT: F 509 TYR cc_start: 0.7450 (p90) cc_final: 0.6950 (p90) REVERT: F 510 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6688 (mm-30) REVERT: G 32 TYR cc_start: 0.8583 (m-80) cc_final: 0.8304 (m-10) REVERT: G 68 SER cc_start: 0.8624 (t) cc_final: 0.8422 (t) REVERT: G 73 VAL cc_start: 0.8135 (OUTLIER) cc_final: 0.6772 (t) REVERT: G 109 LYS cc_start: 0.8863 (mmtm) cc_final: 0.8451 (mptt) REVERT: G 165 PHE cc_start: 0.8100 (p90) cc_final: 0.7715 (p90) REVERT: G 206 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7732 (ttpt) REVERT: G 216 ASP cc_start: 0.9176 (t70) cc_final: 0.8834 (t0) REVERT: G 262 LEU cc_start: 0.9330 (tt) cc_final: 0.8959 (tp) REVERT: G 265 GLN cc_start: 0.9268 (mm110) cc_final: 0.8937 (mp10) REVERT: G 297 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8764 (tm) REVERT: G 311 LYS cc_start: 0.8926 (tmtt) cc_final: 0.8059 (tppt) REVERT: G 348 TYR cc_start: 0.9264 (t80) cc_final: 0.8876 (t80) REVERT: G 352 GLU cc_start: 0.8822 (tp30) cc_final: 0.8024 (tp30) REVERT: G 386 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8188 (ppp) REVERT: G 407 ARG cc_start: 0.7698 (ttt180) cc_final: 0.7216 (tpt-90) REVERT: G 420 MET cc_start: 0.6626 (mmm) cc_final: 0.6284 (mmm) REVERT: G 466 HIS cc_start: 0.8835 (OUTLIER) cc_final: 0.8346 (t-90) REVERT: G 470 ASP cc_start: 0.8613 (m-30) cc_final: 0.8281 (m-30) REVERT: G 482 MET cc_start: 0.8845 (tpt) cc_final: 0.8446 (tpt) REVERT: G 484 TYR cc_start: 0.9172 (m-10) cc_final: 0.8813 (m-80) REVERT: G 487 GLU cc_start: 0.8599 (pm20) cc_final: 0.8028 (pm20) REVERT: G 489 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7949 (ttmt) REVERT: G 490 PHE cc_start: 0.8316 (m-80) cc_final: 0.7852 (m-80) REVERT: G 509 TYR cc_start: 0.7896 (p90) cc_final: 0.7526 (p90) REVERT: G 510 GLU cc_start: 0.6889 (mm-30) cc_final: 0.6674 (mm-30) REVERT: H 65 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8746 (pt) REVERT: H 66 VAL cc_start: 0.9138 (OUTLIER) cc_final: 0.8868 (p) REVERT: H 73 VAL cc_start: 0.8345 (OUTLIER) cc_final: 0.7073 (t) REVERT: H 165 PHE cc_start: 0.8085 (p90) cc_final: 0.7747 (p90) REVERT: H 179 MET cc_start: 0.6910 (ttp) cc_final: 0.6709 (tmm) REVERT: H 199 GLU cc_start: 0.9481 (tp30) cc_final: 0.9182 (mt-10) REVERT: H 202 GLN cc_start: 0.9385 (mm-40) cc_final: 0.8440 (pp30) REVERT: H 203 ARG cc_start: 0.9312 (ptp-110) cc_final: 0.9086 (ptp90) REVERT: H 206 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7922 (ttpt) REVERT: H 208 LYS cc_start: 0.8243 (ttmm) cc_final: 0.8018 (mtpp) REVERT: H 216 ASP cc_start: 0.9118 (t70) cc_final: 0.8795 (t0) REVERT: H 283 GLN cc_start: 0.8768 (tt0) cc_final: 0.8461 (mt0) REVERT: H 297 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8809 (tm) REVERT: H 311 LYS cc_start: 0.8844 (tmtt) cc_final: 0.8273 (tptt) REVERT: H 352 GLU cc_start: 0.8713 (tp30) cc_final: 0.7971 (tp30) REVERT: H 386 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8092 (pmm) REVERT: H 466 HIS cc_start: 0.8702 (OUTLIER) cc_final: 0.8211 (t-90) REVERT: H 470 ASP cc_start: 0.8639 (m-30) cc_final: 0.8283 (m-30) REVERT: H 482 MET cc_start: 0.8845 (tpt) cc_final: 0.8446 (tpt) REVERT: H 484 TYR cc_start: 0.9009 (m-10) cc_final: 0.8587 (m-80) REVERT: H 487 GLU cc_start: 0.8566 (pm20) cc_final: 0.8018 (pm20) REVERT: H 489 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7855 (tttt) REVERT: H 490 PHE cc_start: 0.8356 (m-80) cc_final: 0.7739 (m-80) REVERT: H 509 TYR cc_start: 0.7495 (p90) cc_final: 0.7026 (p90) outliers start: 295 outliers final: 191 residues processed: 1185 average time/residue: 0.4165 time to fit residues: 783.6227 Evaluate side-chains 1215 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 976 time to evaluate : 3.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 489 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 489 LYS Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 466 HIS Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 489 LYS Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 466 HIS Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 489 LYS Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 466 HIS Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 449 ASP Chi-restraints excluded: chain G residue 466 HIS Chi-restraints excluded: chain G residue 467 SER Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 466 HIS Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 489 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 0.9980 chunk 334 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 371 optimal weight: 3.9990 chunk 308 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 ASN ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31576 Z= 0.232 Angle : 0.774 11.617 42888 Z= 0.366 Chirality : 0.048 0.195 4888 Planarity : 0.005 0.060 5328 Dihedral : 16.543 141.052 5350 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 22.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 10.15 % Allowed : 28.29 % Favored : 61.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -2.47 (0.13), residues: 3880 helix: -1.99 (0.13), residues: 1264 sheet: -2.23 (0.24), residues: 416 loop : -1.24 (0.13), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 504 PHE 0.025 0.001 PHE E 90 TYR 0.025 0.002 TYR E 484 ARG 0.009 0.001 ARG D 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1360 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 324 poor density : 1036 time to evaluate : 3.685 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: 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 32 TYR cc_start: 0.8561 (m-10) cc_final: 0.8270 (m-10) REVERT: A 68 SER cc_start: 0.8677 (t) cc_final: 0.8255 (t) REVERT: A 73 VAL cc_start: 0.8025 (OUTLIER) cc_final: 0.6226 (t) REVERT: A 74 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8074 (p) REVERT: A 78 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7701 (ttt) REVERT: A 109 LYS cc_start: 0.8950 (mmtm) cc_final: 0.8565 (mptt) REVERT: A 128 ARG cc_start: 0.8779 (mmt90) cc_final: 0.8488 (mmt90) REVERT: A 165 PHE cc_start: 0.8106 (p90) cc_final: 0.7858 (p90) REVERT: A 202 GLN cc_start: 0.9291 (mm-40) cc_final: 0.8458 (pp30) REVERT: A 203 ARG cc_start: 0.9583 (ptp-110) cc_final: 0.8939 (ptp90) REVERT: A 206 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7690 (ttpt) REVERT: A 208 LYS cc_start: 0.8476 (mtpp) cc_final: 0.7916 (mtmt) REVERT: A 216 ASP cc_start: 0.9108 (t70) cc_final: 0.8739 (t0) REVERT: A 283 GLN cc_start: 0.8676 (tt0) cc_final: 0.8339 (mt0) REVERT: A 285 ASN cc_start: 0.9463 (m110) cc_final: 0.9168 (m110) REVERT: A 297 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8669 (tm) REVERT: A 311 LYS cc_start: 0.8858 (tmtt) cc_final: 0.7927 (tppt) REVERT: A 337 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7308 (tt) REVERT: A 385 MET cc_start: 0.7839 (ttp) cc_final: 0.6788 (tpp) REVERT: A 386 MET cc_start: 0.8814 (ppp) cc_final: 0.8321 (ppp) REVERT: A 420 MET cc_start: 0.6595 (mmm) cc_final: 0.6189 (mmm) REVERT: A 466 HIS cc_start: 0.8626 (OUTLIER) cc_final: 0.8012 (t-90) REVERT: A 469 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8166 (pt0) REVERT: A 470 ASP cc_start: 0.8500 (m-30) cc_final: 0.8089 (m-30) REVERT: A 490 PHE cc_start: 0.8315 (m-80) cc_final: 0.7839 (m-80) REVERT: A 509 TYR cc_start: 0.7750 (p90) cc_final: 0.7459 (p90) REVERT: A 510 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6862 (mm-30) REVERT: B 78 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7983 (ttm) REVERT: B 109 LYS cc_start: 0.8758 (mmtm) cc_final: 0.8388 (mptt) REVERT: B 128 ARG cc_start: 0.9004 (mmm-85) cc_final: 0.8630 (mmt90) REVERT: B 165 PHE cc_start: 0.8073 (p90) cc_final: 0.7746 (p90) REVERT: B 208 LYS cc_start: 0.8535 (mtpp) cc_final: 0.8317 (mtmt) REVERT: B 214 GLU cc_start: 0.9354 (mm-30) cc_final: 0.9125 (mp0) REVERT: B 216 ASP cc_start: 0.9098 (t70) cc_final: 0.8727 (t0) REVERT: B 297 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8839 (tm) REVERT: B 352 GLU cc_start: 0.8323 (tp30) cc_final: 0.8072 (tp30) REVERT: B 386 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8420 (pmm) REVERT: B 407 ARG cc_start: 0.7264 (ttt-90) cc_final: 0.6868 (ttt-90) REVERT: B 420 MET cc_start: 0.6819 (mmm) cc_final: 0.6472 (mmm) REVERT: B 466 HIS cc_start: 0.8692 (OUTLIER) cc_final: 0.8431 (t-90) REVERT: B 482 MET cc_start: 0.8842 (tpt) cc_final: 0.8434 (tpt) REVERT: B 484 TYR cc_start: 0.8875 (m-80) cc_final: 0.8533 (m-80) REVERT: B 487 GLU cc_start: 0.8409 (pm20) cc_final: 0.7816 (pm20) REVERT: B 489 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7155 (tptm) REVERT: B 490 PHE cc_start: 0.8233 (m-80) cc_final: 0.7725 (m-80) REVERT: B 509 TYR cc_start: 0.7426 (p90) cc_final: 0.7107 (p90) REVERT: B 510 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6763 (mm-30) REVERT: C 32 TYR