Starting phenix.real_space_refine on Thu Jul 25 13:10:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u66_41946/07_2024/8u66_41946_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u66_41946/07_2024/8u66_41946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u66_41946/07_2024/8u66_41946.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u66_41946/07_2024/8u66_41946.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u66_41946/07_2024/8u66_41946_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u66_41946/07_2024/8u66_41946_neut.cif" } resolution = 2.21 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= -0.001 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 128 5.16 5 C 17968 2.51 5 N 5064 2.21 5 O 6181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 29365 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "B" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 125 Classifications: {'water': 125} Link IDs: {None: 124} Chain: "C" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Classifications: {'water': 121} Link IDs: {None: 120} Chain: "E" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 125 Classifications: {'water': 125} Link IDs: {None: 124} Chain: "F" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Classifications: {'water': 121} Link IDs: {None: 120} Chain: "G" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Classifications: {'water': 121} Link IDs: {None: 120} Chain: "H" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Time building chain proxies: 15.29, per 1000 atoms: 0.52 Number of scatterers: 29365 At special positions: 0 Unit cell: (122.85, 122.85, 108.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 128 16.00 P 16 15.00 Mg 8 11.99 O 6181 8.00 N 5064 7.00 C 17968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.66 Conformation dependent library (CDL) restraints added in 5.2 seconds 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 24 sheets defined 54.2% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 Processing helix chain 'A' and resid 42 through 56 Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 98 through 107 Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.614A pdb=" N PHE A 113 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 140 through 149 Processing helix chain 'A' and resid 167 through 182 Processing helix chain 'A' and resid 199 through 219 Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 259 through 274 Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.553A pdb=" N ARG A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL A 300 " --> pdb=" O HIS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 337 Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 398 through 419 Processing helix chain 'A' and resid 422 through 436 removed outlier: 5.851A pdb=" N ARG A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 448 Processing helix chain 'B' and resid 13 through 18 Processing helix chain 'B' and resid 42 through 56 Processing helix chain 'B' and resid 62 through 68 Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'B' and resid 98 through 107 Processing helix chain 'B' and resid 109 through 113 removed outlier: 3.614A pdb=" N PHE B 113 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 140 through 149 Processing helix chain 'B' and resid 167 through 182 Processing helix chain 'B' and resid 199 through 219 Processing helix chain 'B' and resid 232 through 246 Processing helix chain 'B' and resid 255 through 259 Processing helix chain 'B' and resid 259 through 274 Processing helix chain 'B' and resid 284 through 289 removed outlier: 3.552A pdb=" N ARG B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL B 300 " --> pdb=" O HIS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 337 Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 389 through 394 Processing helix chain 'B' and resid 398 through 419 Processing helix chain 'B' and resid 422 through 436 removed outlier: 5.851A pdb=" N ARG B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 Processing helix chain 'C' and resid 13 through 18 Processing helix chain 'C' and resid 42 through 56 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 69 through 74 Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 98 through 107 Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.614A pdb=" N PHE C 113 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 132 Processing helix chain 'C' and