cc_start: 0.8551 (m-10) cc_final: 0.8329 (m-10) REVERT: C 62 LYS cc_start: 0.9045 (mmtt) cc_final: 0.8733 (mtmm) REVERT: C 109 LYS cc_start: 0.8838 (mmtm) cc_final: 0.8470 (mptt) REVERT: C 128 ARG cc_start: 0.9153 (mmm-85) cc_final: 0.8726 (mmt90) REVERT: C 132 GLU cc_start: 0.9472 (mp0) cc_final: 0.9234 (mp0) REVERT: C 165 PHE cc_start: 0.8172 (p90) cc_final: 0.7257 (p90) REVERT: C 199 GLU cc_start: 0.9459 (tp30) cc_final: 0.9244 (mt-10) REVERT: C 202 GLN cc_start: 0.9368 (mm-40) cc_final: 0.8390 (pp30) REVERT: C 203 ARG cc_start: 0.9307 (ptp-110) cc_final: 0.9087 (ptp90) REVERT: C 208 LYS cc_start: 0.8546 (mtpp) cc_final: 0.8064 (mtpp) REVERT: C 214 GLU cc_start: 0.9405 (mm-30) cc_final: 0.9111 (mp0) REVERT: C 216 ASP cc_start: 0.9147 (t70) cc_final: 0.8772 (t0) REVERT: C 250 ILE cc_start: 0.8646 (pp) cc_final: 0.8348 (pp) REVERT: C 285 ASN cc_start: 0.9453 (m110) cc_final: 0.9174 (m110) REVERT: C 311 LYS cc_start: 0.8846 (tmtt) cc_final: 0.7975 (tppt) REVERT: C 337 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7396 (tt) REVERT: C 352 GLU cc_start: 0.8761 (tp30) cc_final: 0.7917 (tp30) REVERT: C 386 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8323 (ppp) REVERT: C 420 MET cc_start: 0.6994 (mmm) cc_final: 0.6529 (mmm) REVERT: C 466 HIS cc_start: 0.8739 (OUTLIER) cc_final: 0.8179 (t-90) REVERT: C 470 ASP cc_start: 0.8355 (m-30) cc_final: 0.7980 (m-30) REVERT: C 484 TYR cc_start: 0.9051 (m-80) cc_final: 0.8544 (m-80) REVERT: C 490 PHE cc_start: 0.8325 (m-80) cc_final: 0.7864 (m-80) REVERT: C 510 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6698 (mm-30) REVERT: D 32 TYR cc_start: 0.8462 (m-10) cc_final: 0.8229 (m-10) REVERT: D 73 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.6418 (t) REVERT: D 78 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7817 (ttt) REVERT: D 109 LYS cc_start: 0.8783 (mmtm) cc_final: 0.8343 (mptt) REVERT: D 165 PHE cc_start: 0.8031 (p90) cc_final: 0.7162 (p90) REVERT: D 166 LEU cc_start: 0.8309 (tp) cc_final: 0.8024 (tp) REVERT: D 206 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7781 (ttpt) REVERT: D 208 LYS cc_start: 0.8472 (mtpp) cc_final: 0.8092 (ttmm) REVERT: D 214 GLU cc_start: 0.9397 (mm-30) cc_final: 0.9156 (mp0) REVERT: D 216 ASP cc_start: 0.9188 (t70) cc_final: 0.8841 (t0) REVERT: D 283 GLN cc_start: 0.8633 (tt0) cc_final: 0.8328 (mt0) REVERT: D 297 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8874 (tm) REVERT: D 311 LYS cc_start: 0.8841 (tmtt) cc_final: 0.8251 (tptt) REVERT: D 390 LEU cc_start: 0.9045 (tt) cc_final: 0.8623 (tt) REVERT: D 420 MET cc_start: 0.7052 (mmm) cc_final: 0.6632 (mmm) REVERT: D 488 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7628 (tp) REVERT: D 490 PHE cc_start: 0.8275 (m-80) cc_final: 0.7824 (m-80) REVERT: D 509 TYR cc_start: 0.7420 (p90) cc_final: 0.7130 (p90) REVERT: D 510 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6872 (mm-30) REVERT: E 78 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8132 (ttm) REVERT: E 109 LYS cc_start: 0.8857 (mmtm) cc_final: 0.8431 (mptt) REVERT: E 128 ARG cc_start: 0.8819 (mmt90) cc_final: 0.8540 (mmt90) REVERT: E 132 GLU cc_start: 0.9491 (mp0) cc_final: 0.9262 (mp0) REVERT: E 208 LYS cc_start: 0.8256 (ttmm) cc_final: 0.7690 (mtmt) REVERT: E 214 GLU cc_start: 0.9382 (mm-30) cc_final: 0.9139 (mp0) REVERT: E 216 ASP cc_start: 0.9179 (t70) cc_final: 0.8812 (t0) REVERT: E 297 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8793 (tm) REVERT: E 348 TYR cc_start: 0.9191 (t80) cc_final: 0.8939 (t80) REVERT: E 386 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8483 (pmm) REVERT: E 408 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8599 (mp) REVERT: E 420 MET cc_start: 0.6999 (mmm) cc_final: 0.6576 (mmm) REVERT: E 466 HIS cc_start: 0.8694 (OUTLIER) cc_final: 0.7828 (t-90) REVERT: E 469 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8140 (pt0) REVERT: E 470 ASP cc_start: 0.8459 (m-30) cc_final: 0.8081 (m-30) REVERT: E 489 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7951 (ttmt) REVERT: E 490 PHE cc_start: 0.8305 (m-80) cc_final: 0.7874 (m-80) REVERT: E 509 TYR cc_start: 0.7841 (p90) cc_final: 0.7606 (p90) REVERT: E 510 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6440 (mm-30) REVERT: F 32 TYR cc_start: 0.8481 (m-10) cc_final: 0.8236 (m-10) REVERT: F 109 LYS cc_start: 0.8816 (mmtm) cc_final: 0.8469 (mptt) REVERT: F 165 PHE cc_start: 0.8257 (p90) cc_final: 0.7714 (p90) REVERT: F 166 LEU cc_start: 0.8190 (tp) cc_final: 0.7871 (tp) REVERT: F 185 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7776 (mt) REVERT: F 216 ASP cc_start: 0.9215 (t70) cc_final: 0.8851 (t0) REVERT: F 311 LYS cc_start: 0.8865 (tmtt) cc_final: 0.8330 (tptt) REVERT: F 386 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8192 (ppp) REVERT: F 407 ARG cc_start: 0.7412 (ttt180) cc_final: 0.6965 (ttt-90) REVERT: F 466 HIS cc_start: 0.8742 (OUTLIER) cc_final: 0.8319 (t-90) REVERT: F 470 ASP cc_start: 0.8552 (m-30) cc_final: 0.8236 (m-30) REVERT: F 482 MET cc_start: 0.8891 (tpt) cc_final: 0.8546 (tpt) REVERT: F 487 GLU cc_start: 0.8567 (pm20) cc_final: 0.7990 (pm20) REVERT: F 488 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7689 (tp) REVERT: F 490 PHE cc_start: 0.8267 (m-80) cc_final: 0.7893 (m-80) REVERT: F 509 TYR cc_start: 0.7512 (p90) cc_final: 0.7030 (p90) REVERT: F 510 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6553 (mm-30) REVERT: G 32 TYR cc_start: 0.8598 (m-10) cc_final: 0.8323 (m-10) REVERT: G 109 LYS cc_start: 0.8871 (mmtm) cc_final: 0.8480 (mptt) REVERT: G 132 GLU cc_start: 0.9477 (mp0) cc_final: 0.9256 (mp0) REVERT: G 165 PHE cc_start: 0.8219 (p90) cc_final: 0.7896 (p90) REVERT: G 199 GLU cc_start: 0.9491 (tp30) cc_final: 0.8842 (tp30) REVERT: G 202 GLN cc_start: 0.9397 (mm-40) cc_final: 0.8434 (pp30) REVERT: G 203 ARG cc_start: 0.9317 (ptp-110) cc_final: 0.8777 (ptp-110) REVERT: G 206 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7803 (ttpt) REVERT: G 216 ASP cc_start: 0.9198 (t70) cc_final: 0.8883 (t0) REVERT: G 250 ILE cc_start: 0.8781 (pp) cc_final: 0.8525 (pp) REVERT: G 297 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8850 (mm) REVERT: G 311 LYS cc_start: 0.8717 (tmtt) cc_final: 0.7903 (tppt) REVERT: G 348 TYR cc_start: 0.9263 (t80) cc_final: 0.9041 (t80) REVERT: G 385 MET cc_start: 0.7122 (ttt) cc_final: 0.6919 (mmm) REVERT: G 386 MET cc_start: 0.8645 (ppp) cc_final: 0.8365 (ppp) REVERT: G 407 ARG cc_start: 0.7526 (ttt180) cc_final: 0.7190 (tpt-90) REVERT: G 408 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8480 (mp) REVERT: G 420 MET cc_start: 0.6589 (mmm) cc_final: 0.6238 (mmm) REVERT: G 466 HIS cc_start: 0.8874 (OUTLIER) cc_final: 0.8456 (t-90) REVERT: G 470 ASP cc_start: 0.8512 (m-30) cc_final: 0.8227 (m-30) REVERT: G 489 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7995 (ttmt) REVERT: G 490 PHE cc_start: 0.8328 (m-80) cc_final: 0.7869 (m-80) REVERT: G 509 TYR cc_start: 0.7839 (p90) cc_final: 0.7499 (p90) REVERT: G 510 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6892 (mm-30) REVERT: H 32 TYR cc_start: 0.8372 (m-10) cc_final: 0.8106 (m-10) REVERT: H 65 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8760 (pt) REVERT: H 66 VAL cc_start: 0.9210 (OUTLIER) cc_final: 0.8848 (p) REVERT: H 73 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.7127 (t) REVERT: H 109 LYS cc_start: 0.8845 (mmtm) cc_final: 0.8534 (mptt) REVERT: H 165 PHE cc_start: 0.8040 (p90) cc_final: 0.7430 (p90) REVERT: H 199 GLU cc_start: 0.9490 (tp30) cc_final: 0.8936 (tp30) REVERT: H 202 GLN cc_start: 0.9410 (mm-40) cc_final: 0.8467 (pp30) REVERT: H 203 ARG cc_start: 0.9324 (ptp-110) cc_final: 0.8675 (ptp-110) REVERT: H 206 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7985 (ttpt) REVERT: H 208 LYS cc_start: 0.8268 (ttmm) cc_final: 0.7475 (mtmt) REVERT: H 216 ASP cc_start: 0.9117 (t70) cc_final: 0.8827 (t0) REVERT: H 283 GLN cc_start: 0.8737 (tt0) cc_final: 0.8447 (mt0) REVERT: H 297 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8797 (tm) REVERT: H 311 LYS cc_start: 0.8779 (tmtt) cc_final: 0.8215 (tptt) REVERT: H 386 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8042 (pmm) REVERT: H 466 HIS cc_start: 0.8641 (OUTLIER) cc_final: 0.8233 (t-90) REVERT: H 470 ASP cc_start: 0.8558 (m-30) cc_final: 0.8251 (m-30) REVERT: H 482 MET cc_start: 0.8870 (tpt) cc_final: 0.8448 (tpt) REVERT: H 487 GLU cc_start: 0.8507 (pm20) cc_final: 0.7962 (pm20) REVERT: H 489 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7832 (ttmt) REVERT: H 490 PHE cc_start: 0.8312 (m-80) cc_final: 0.7747 (m-80) REVERT: H 509 TYR cc_start: 0.7602 (p90) cc_final: 0.7283 (p90) outliers start: 324 outliers final: 221 residues processed: 1190 average time/residue: 0.4099 time to fit residues: 777.7668 Evaluate side-chains 1235 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 967 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 489 LYS Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 466 HIS Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 355 ARG Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 489 LYS Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 466 HIS Chi-restraints excluded: chain F residue 467 SER Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 449 ASP Chi-restraints excluded: chain G residue 466 HIS Chi-restraints excluded: chain G residue 467 SER Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 466 HIS Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 489 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 211 optimal weight: 6.9990 chunk 271 optimal weight: 0.9990 chunk 210 optimal weight: 4.9990 chunk 312 optimal weight: 3.9990 chunk 207 optimal weight: 0.0980 chunk 370 optimal weight: 0.0020 chunk 231 optimal weight: 2.9990 chunk 225 optimal weight: 0.6980 chunk 170 optimal weight: 0.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN A 243 GLN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 243 GLN B 283 GLN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN C 243 GLN ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN D 243 GLN D 298 GLN D 303 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN E 343 GLN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN F 243 GLN F 283 GLN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 GLN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN H 243 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31576 Z= 0.184 Angle : 0.783 12.206 42888 Z= 0.364 Chirality : 0.047 0.196 4888 Planarity : 0.005 0.057 5328 Dihedral : 16.037 137.933 5342 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 7.77 % Allowed : 31.14 % Favored : 61.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -2.37 (0.13), residues: 3880 helix: -1.94 (0.13), residues: 1200 sheet: -2.41 (0.22), residues: 480 loop : -1.07 (0.13), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 504 PHE 0.012 0.001 PHE G 90 TYR 0.028 0.002 TYR C 509 ARG 0.018 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1338 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1090 time to evaluate : 3.902 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: 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 32 TYR cc_start: 0.8462 (m-10) cc_final: 0.8183 (m-10) REVERT: A 109 LYS cc_start: 0.8883 (mmtm) cc_final: 0.8497 (mptt) REVERT: A 150 MET cc_start: 0.9192 (tmm) cc_final: 0.8748 (tpt) REVERT: A 166 LEU cc_start: 0.8208 (tp) cc_final: 0.7971 (tp) REVERT: A 202 GLN cc_start: 0.9265 (mm-40) cc_final: 0.8416 (pp30) REVERT: A 206 LYS cc_start: 0.8144 (mtmt) cc_final: 0.7666 (ttpt) REVERT: A 208 LYS cc_start: 0.8430 (mtpp) cc_final: 0.7910 (mtmt) REVERT: A 214 GLU cc_start: 0.9390 (mm-30) cc_final: 0.9117 (mp0) REVERT: A 216 ASP cc_start: 0.9091 (t70) cc_final: 0.8723 (t0) REVERT: A 283 GLN cc_start: 0.8489 (tt0) cc_final: 0.8269 (tt0) REVERT: A 297 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8655 (tm) REVERT: A 311 LYS cc_start: 0.8754 (tmtt) cc_final: 0.7843 (tppt) REVERT: A 337 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7385 (tt) REVERT: A 352 GLU cc_start: 0.8493 (tp30) cc_final: 0.8255 (tp30) REVERT: A 386 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8189 (ppp) REVERT: A 420 MET cc_start: 0.6618 (mmm) cc_final: 0.6241 (mmm) REVERT: A 466 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.7930 (t-90) REVERT: A 469 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8033 (pt0) REVERT: A 470 ASP cc_start: 0.8393 (m-30) cc_final: 0.8023 (m-30) REVERT: A 489 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7893 (ttmt) REVERT: A 490 PHE cc_start: 0.8300 (m-80) cc_final: 0.7768 (m-80) REVERT: A 509 TYR cc_start: 0.7690 (p90) cc_final: 0.7409 (p90) REVERT: A 510 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7058 (mm-30) REVERT: B 32 TYR cc_start: 0.8384 (m-10) cc_final: 0.8149 (m-10) REVERT: B 47 ASP cc_start: 0.9123 (m-30) cc_final: 0.8406 (p0) REVERT: B 109 LYS cc_start: 0.8824 (mmtm) cc_final: 0.8450 (mptt) REVERT: B 128 ARG cc_start: 0.9003 (mmm-85) cc_final: 0.8587 (mmt90) REVERT: B 165 PHE cc_start: 0.8010 (p90) cc_final: 0.7327 (p90) REVERT: B 166 LEU cc_start: 0.8336 (tp) cc_final: 0.8020 (tp) REVERT: B 199 GLU cc_start: 0.9360 (tp30) cc_final: 0.9134 (mt-10) REVERT: B 214 GLU cc_start: 0.9353 (mm-30) cc_final: 0.9120 (mp0) REVERT: B 216 ASP cc_start: 0.9075 (t70) cc_final: 0.8690 (t0) REVERT: B 297 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8743 (tm) REVERT: B 309 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8388 (pt0) REVERT: B 407 ARG cc_start: 0.7252 (ttt180) cc_final: 0.6880 (ttt-90) REVERT: B 420 MET cc_start: 0.6790 (mmm) cc_final: 0.6468 (mmm) REVERT: B 489 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7124 (tptm) REVERT: B 490 PHE cc_start: 0.8161 (m-80) cc_final: 0.7714 (m-80) REVERT: B 509 TYR cc_start: 0.7504 (p90) cc_final: 0.7083 (p90) REVERT: C 32 TYR cc_start: 0.8436 (m-10) cc_final: 0.8183 (m-10) REVERT: C 47 ASP cc_start: 0.9071 (m-30) cc_final: 0.8282 (p0) REVERT: C 62 LYS cc_start: 0.9043 (mmtt) cc_final: 0.8792 (mtmm) REVERT: C 109 LYS cc_start: 0.8825 (mmtm) cc_final: 0.8420 (mptt) REVERT: C 128 ARG cc_start: 0.9126 (mmm-85) cc_final: 0.8575 (mmt90) REVERT: C 150 MET cc_start: 0.9121 (tmm) cc_final: 0.8662 (tpt) REVERT: C 165 PHE cc_start: 0.8039 (p90) cc_final: 0.7109 (p90) REVERT: C 166 LEU cc_start: 0.8347 (tp) cc_final: 0.8022 (tp) REVERT: C 199 GLU cc_start: 0.9445 (tp30) cc_final: 0.9135 (tp30) REVERT: C 203 ARG cc_start: 0.9296 (ptp-110) cc_final: 0.9086 (ptp-110) REVERT: C 214 GLU cc_start: 0.9395 (mm-30) cc_final: 0.9092 (mp0) REVERT: C 216 ASP cc_start: 0.9135 (t70) cc_final: 0.8783 (t0) REVERT: C 250 ILE cc_start: 0.8647 (pp) cc_final: 0.8436 (pp) REVERT: C 285 ASN cc_start: 0.9454 (m110) cc_final: 0.9167 (m110) REVERT: C 297 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8648 (tm) REVERT: C 313 LEU cc_start: 0.9302 (mp) cc_final: 0.9059 (mp) REVERT: C 337 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7430 (tt) REVERT: C 386 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8134 (ppp) REVERT: C 420 MET cc_start: 0.7085 (mmm) cc_final: 0.6632 (mmm) REVERT: C 466 HIS cc_start: 0.8605 (OUTLIER) cc_final: 0.8323 (t-90) REVERT: C 470 ASP cc_start: 0.8167 (m-30) cc_final: 0.7914 (m-30) REVERT: C 490 PHE cc_start: 0.8334 (m-80) cc_final: 0.7901 (m-80) REVERT: C 509 TYR cc_start: 0.7280 (p90) cc_final: 0.6705 (p90) REVERT: C 510 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6841 (mm-30) REVERT: D 65 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8892 (pt) REVERT: D 109 LYS cc_start: 0.8743 (mmtm) cc_final: 0.8484 (mptt) REVERT: D 111 GLU cc_start: 0.8745 (mp0) cc_final: 0.8398 (pm20) REVERT: D 132 GLU cc_start: 0.9501 (mp0) cc_final: 0.9269 (mp0) REVERT: D 165 PHE cc_start: 0.7994 (p90) cc_final: 0.7039 (p90) REVERT: D 166 LEU cc_start: 0.8312 (tp) cc_final: 0.7983 (tp) REVERT: D 206 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7704 (ttpt) REVERT: D 214 GLU cc_start: 0.9389 (mm-30) cc_final: 0.9133 (mp0) REVERT: D 216 ASP cc_start: 0.9156 (t70) cc_final: 0.8764 (t0) REVERT: D 283 GLN cc_start: 0.8555 (tt0) cc_final: 0.8301 (mt0) REVERT: D 297 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8788 (tm) REVERT: D 311 LYS cc_start: 0.8848 (tmtt) cc_final: 0.8246 (tptt) REVERT: D 390 LEU cc_start: 0.8820 (tt) cc_final: 0.8607 (tt) REVERT: D 407 ARG cc_start: 0.7076 (ttt90) cc_final: 0.6833 (ttt-90) REVERT: D 420 MET cc_start: 0.7136 (mmm) cc_final: 0.6782 (mmm) REVERT: D 488 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7678 (tp) REVERT: D 490 PHE cc_start: 0.8170 (m-80) cc_final: 0.7805 (m-80) REVERT: D 509 TYR cc_start: 0.7318 (p90) cc_final: 0.6985 (p90) REVERT: D 510 GLU cc_start: 0.7255 (mm-30) cc_final: 0.7035 (mm-30) REVERT: E 32 TYR cc_start: 0.8516 (m-10) cc_final: 0.8219 (m-10) REVERT: E 47 ASP cc_start: 0.9057 (m-30) cc_final: 0.8276 (p0) REVERT: E 78 MET cc_start: 0.8437 (ttm) cc_final: 0.8029 (ttm) REVERT: E 109 LYS cc_start: 0.8846 (mmtm) cc_final: 0.8483 (mptt) REVERT: E 128 ARG cc_start: 0.8812 (mmt90) cc_final: 0.8489 (mmt90) REVERT: E 166 LEU cc_start: 0.8276 (tp) cc_final: 0.8012 (tp) REVERT: E 199 GLU cc_start: 0.9492 (tp30) cc_final: 0.9272 (mt-10) REVERT: E 202 GLN cc_start: 0.9354 (mm-40) cc_final: 0.8335 (pp30) REVERT: E 203 ARG cc_start: 0.9380 (ptp-110) cc_final: 0.9083 (ptp90) REVERT: E 206 LYS cc_start: 0.7898 (ptpt) cc_final: 0.7526 (ptpt) REVERT: E 208 LYS cc_start: 0.8180 (ttmm) cc_final: 0.7700 (mtmt) REVERT: E 214 GLU cc_start: 0.9370 (mm-30) cc_final: 0.9120 (mp0) REVERT: E 216 ASP cc_start: 0.9169 (t70) cc_final: 0.8801 (t0) REVERT: E 250 ILE cc_start: 0.8760 (pp) cc_final: 0.8482 (pp) REVERT: E 297 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8651 (tm) REVERT: E 352 GLU cc_start: 0.8521 (tp30) cc_final: 0.8248 (tp30) REVERT: E 386 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8410 (pmm) REVERT: E 408 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8483 (mp) REVERT: E 420 MET cc_start: 0.7070 (mmm) cc_final: 0.6679 (mmm) REVERT: E 466 HIS cc_start: 0.8629 (OUTLIER) cc_final: 0.8154 (t-90) REVERT: E 470 ASP cc_start: 0.8515 (m-30) cc_final: 0.8117 (m-30) REVERT: E 489 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7916 (ttmt) REVERT: E 490 PHE cc_start: 0.8296 (m-80) cc_final: 0.7829 (m-80) REVERT: E 509 TYR cc_start: 0.7837 (p90) cc_final: 0.7593 (p90) REVERT: F 65 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8824 (pt) REVERT: F 109 LYS cc_start: 0.8881 (mmtm) cc_final: 0.8558 (mptt) REVERT: F 111 GLU cc_start: 0.8703 (mp0) cc_final: 0.8144 (mp0) REVERT: F 165 PHE cc_start: 0.8186 (p90) cc_final: 0.7826 (p90) REVERT: F 166 LEU cc_start: 0.8260 (tp) cc_final: 0.7904 (tp) REVERT: F 185 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7722 (mt) REVERT: F 216 ASP cc_start: 0.9194 (t70) cc_final: 0.8820 (t0) REVERT: F 297 LEU cc_start: 0.8981 (mm) cc_final: 0.8737 (mm) REVERT: F 309 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8515 (pt0) REVERT: F 311 LYS cc_start: 0.8875 (tmtt) cc_final: 0.8319 (tptt) REVERT: F 386 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8501 (pmm) REVERT: F 399 GLU cc_start: 0.8798 (pm20) cc_final: 0.8146 (tt0) REVERT: F 407 ARG cc_start: 0.7438 (ttt180) cc_final: 0.7188 (ttt180) REVERT: F 466 HIS cc_start: 0.8680 (OUTLIER) cc_final: 0.8335 (t-90) REVERT: F 470 ASP cc_start: 0.8472 (m-30) cc_final: 0.8098 (m-30) REVERT: F 490 PHE cc_start: 0.8264 (m-80) cc_final: 0.7821 (m-80) REVERT: F 509 TYR cc_start: 0.7529 (p90) cc_final: 0.7113 (p90) REVERT: F 510 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6940 (mm-30) REVERT: G 32 TYR cc_start: 0.8500 (m-10) cc_final: 0.8242 (m-10) REVERT: G 68 SER cc_start: 0.8403 (t) cc_final: 0.8107 (t) REVERT: G 73 VAL cc_start: 0.8076 (OUTLIER) cc_final: 0.6490 (t) REVERT: G 78 MET cc_start: 0.7713 (ttt) cc_final: 0.7357 (ttt) REVERT: G 109 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8612 (mptt) REVERT: G 111 GLU cc_start: 0.8579 (mp0) cc_final: 0.8206 (mp0) REVERT: G 150 MET cc_start: 0.9145 (tmm) cc_final: 0.8720 (tpt) REVERT: G 165 PHE cc_start: 0.8182 (p90) cc_final: 0.7828 (p90) REVERT: G 166 LEU cc_start: 0.8259 (tp) cc_final: 0.7873 (tp) REVERT: G 199 GLU cc_start: 0.9471 (tp30) cc_final: 0.8908 (tp30) REVERT: G 202 GLN cc_start: 0.9381 (mm-40) cc_final: 0.8382 (pp30) REVERT: G 203 ARG cc_start: 0.9317 (ptp-110) cc_final: 0.8766 (ptp-110) REVERT: G 206 LYS cc_start: 0.8264 (mtmt) cc_final: 0.7827 (ttpt) REVERT: G 214 GLU cc_start: 0.9415 (mm-30) cc_final: 0.9137 (mp0) REVERT: G 216 ASP cc_start: 0.9166 (t70) cc_final: 0.8836 (t0) REVERT: G 297 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8701 (tm) REVERT: G 311 LYS cc_start: 0.8689 (tmtt) cc_final: 0.7829 (tppt) REVERT: G 420 MET cc_start: 0.6736 (mmm) cc_final: 0.6440 (mmm) REVERT: G 466 HIS cc_start: 0.8686 (OUTLIER) cc_final: 0.8363 (t-90) REVERT: G 470 ASP cc_start: 0.8394 (m-30) cc_final: 0.8041 (m-30) REVERT: G 480 ARG cc_start: 0.9046 (mmt180) cc_final: 0.8836 (mmt180) REVERT: G 489 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7977 (ttmt) REVERT: G 490 PHE cc_start: 0.8338 (m-80) cc_final: 0.7915 (m-80) REVERT: G 509 TYR cc_start: 0.7824 (p90) cc_final: 0.7396 (p90) REVERT: G 510 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6894 (mm-30) REVERT: H 78 MET cc_start: 0.7608 (ttt) cc_final: 0.7312 (ttt) REVERT: H 103 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8215 (tp30) REVERT: H 109 LYS cc_start: 0.8889 (mmtm) cc_final: 0.8387 (mptt) REVERT: H 165 PHE cc_start: 0.8017 (p90) cc_final: 0.7613 (p90) REVERT: H 166 LEU cc_start: 0.8253 (tp) cc_final: 0.7950 (tp) REVERT: H 202 GLN cc_start: 0.9379 (mm-40) cc_final: 0.8386 (pp30) REVERT: H 203 ARG cc_start: 0.9321 (ptp-110) cc_final: 0.8747 (ptp-110) REVERT: H 208 LYS cc_start: 0.8102 (ttmm) cc_final: 0.7602 (mtmt) REVERT: H 216 ASP cc_start: 0.9077 (t70) cc_final: 0.8770 (t0) REVERT: H 283 GLN cc_start: 0.8630 (tt0) cc_final: 0.8329 (mt0) REVERT: H 297 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8691 (tm) REVERT: H 309 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8542 (pt0) REVERT: H 311 LYS cc_start: 0.8850 (tmtt) cc_final: 0.8249 (tptt) REVERT: H 337 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7218 (tt) REVERT: H 466 HIS cc_start: 0.8525 (OUTLIER) cc_final: 0.8132 (t-90) REVERT: H 470 ASP cc_start: 0.8439 (m-30) cc_final: 0.8120 (m-30) REVERT: H 490 PHE cc_start: 0.8296 (m-80) cc_final: 0.7754 (m-80) REVERT: H 509 TYR cc_start: 0.7615 (p90) cc_final: 0.7247 (p90) outliers start: 248 outliers final: 164 residues processed: 1214 average time/residue: 0.4096 time to fit residues: 793.5971 Evaluate side-chains 1213 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1011 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 489 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 489 LYS Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 466 HIS Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 489 LYS Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 309 GLN Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 466 HIS Chi-restraints excluded: chain F residue 467 SER Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 466 HIS Chi-restraints excluded: chain G residue 467 SER Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 449 ASP Chi-restraints excluded: chain H residue 466 HIS Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 488 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 0.0020 chunk 147 optimal weight: 0.0770 chunk 221 optimal weight: 10.0000 chunk 111 optimal weight: 0.1980 chunk 72 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 235 optimal weight: 0.7980 chunk 252 optimal weight: 10.0000 chunk 182 optimal weight: 0.0670 chunk 34 optimal weight: 0.9990 chunk 290 optimal weight: 2.9990 overall best weight: 0.2284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 HIS ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31576 Z= 0.189 Angle : 0.813 12.881 42888 Z= 0.374 Chirality : 0.048 0.247 4888 Planarity : 0.005 0.057 5328 Dihedral : 15.610 136.491 5335 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 7.08 % Allowed : 32.52 % Favored : 60.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -2.31 (0.13), residues: 3880 helix: -1.79 (0.13), residues: 1144 sheet: -2.36 (0.22), residues: 480 loop : -1.14 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 466 PHE 0.012 0.001 PHE D 90 TYR 0.042 0.002 TYR E 484 ARG 0.011 0.001 ARG C 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1318 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1092 time to evaluate : 3.769 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: 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 47 ASP cc_start: 0.8951 (m-30) cc_final: 0.8226 (p0) REVERT: A 59 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7857 (pt) REVERT: A 73 VAL cc_start: 0.7767 (OUTLIER) cc_final: 0.6362 (t) REVERT: A 109 LYS cc_start: 0.8935 (mmtm) cc_final: 0.8577 (mptt) REVERT: A 150 MET cc_start: 0.9221 (tmm) cc_final: 0.8797 (tpt) REVERT: A 166 LEU cc_start: 0.8118 (tp) cc_final: 0.7895 (tp) REVERT: A 203 ARG cc_start: 0.9559 (ptp-110) cc_final: 0.9301 (ptp90) REVERT: A 206 LYS cc_start: 0.8180 (mtmt) cc_final: 0.7709 (ttpt) REVERT: A 214 GLU cc_start: 0.9394 (mm-30) cc_final: 0.9111 (mp0) REVERT: A 216 ASP cc_start: 0.9092 (t70) cc_final: 0.8735 (t0) REVERT: A 250 ILE cc_start: 0.8517 (pp) cc_final: 0.8258 (pp) REVERT: A 253 HIS cc_start: 0.9072 (m90) cc_final: 0.8864 (m-70) REVERT: A 283 GLN cc_start: 0.8469 (tt0) cc_final: 0.8242 (mt0) REVERT: A 311 LYS cc_start: 0.8771 (tmtt) cc_final: 0.7828 (tppt) REVERT: A 337 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7407 (tt) REVERT: A 352 GLU cc_start: 0.8460 (tp30) cc_final: 0.7798 (tp30) REVERT: A 389 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8070 (tp) REVERT: A 420 MET cc_start: 0.6573 (mmm) cc_final: 0.6182 (mmm) REVERT: A 466 HIS cc_start: 0.8480 (OUTLIER) cc_final: 0.7865 (t-90) REVERT: A 469 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.7977 (pt0) REVERT: A 470 ASP cc_start: 0.8396 (m-30) cc_final: 0.7976 (m-30) REVERT: A 489 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7951 (tttm) REVERT: A 490 PHE cc_start: 0.8207 (m-80) cc_final: 0.7757 (m-80) REVERT: A 509 TYR cc_start: 0.7705 (p90) cc_final: 0.7420 (p90) REVERT: A 510 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7034 (mm-30) REVERT: B 47 ASP cc_start: 0.9051 (m-30) cc_final: 0.8413 (p0) REVERT: B 109 LYS cc_start: 0.8832 (mmtm) cc_final: 0.8501 (mptt) REVERT: B 128 ARG cc_start: 0.8980 (mmm-85) cc_final: 0.8463 (mmt90) REVERT: B 165 PHE cc_start: 0.7956 (p90) cc_final: 0.7115 (p90) REVERT: B 166 LEU cc_start: 0.8308 (tp) cc_final: 0.7986 (tp) REVERT: B 202 GLN cc_start: 0.9332 (mm-40) cc_final: 0.8722 (pp30) REVERT: B 214 GLU cc_start: 0.9355 (mm-30) cc_final: 0.9116 (mp0) REVERT: B 216 ASP cc_start: 0.9069 (t70) cc_final: 0.8726 (t0) REVERT: B 297 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8687 (tm) REVERT: B 313 LEU cc_start: 0.9249 (mp) cc_final: 0.9038 (mt) REVERT: B 407 ARG cc_start: 0.7372 (ttt180) cc_final: 0.6924 (ttt-90) REVERT: B 420 MET cc_start: 0.6816 (mmm) cc_final: 0.6492 (mmm) REVERT: B 490 PHE cc_start: 0.8152 (m-80) cc_final: 0.7744 (m-80) REVERT: B 509 TYR cc_start: 0.7505 (p90) cc_final: 0.7215 (p90) REVERT: C 47 ASP cc_start: 0.8964 (m-30) cc_final: 0.8290 (p0) REVERT: C 103 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8114 (tp30) REVERT: C 109 LYS cc_start: 0.8846 (mmtm) cc_final: 0.8601 (mptt) REVERT: C 111 GLU cc_start: 0.8113 (mp0) cc_final: 0.7233 (pm20) REVERT: C 132 GLU cc_start: 0.9439 (mp0) cc_final: 0.9181 (mp0) REVERT: C 150 MET cc_start: 0.9145 (tmm) cc_final: 0.8699 (tpt) REVERT: C 165 PHE cc_start: 0.7966 (p90) cc_final: 0.7327 (p90) REVERT: C 166 LEU cc_start: 0.8359 (tp) cc_final: 0.8050 (tp) REVERT: C 206 LYS cc_start: 0.8218 (mtmt) cc_final: 0.7783 (ttpt) REVERT: C 208 LYS cc_start: 0.6857 (mtmt) cc_final: 0.6206 (mtmt) REVERT: C 214 GLU cc_start: 0.9400 (mm-30) cc_final: 0.9091 (mp0) REVERT: C 216 ASP cc_start: 0.9143 (t70) cc_final: 0.8745 (t0) REVERT: C 250 ILE cc_start: 0.8691 (pp) cc_final: 0.8476 (pp) REVERT: C 285 ASN cc_start: 0.9449 (m110) cc_final: 0.9155 (m110) REVERT: C 297 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8536 (tm) REVERT: C 337 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7433 (tt) REVERT: C 348 TYR cc_start: 0.8800 (t80) cc_final: 0.8585 (t80) REVERT: C 420 MET cc_start: 0.7079 (mmm) cc_final: 0.6666 (mmm) REVERT: C 466 HIS cc_start: 0.8799 (OUTLIER) cc_final: 0.8476 (t-90) REVERT: C 470 ASP cc_start: 0.8246 (m-30) cc_final: 0.8020 (m-30) REVERT: C 483 MET cc_start: 0.9499 (tmm) cc_final: 0.9245 (tmm) REVERT: C 490 PHE cc_start: 0.8266 (m-80) cc_final: 0.7928 (m-80) REVERT: C 509 TYR cc_start: 0.7211 (p90) cc_final: 0.6739 (p90) REVERT: C 510 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.7095 (mm-30) REVERT: D 65 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8815 (pt) REVERT: D 73 VAL cc_start: 0.7642 (OUTLIER) cc_final: 0.5855 (t) REVERT: D 74 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.7703 (p) REVERT: D 78 MET cc_start: 0.7434 (ttt) cc_final: 0.7182 (ttt) REVERT: D 109 LYS cc_start: 0.8717 (mmtm) cc_final: 0.8453 (mptt) REVERT: D 111 GLU cc_start: 0.8697 (mp0) cc_final: 0.8416 (mp0) REVERT: D 165 PHE cc_start: 0.7899 (p90) cc_final: 0.6854 (p90) REVERT: D 166 LEU cc_start: 0.8278 (tp) cc_final: 0.7957 (tp) REVERT: D 179 MET cc_start: 0.7705 (mtm) cc_final: 0.7265 (pmm) REVERT: D 206 LYS cc_start: 0.8020 (mtmt) cc_final: 0.7687 (ttpt) REVERT: D 214 GLU cc_start: 0.9400 (mm-30) cc_final: 0.9140 (mp0) REVERT: D 216 ASP cc_start: 0.9083 (t70) cc_final: 0.8705 (t0) REVERT: D 283 GLN cc_start: 0.8500 (tt0) cc_final: 0.8274 (mt0) REVERT: D 311 LYS cc_start: 0.8829 (tmtt) cc_final: 0.8200 (tptt) REVERT: D 407 ARG cc_start: 0.7100 (ttt90) cc_final: 0.6793 (ttt-90) REVERT: D 420 MET cc_start: 0.7159 (mmm) cc_final: 0.6859 (mmm) REVERT: D 488 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7399 (tp) REVERT: D 490 PHE cc_start: 0.8255 (m-80) cc_final: 0.7754 (m-80) REVERT: D 509 TYR cc_start: 0.7347 (p90) cc_final: 0.7052 (p90) REVERT: D 510 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7089 (mm-30) REVERT: E 32 TYR cc_start: 0.8467 (m-10) cc_final: 0.8216 (m-10) REVERT: E 47 ASP cc_start: 0.8954 (m-30) cc_final: 0.8276 (p0) REVERT: E 74 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.7888 (p) REVERT: E 78 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7754 (ttm) REVERT: E 109 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8604 (mptt) REVERT: E 132 GLU cc_start: 0.9486 (mp0) cc_final: 0.9248 (mp0) REVERT: E 166 LEU cc_start: 0.8287 (tp) cc_final: 0.7995 (tp) REVERT: E 179 MET cc_start: 0.7694 (mtm) cc_final: 0.7370 (pmm) REVERT: E 199 GLU cc_start: 0.9497 (tp30) cc_final: 0.9189 (mt-10) REVERT: E 202 GLN cc_start: 0.9309 (mm-40) cc_final: 0.8198 (pp30) REVERT: E 203 ARG cc_start: 0.9392 (ptp-110) cc_final: 0.8949 (ptp90) REVERT: E 206 LYS cc_start: 0.8018 (ptpt) cc_final: 0.7638 (ptmt) REVERT: E 208 LYS cc_start: 0.8056 (ttmm) cc_final: 0.7570 (mtmt) REVERT: E 214 GLU cc_start: 0.9353 (mm-30) cc_final: 0.9086 (mp0) REVERT: E 216 ASP cc_start: 0.9149 (t70) cc_final: 0.8775 (t0) REVERT: E 253 HIS cc_start: 0.8960 (m90) cc_final: 0.8631 (m-70) REVERT: E 408 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8458 (mp) REVERT: E 420 MET cc_start: 0.7072 (mmm) cc_final: 0.6465 (mmm) REVERT: E 466 HIS cc_start: 0.8546 (OUTLIER) cc_final: 0.8105 (t-90) REVERT: E 470 ASP cc_start: 0.8500 (m-30) cc_final: 0.8230 (m-30) REVERT: E 489 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7907 (ttmt) REVERT: E 490 PHE cc_start: 0.8234 (m-80) cc_final: 0.7812 (m-80) REVERT: E 509 TYR cc_start: 0.7830 (p90) cc_final: 0.7607 (p90) REVERT: E 510 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6736 (mm-30) REVERT: F 47 ASP cc_start: 0.9098 (m-30) cc_final: 0.8337 (p0) REVERT: F 55 LEU cc_start: 0.9033 (tt) cc_final: 0.8541 (tp) REVERT: F 66 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8586 (p) REVERT: F 109 LYS cc_start: 0.8896 (mmtm) cc_final: 0.8618 (mptt) REVERT: F 165 PHE cc_start: 0.8210 (p90) cc_final: 0.7763 (p90) REVERT: F 166 LEU cc_start: 0.8246 (tp) cc_final: 0.7901 (tp) REVERT: F 179 MET cc_start: 0.7709 (mtm) cc_final: 0.7326 (pmm) REVERT: F 185 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7732 (mt) REVERT: F 203 ARG cc_start: 0.9353 (ptp-110) cc_final: 0.8875 (ptp90) REVERT: F 216 ASP cc_start: 0.9189 (t70) cc_final: 0.8814 (t0) REVERT: F 386 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8438 (pmm) REVERT: F 399 GLU cc_start: 0.8746 (pm20) cc_final: 0.8130 (tt0) REVERT: F 466 HIS cc_start: 0.8526 (OUTLIER) cc_final: 0.8210 (t-90) REVERT: F 470 ASP cc_start: 0.8418 (m-30) cc_final: 0.8108 (m-30) REVERT: F 490 PHE cc_start: 0.8312 (m-80) cc_final: 0.7905 (m-80) REVERT: F 509 TYR cc_start: 0.7475 (p90) cc_final: 0.7107 (p90) REVERT: G 68 SER cc_start: 0.8352 (t) cc_final: 0.8007 (t) REVERT: G 73 VAL cc_start: 0.7777 (OUTLIER) cc_final: 0.6212 (t) REVERT: G 78 MET cc_start: 0.7503 (ttt) cc_final: 0.7204 (ttt) REVERT: G 103 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8295 (tp30) REVERT: G 109 LYS cc_start: 0.8904 (mmtm) cc_final: 0.8654 (mptt) REVERT: G 111 GLU cc_start: 0.8542 (mp0) cc_final: 0.8163 (mp0) REVERT: G 128 ARG cc_start: 0.8884 (mmt90) cc_final: 0.8626 (mmt180) REVERT: G 132 GLU cc_start: 0.9472 (mp0) cc_final: 0.9236 (mp0) REVERT: G 199 GLU cc_start: 0.9456 (tp30) cc_final: 0.8924 (tp30) REVERT: G 202 GLN cc_start: 0.9390 (mm-40) cc_final: 0.8365 (pp30) REVERT: G 206 LYS cc_start: 0.8267 (mtmt) cc_final: 0.7818 (ttpt) REVERT: G 214 GLU cc_start: 0.9404 (mm-30) cc_final: 0.9127 (mp0) REVERT: G 216 ASP cc_start: 0.9155 (t70) cc_final: 0.8827 (t0) REVERT: G 297 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8632 (tm) REVERT: G 311 LYS cc_start: 0.8727 (tmtt) cc_final: 0.7782 (tppt) REVERT: G 385 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.6140 (mmm) REVERT: G 420 MET cc_start: 0.6622 (mmm) cc_final: 0.6293 (mmm) REVERT: G 489 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7938 (ttmt) REVERT: G 490 PHE cc_start: 0.8239 (m-80) cc_final: 0.7853 (m-80) REVERT: G 509 TYR cc_start: 0.7826 (p90) cc_final: 0.7353 (p90) REVERT: G 510 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6897 (mm-30) REVERT: H 78 MET cc_start: 0.7446 (ttt) cc_final: 0.7183 (ttt) REVERT: H 103 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8222 (tp30) REVERT: H 111 GLU cc_start: 0.8666 (mp0) cc_final: 0.8388 (pm20) REVERT: H 150 MET cc_start: 0.9037 (tmm) cc_final: 0.8601 (tpt) REVERT: H 161 ARG cc_start: 0.9421 (mpp-170) cc_final: 0.8877 (mtt90) REVERT: H 165 PHE cc_start: 0.8000 (p90) cc_final: 0.7592 (p90) REVERT: H 166 LEU cc_start: 0.8303 (tp) cc_final: 0.7981 (tp) REVERT: H 202 GLN cc_start: 0.9342 (mm-40) cc_final: 0.8403 (pp30) REVERT: H 203 ARG cc_start: 0.9360 (ptp-110) cc_final: 0.8789 (ptp-110) REVERT: H 208 LYS cc_start: 0.8007 (ttmm) cc_final: 0.7533 (mtmt) REVERT: H 216 ASP cc_start: 0.9025 (t70) cc_final: 0.8677 (t0) REVERT: H 268 VAL cc_start: 0.8748 (t) cc_final: 0.8461 (t) REVERT: H 466 HIS cc_start: 0.8362 (OUTLIER) cc_final: 0.8127 (t-90) REVERT: H 470 ASP cc_start: 0.8390 (m-30) cc_final: 0.7980 (m-30) REVERT: H 471 ILE cc_start: 0.9016 (mp) cc_final: 0.8802 (mp) REVERT: H 490 PHE cc_start: 0.8401 (m-80) cc_final: 0.7877 (m-80) REVERT: H 509 TYR cc_start: 0.7697 (p90) cc_final: 0.7339 (p90) outliers start: 226 outliers final: 152 residues processed: 1208 average time/residue: 0.4509 time to fit residues: 884.3293 Evaluate side-chains 1234 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1048 time to evaluate : 5.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 489 LYS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain C residue 466 HIS Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 489 LYS Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 466 HIS Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 385 MET Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 467 SER Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 449 ASP Chi-restraints excluded: chain H residue 466 HIS Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 488 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 20.0000 chunk 354 optimal weight: 5.9990 chunk 323 optimal weight: 0.6980 chunk 344 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 270 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 311 optimal weight: 9.9990 chunk 326 optimal weight: 0.4980 chunk 343 optimal weight: 3.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS E 303 ASN ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 31576 Z= 0.335 Angle : 0.879 13.143 42888 Z= 0.421 Chirality : 0.050 0.239 4888 Planarity : 0.006 0.090 5328 Dihedral : 15.536 133.943 5330 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 27.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 7.55 % Allowed : 33.40 % Favored : 59.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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 (0.13), residues: 3880 helix: -1.97 (0.13), residues: 1248 sheet: -2.46 (0.21), residues: 528 loop : -1.18 (0.14), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 466 PHE 0.023 0.002 PHE G 90 TYR 0.043 0.002 TYR E 484 ARG 0.013 0.001 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1229 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 988 time to evaluate : 3.452 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: 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 73 VAL cc_start: 0.8214 (OUTLIER) cc_final: 0.6997 (t) REVERT: A 109 LYS cc_start: 0.8973 (mmtm) cc_final: 0.8759 (mmtm) REVERT: A 150 MET cc_start: 0.9165 (tmm) cc_final: 0.8729 (tpt) REVERT: A 202 GLN cc_start: 0.9356 (mm-40) cc_final: 0.8414 (pp30) REVERT: A 203 ARG cc_start: 0.9567 (ptp-110) cc_final: 0.8838 (ptp90) REVERT: A 206 LYS cc_start: 0.8443 (mtmt) cc_final: 0.7780 (ttpt) REVERT: A 214 GLU cc_start: 0.9402 (mm-30) cc_final: 0.9120 (mp0) REVERT: A 216 ASP cc_start: 0.9121 (t70) cc_final: 0.8776 (t0) REVERT: A 311 LYS cc_start: 0.8676 (tmtt) cc_final: 0.7741 (tppt) REVERT: A 337 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7299 (tt) REVERT: A 352 GLU cc_start: 0.8512 (tp30) cc_final: 0.8124 (tp30) REVERT: A 420 MET cc_start: 0.6948 (mmm) cc_final: 0.6446 (mmm) REVERT: A 466 HIS cc_start: 0.8661 (OUTLIER) cc_final: 0.7938 (t-90) REVERT: A 469 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7955 (pt0) REVERT: A 470 ASP cc_start: 0.8497 (m-30) cc_final: 0.8111 (m-30) REVERT: A 488 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7740 (tp) REVERT: A 489 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7287 (tptm) REVERT: A 490 PHE cc_start: 0.8313 (m-80) cc_final: 0.7843 (m-80) REVERT: A 510 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6939 (mm-30) REVERT: B 32 TYR cc_start: 0.8557 (m-10) cc_final: 0.8289 (m-10) REVERT: B 47 ASP cc_start: 0.9082 (m-30) cc_final: 0.8459 (p0) REVERT: B 78 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8036 (ttm) REVERT: B 109 LYS cc_start: 0.8841 (mmtm) cc_final: 0.8541 (mptt) REVERT: B 165 PHE cc_start: 0.8020 (p90) cc_final: 0.7298 (p90) REVERT: B 203 ARG cc_start: 0.9533 (ptp-110) cc_final: 0.8981 (ptp-110) REVERT: B 214 GLU cc_start: 0.9369 (mm-30) cc_final: 0.9139 (mp0) REVERT: B 216 ASP cc_start: 0.9129 (t70) cc_final: 0.8733 (t0) REVERT: B 297 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8862 (tm) REVERT: B 420 MET cc_start: 0.7249 (mmm) cc_final: 0.6776 (mmm) REVERT: B 490 PHE cc_start: 0.8293 (m-80) cc_final: 0.7812 (m-80) REVERT: B 503 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8424 (p) REVERT: C 47 ASP cc_start: 0.9057 (m-30) cc_final: 0.8319 (p0) REVERT: C 73 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.7183 (t) REVERT: C 103 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8151 (tp30) REVERT: C 109 LYS cc_start: 0.8857 (mmtm) cc_final: 0.8645 (mptt) REVERT: C 165 PHE cc_start: 0.8155 (p90) cc_final: 0.7100 (p90) REVERT: C 199 GLU cc_start: 0.9450 (tp30) cc_final: 0.8438 (tp30) REVERT: C 202 GLN cc_start: 0.9403 (mm-40) cc_final: 0.8644 (pp30) REVERT: C 214 GLU cc_start: 0.9409 (mm-30) cc_final: 0.9097 (mp0) REVERT: C 216 ASP cc_start: 0.9162 (t70) cc_final: 0.8768 (t0) REVERT: C 250 ILE cc_start: 0.8676 (pp) cc_final: 0.8329 (pp) REVERT: C 285 ASN cc_start: 0.9476 (m110) cc_final: 0.9179 (m110) REVERT: C 297 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8702 (tm) REVERT: C 337 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7393 (tt) REVERT: C 352 GLU cc_start: 0.8660 (tp30) cc_final: 0.8349 (tp30) REVERT: C 414 MET cc_start: 0.8040 (pmm) cc_final: 0.7830 (pmm) REVERT: C 420 MET cc_start: 0.7244 (mmm) cc_final: 0.6727 (mmm) REVERT: C 466 HIS cc_start: 0.8903 (OUTLIER) cc_final: 0.8364 (t-90) REVERT: C 470 ASP cc_start: 0.8394 (m-30) cc_final: 0.8158 (m-30) REVERT: C 490 PHE cc_start: 0.8437 (m-80) cc_final: 0.8009 (m-80) REVERT: C 498 GLN cc_start: 0.9032 (pm20) cc_final: 0.8818 (pm20) REVERT: C 510 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6754 (mm-30) REVERT: D 32 TYR cc_start: 0.8457 (m-10) cc_final: 0.8066 (m-10) REVERT: D 38 LEU cc_start: 0.9126 (pt) cc_final: 0.8672 (pt) REVERT: D 73 VAL cc_start: 0.8126 (OUTLIER) cc_final: 0.6978 (t) REVERT: D 109 LYS cc_start: 0.8701 (mmtm) cc_final: 0.8464 (mptt) REVERT: D 111 GLU cc_start: 0.8784 (mp0) cc_final: 0.8507 (mp0) REVERT: D 132 GLU cc_start: 0.9503 (mp0) cc_final: 0.9275 (mp0) REVERT: D 165 PHE cc_start: 0.8003 (p90) cc_final: 0.7054 (p90) REVERT: D 216 ASP cc_start: 0.9132 (t70) cc_final: 0.8786 (t0) REVERT: D 311 LYS cc_start: 0.8888 (tmtt) cc_final: 0.8269 (tptt) REVERT: D 420 MET cc_start: 0.7326 (mmm) cc_final: 0.6965 (mmm) REVERT: D 469 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8174 (pt0) REVERT: D 482 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8612 (tpt) REVERT: D 488 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7406 (tp) REVERT: D 490 PHE cc_start: 0.8394 (m-80) cc_final: 0.7845 (m-80) REVERT: D 509 TYR cc_start: 0.7306 (p90) cc_final: 0.7059 (p90) REVERT: D 510 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6923 (mm-30) REVERT: E 47 ASP cc_start: 0.9046 (m-30) cc_final: 0.8297 (p0) REVERT: E 109 LYS cc_start: 0.8904 (mmtm) cc_final: 0.8641 (mptt) REVERT: E 128 ARG cc_start: 0.8798 (mmt90) cc_final: 0.8480 (ttm-80) REVERT: E 199 GLU cc_start: 0.9528 (tp30) cc_final: 0.9191 (mt-10) REVERT: E 202 GLN cc_start: 0.9368 (mm-40) cc_final: 0.8370 (pp30) REVERT: E 203 ARG cc_start: 0.9377 (ptp-110) cc_final: 0.8945 (ptp90) REVERT: E 206 LYS cc_start: 0.8250 (ptpt) cc_final: 0.7780 (ptpt) REVERT: E 208 LYS cc_start: 0.8238 (ttmm) cc_final: 0.7718 (mtmt) REVERT: E 214 GLU cc_start: 0.9352 (mm-30) cc_final: 0.9097 (mp0) REVERT: E 216 ASP cc_start: 0.9177 (t70) cc_final: 0.8799 (t0) REVERT: E 283 GLN cc_start: 0.8681 (tt0) cc_final: 0.8473 (tt0) REVERT: E 285 ASN cc_start: 0.9458 (m110) cc_final: 0.9159 (m110) REVERT: E 352 GLU cc_start: 0.8899 (tp30) cc_final: 0.8628 (tp30) REVERT: E 420 MET cc_start: 0.7351 (mmm) cc_final: 0.6907 (mmm) REVERT: E 466 HIS cc_start: 0.8733 (OUTLIER) cc_final: 0.8180 (t-90) REVERT: E 470 ASP cc_start: 0.8457 (m-30) cc_final: 0.8238 (m-30) REVERT: E 488 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7929 (tp) REVERT: E 489 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7826 (ttmt) REVERT: E 490 PHE cc_start: 0.8355 (m-80) cc_final: 0.7932 (m-80) REVERT: F 32 TYR cc_start: 0.8573 (m-10) cc_final: 0.8090 (m-10) REVERT: F 47 ASP cc_start: 0.9159 (m-30) cc_final: 0.8424 (p0) REVERT: F 109 LYS cc_start: 0.8919 (mmtm) cc_final: 0.8672 (mptt) REVERT: F 165 PHE cc_start: 0.8212 (p90) cc_final: 0.7547 (p90) REVERT: F 166 LEU cc_start: 0.8282 (tp) cc_final: 0.8038 (tp) REVERT: F 185 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7626 (mt) REVERT: F 202 GLN cc_start: 0.9378 (mm-40) cc_final: 0.9157 (mm-40) REVERT: F 216 ASP cc_start: 0.9229 (t70) cc_final: 0.8884 (t0) REVERT: F 386 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8156 (ppp) REVERT: F 399 GLU cc_start: 0.8768 (pm20) cc_final: 0.8070 (tt0) REVERT: F 466 HIS cc_start: 0.8635 (OUTLIER) cc_final: 0.8248 (t-90) REVERT: F 470 ASP cc_start: 0.8557 (m-30) cc_final: 0.8197 (m-30) REVERT: F 488 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7742 (tp) REVERT: F 490 PHE cc_start: 0.8322 (m-80) cc_final: 0.7914 (m-80) REVERT: G 32 TYR cc_start: 0.8592 (m-10) cc_final: 0.8384 (m-10) REVERT: G 68 SER cc_start: 0.9066 (t) cc_final: 0.8778 (t) REVERT: G 73 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.6875 (t) REVERT: G 78 MET cc_start: 0.7651 (ttt) cc_final: 0.7320 (ttt) REVERT: G 103 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8264 (tp30) REVERT: G 109 LYS cc_start: 0.8898 (mmtm) cc_final: 0.8645 (mptt) REVERT: G 132 GLU cc_start: 0.9461 (mp0) cc_final: 0.9235 (mp0) REVERT: G 150 MET cc_start: 0.9148 (tmm) cc_final: 0.8696 (tpt) REVERT: G 199 GLU cc_start: 0.9459 (tp30) cc_final: 0.8991 (tp30) REVERT: G 202 GLN cc_start: 0.9471 (mm-40) cc_final: 0.8466 (pp30) REVERT: G 214 GLU cc_start: 0.9427 (mm-30) cc_final: 0.9138 (mp0) REVERT: G 216 ASP cc_start: 0.9205 (t70) cc_final: 0.8871 (t0) REVERT: G 297 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8827 (tm) REVERT: G 311 LYS cc_start: 0.8706 (tmtt) cc_final: 0.7796 (tppt) REVERT: G 385 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7230 (tmm) REVERT: G 420 MET cc_start: 0.7072 (mmm) cc_final: 0.6656 (mmm) REVERT: G 469 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8208 (pt0) REVERT: G 470 ASP cc_start: 0.8401 (m-30) cc_final: 0.8065 (m-30) REVERT: G 488 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7834 (tp) REVERT: G 489 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7841 (ttmt) REVERT: G 490 PHE cc_start: 0.8384 (m-80) cc_final: 0.7932 (m-80) REVERT: G 509 TYR cc_start: 0.7951 (p90) cc_final: 0.7742 (p90) REVERT: G 510 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6905 (mm-30) REVERT: H 32 TYR cc_start: 0.8455 (m-10) cc_final: 0.7974 (m-10) REVERT: H 73 VAL cc_start: 0.8352 (OUTLIER) cc_final: 0.7082 (t) REVERT: H 74 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8226 (p) REVERT: H 103 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8219 (tp30) REVERT: H 132 GLU cc_start: 0.9489 (mp0) cc_final: 0.9235 (mp0) REVERT: H 202 GLN cc_start: 0.9422 (mm-40) cc_final: 0.8461 (pp30) REVERT: H 203 ARG cc_start: 0.9339 (ptp-110) cc_final: 0.8787 (ptp-110) REVERT: H 208 LYS cc_start: 0.8212 (ttmm) cc_final: 0.7706 (mtmt) REVERT: H 216 ASP cc_start: 0.9058 (t70) cc_final: 0.8755 (t0) REVERT: H 337 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7259 (tt) REVERT: H 407 ARG cc_start: 0.7466 (ttt180) cc_final: 0.6866 (ttt180) REVERT: H 466 HIS cc_start: 0.8683 (OUTLIER) cc_final: 0.8233 (t-90) REVERT: H 470 ASP cc_start: 0.8347 (m-30) cc_final: 0.8031 (m-30) REVERT: H 488 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7816 (tp) REVERT: H 490 PHE cc_start: 0.8527 (m-80) cc_final: 0.8096 (m-80) REVERT: H 509 TYR cc_start: 0.7740 (p90) cc_final: 0.7519 (p90) outliers start: 241 outliers final: 175 residues processed: 1102 average time/residue: 0.4475 time to fit residues: 799.2684 Evaluate side-chains 1184 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 969 time to evaluate : 3.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 489 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 482 MET Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 466 HIS Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 353 TYR Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 489 LYS Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 466 HIS Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 385 MET Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 467 SER Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 482 MET Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 353 TYR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 466 HIS Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 488 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 3.9990 chunk 364 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 253 optimal weight: 8.9990 chunk 382 optimal weight: 2.9990 chunk 352 optimal weight: 5.9990 chunk 304 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 235 optimal weight: 0.9980 chunk 186 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 31576 Z= 0.315 Angle : 0.884 13.449 42888 Z= 0.422 Chirality : 0.051 0.245 4888 Planarity : 0.006 0.094 5328 Dihedral : 15.438 134.566 5326 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 27.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 7.46 % Allowed : 33.74 % Favored : 58.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -2.45 (0.13), residues: 3880 helix: -1.94 (0.13), residues: 1216 sheet: -2.17 (0.22), residues: 464 loop : -1.24 (0.13), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 466 PHE 0.018 0.002 PHE G 90 TYR 0.034 0.002 TYR E 484 ARG 0.016 0.001 ARG F 407 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1229 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 991 time to evaluate : 3.318 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: 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 32 TYR cc_start: 0.8591 (m-10) cc_final: 0.8257 (m-10) REVERT: A 73 VAL cc_start: 0.8270 (OUTLIER) cc_final: 0.7034 (t) REVERT: A 100 GLN cc_start: 0.8959 (tt0) cc_final: 0.8612 (tp40) REVERT: A 109 LYS cc_start: 0.8972 (mmtm) cc_final: 0.8708 (mmtm) REVERT: A 128 ARG cc_start: 0.8990 (mmm-85) cc_final: 0.8673 (mmt90) REVERT: A 202 GLN cc_start: 0.9338 (mm-40) cc_final: 0.8526 (pp30) REVERT: A 206 LYS cc_start: 0.8430 (mtmt) cc_final: 0.7702 (ttpt) REVERT: A 216 ASP cc_start: 0.9141 (t70) cc_final: 0.8809 (t0) REVERT: A 311 LYS cc_start: 0.8659 (tmtt) cc_final: 0.8253 (tmtt) REVERT: A 335 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8160 (mm-30) REVERT: A 337 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7419 (tt) REVERT: A 352 GLU cc_start: 0.8533 (tp30) cc_final: 0.8142 (tp30) REVERT: A 407 ARG cc_start: 0.7585 (ttt180) cc_final: 0.7242 (ttt180) REVERT: A 420 MET cc_start: 0.7167 (mmm) cc_final: 0.6640 (mmm) REVERT: A 466 HIS cc_start: 0.8674 (OUTLIER) cc_final: 0.7909 (t-90) REVERT: A 469 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7952 (pt0) REVERT: A 470 ASP cc_start: 0.8476 (m-30) cc_final: 0.8016 (m-30) REVERT: A 488 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7752 (tp) REVERT: A 489 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7323 (tptm) REVERT: A 490 PHE cc_start: 0.8367 (m-80) cc_final: 0.7841 (m-80) REVERT: A 509 TYR cc_start: 0.7350 (p90) cc_final: 0.7003 (p90) REVERT: A 510 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6914 (mm-30) REVERT: B 32 TYR cc_start: 0.8616 (m-10) cc_final: 0.8381 (m-10) REVERT: B 47 ASP cc_start: 0.9111 (m-30) cc_final: 0.8441 (p0) REVERT: B 78 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8159 (ttm) REVERT: B 109 LYS cc_start: 0.8808 (mmtm) cc_final: 0.8581 (mptt) REVERT: B 165 PHE cc_start: 0.8017 (p90) cc_final: 0.7576 (p90) REVERT: B 214 GLU cc_start: 0.9337 (mm-30) cc_final: 0.9102 (mp0) REVERT: B 216 ASP cc_start: 0.9114 (t70) cc_final: 0.8718 (t0) REVERT: B 250 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7672 (pp) REVERT: B 420 MET cc_start: 0.7337 (mmm) cc_final: 0.6537 (mmt) REVERT: B 490 PHE cc_start: 0.8322 (m-80) cc_final: 0.7797 (m-80) REVERT: B 503 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8536 (t) REVERT: C 32 TYR cc_start: 0.8606 (m-10) cc_final: 0.8273 (m-10) REVERT: C 103 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8149 (tp30) REVERT: C 109 LYS cc_start: 0.8847 (mmtm) cc_final: 0.8492 (mptt) REVERT: C 132 GLU cc_start: 0.9455 (mp0) cc_final: 0.9213 (mp0) REVERT: C 150 MET cc_start: 0.9094 (tmm) cc_final: 0.8531 (tpt) REVERT: C 165 PHE cc_start: 0.8117 (p90) cc_final: 0.7762 (p90) REVERT: C 199 GLU cc_start: 0.9470 (tp30) cc_final: 0.9111 (mt-10) REVERT: C 202 GLN cc_start: 0.9356 (mm-40) cc_final: 0.8548 (pp30) REVERT: C 203 ARG cc_start: 0.9301 (ptp-110) cc_final: 0.8794 (ptp90) REVERT: C 214 GLU cc_start: 0.9376 (mm-30) cc_final: 0.9071 (mp0) REVERT: C 216 ASP cc_start: 0.9162 (t70) cc_final: 0.8768 (t0) REVERT: C 250 ILE cc_start: 0.8656 (pp) cc_final: 0.8377 (pp) REVERT: C 337 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7381 (tt) REVERT: C 352 GLU cc_start: 0.8684 (tp30) cc_final: 0.8402 (tp30) REVERT: C 420 MET cc_start: 0.7299 (mmm) cc_final: 0.6360 (mmt) REVERT: C 466 HIS cc_start: 0.8931 (OUTLIER) cc_final: 0.8398 (t-90) REVERT: C 490 PHE cc_start: 0.8338 (m-80) cc_final: 0.7884 (m-80) REVERT: C 510 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6901 (mm-30) REVERT: D 32 TYR cc_start: 0.8560 (m-10) cc_final: 0.8167 (m-10) REVERT: D 73 VAL cc_start: 0.8245 (OUTLIER) cc_final: 0.6934 (t) REVERT: D 109 LYS cc_start: 0.8695 (mmtm) cc_final: 0.8468 (mptt) REVERT: D 165 PHE cc_start: 0.7995 (p90) cc_final: 0.7072 (p90) REVERT: D 179 MET cc_start: 0.6933 (ptp) cc_final: 0.6130 (pmm) REVERT: D 202 GLN cc_start: 0.9457 (mt0) cc_final: 0.8686 (pp30) REVERT: D 203 ARG cc_start: 0.9157 (ptp-110) cc_final: 0.8563 (ptp-110) REVERT: D 208 LYS cc_start: 0.8475 (mtpp) cc_final: 0.8185 (mtmt) REVERT: D 214 GLU cc_start: 0.9382 (mm-30) cc_final: 0.9147 (mp0) REVERT: D 216 ASP cc_start: 0.9113 (t70) cc_final: 0.8780 (t0) REVERT: D 311 LYS cc_start: 0.8800 (tmtt) cc_final: 0.8192 (tptt) REVERT: D 337 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7404 (tt) REVERT: D 420 MET cc_start: 0.7394 (mmm) cc_final: 0.6970 (mmm) REVERT: D 482 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8651 (tpt) REVERT: D 487 GLU cc_start: 0.8272 (pm20) cc_final: 0.7617 (pm20) REVERT: D 488 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7074 (tt) REVERT: D 490 PHE cc_start: 0.8422 (m-80) cc_final: 0.7810 (m-80) REVERT: D 510 GLU cc_start: 0.7283 (mm-30) cc_final: 0.7034 (mm-30) REVERT: E 32 TYR cc_start: 0.8649 (m-10) cc_final: 0.8257 (m-10) REVERT: E 47 ASP cc_start: 0.8991 (m-30) cc_final: 0.8258 (p0) REVERT: E 109 LYS cc_start: 0.8896 (mmtm) cc_final: 0.8629 (mptt) REVERT: E 111 GLU cc_start: 0.8729 (mp0) cc_final: 0.8503 (mp0) REVERT: E 132 GLU cc_start: 0.9503 (mp0) cc_final: 0.9278 (mp0) REVERT: E 179 MET cc_start: 0.6988 (ptp) cc_final: 0.6235 (pmm) REVERT: E 206 LYS cc_start: 0.8248 (ptpt) cc_final: 0.7863 (ptpt) REVERT: E 208 LYS cc_start: 0.8333 (ttmm) cc_final: 0.7893 (mtmt) REVERT: E 214 GLU cc_start: 0.9341 (mm-30) cc_final: 0.9093 (mp0) REVERT: E 216 ASP cc_start: 0.9164 (t70) cc_final: 0.8786 (t0) REVERT: E 352 GLU cc_start: 0.8906 (tp30) cc_final: 0.8669 (tp30) REVERT: E 420 MET cc_start: 0.7364 (mmm) cc_final: 0.6879 (mmm) REVERT: E 466 HIS cc_start: 0.8792 (OUTLIER) cc_final: 0.8291 (t-90) REVERT: E 470 ASP cc_start: 0.8500 (m-30) cc_final: 0.8204 (m-30) REVERT: E 488 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7849 (tp) REVERT: E 489 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7814 (ttmt) REVERT: E 490 PHE cc_start: 0.8366 (m-80) cc_final: 0.7915 (m-80) REVERT: E 509 TYR cc_start: 0.7278 (p90) cc_final: 0.7045 (p90) REVERT: F 32 TYR cc_start: 0.8708 (m-10) cc_final: 0.8232 (m-10) REVERT: F 47 ASP cc_start: 0.9151 (m-30) cc_final: 0.8428 (p0) REVERT: F 65 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9018 (pt) REVERT: F 109 LYS cc_start: 0.8908 (mmtm) cc_final: 0.8669 (mptt) REVERT: F 165 PHE cc_start: 0.8305 (p90) cc_final: 0.7588 (p90) REVERT: F 166 LEU cc_start: 0.8282 (tp) cc_final: 0.7945 (tp) REVERT: F 179 MET cc_start: 0.6912 (ptp) cc_final: 0.6157 (pmm) REVERT: F 185 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7645 (mt) REVERT: F 202 GLN cc_start: 0.9371 (mm-40) cc_final: 0.9164 (mm-40) REVERT: F 216 ASP cc_start: 0.9225 (t70) cc_final: 0.8881 (t0) REVERT: F 386 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8106 (ppp) REVERT: F 399 GLU cc_start: 0.8769 (pm20) cc_final: 0.8046 (tt0) REVERT: F 466 HIS cc_start: 0.8725 (OUTLIER) cc_final: 0.8328 (t-90) REVERT: F 470 ASP cc_start: 0.8518 (m-30) cc_final: 0.8182 (m-30) REVERT: F 488 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7712 (tp) REVERT: F 490 PHE cc_start: 0.8365 (m-80) cc_final: 0.7932 (m-80) REVERT: G 68 SER cc_start: 0.9064 (t) cc_final: 0.8786 (t) REVERT: G 73 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.6859 (t) REVERT: G 74 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8111 (p) REVERT: G 78 MET cc_start: 0.7807 (ttt) cc_final: 0.7377 (ttt) REVERT: G 103 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8257 (tp30) REVERT: G 109 LYS cc_start: 0.8893 (mmtm) cc_final: 0.8620 (mptt) REVERT: G 132 GLU cc_start: 0.9477 (mp0) cc_final: 0.9256 (mp0) REVERT: G 199 GLU cc_start: 0.9473 (tp30) cc_final: 0.8915 (tp30) REVERT: G 202 GLN cc_start: 0.9461 (mm-40) cc_final: 0.8511 (pp30) REVERT: G 206 LYS cc_start: 0.8470 (mtmt) cc_final: 0.7787 (ttpt) REVERT: G 214 GLU cc_start: 0.9420 (mm-30) cc_final: 0.9131 (mp0) REVERT: G 216 ASP cc_start: 0.9194 (t70) cc_final: 0.8858 (t0) REVERT: G 311 LYS cc_start: 0.8691 (tmtt) cc_final: 0.7752 (tppt) REVERT: G 385 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7057 (tmm) REVERT: G 420 MET cc_start: 0.7276 (mmm) cc_final: 0.6843 (mmm) REVERT: G 469 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8162 (pt0) REVERT: G 470 ASP cc_start: 0.8386 (m-30) cc_final: 0.8045 (m-30) REVERT: G 488 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7745 (tp) REVERT: G 489 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7821 (ttmt) REVERT: G 490 PHE cc_start: 0.8453 (m-80) cc_final: 0.7974 (m-80) REVERT: G 510 GLU cc_start: 0.7272 (mm-30) cc_final: 0.7034 (mm-30) REVERT: H 32 TYR cc_start: 0.8613 (m-10) cc_final: 0.8130 (m-10) REVERT: H 47 ASP cc_start: 0.9119 (m-30) cc_final: 0.8348 (p0) REVERT: H 73 VAL cc_start: 0.8448 (OUTLIER) cc_final: 0.6921 (t) REVERT: H 103 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8213 (tp30) REVERT: H 111 GLU cc_start: 0.8764 (mp0) cc_final: 0.8306 (mp0) REVERT: H 128 ARG cc_start: 0.8885 (mmt90) cc_final: 0.8674 (mmt90) REVERT: H 208 LYS cc_start: 0.8239 (ttmm) cc_final: 0.7759 (mtmt) REVERT: H 216 ASP cc_start: 0.9033 (t70) cc_final: 0.8727 (t0) REVERT: H 337 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7338 (tt) REVERT: H 407 ARG cc_start: 0.7447 (ttt180) cc_final: 0.6838 (ttt180) REVERT: H 466 HIS cc_start: 0.8740 (OUTLIER) cc_final: 0.8337 (t-90) REVERT: H 488 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7840 (tp) REVERT: H 490 PHE cc_start: 0.8517 (m-80) cc_final: 0.8077 (m-80) outliers start: 238 outliers final: 187 residues processed: 1106 average time/residue: 0.4237 time to fit residues: 752.9904 Evaluate side-chains 1197 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 972 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 489 LYS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain B residue 482 MET Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 466 HIS Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 482 MET Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 353 TYR Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 466 HIS Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 489 LYS Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 466 HIS Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 385 MET Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 467 SER Chi-restraints excluded: chain G residue 469 GLN Chi-restraints excluded: chain G residue 482 MET Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 43 ASP Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 353 TYR Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 466 HIS Chi-restraints excluded: chain H residue 469 GLN Chi-restraints excluded: chain H residue 488 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 8.9990 chunk 324 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 280 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 305 optimal weight: 8.9990 chunk 127 optimal weight: 0.8980 chunk 313 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN ** F 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.162353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.127099 restraints weight = 52000.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.132477 restraints weight = 29489.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.136157 restraints weight = 19876.900| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31576 Z= 0.240 Angle : 0.873 13.568 42888 Z= 0.413 Chirality : 0.050 0.255 4888 Planarity : 0.005 0.084 5328 Dihedral : 15.135 135.014 5323 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 24.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 7.05 % Allowed : 34.90 % Favored : 58.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -2.44 (0.13), residues: 3880 helix: -1.86 (0.13), residues: 1168 sheet: -2.23 (0.22), residues: 480 loop : -1.29 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 454 PHE 0.014 0.001 PHE C 90 TYR 0.031 0.002 TYR B 233 ARG 0.011 0.001 ARG E 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11022.29 seconds wall clock time: 198 minutes 14.93 seconds (11894.93 seconds total)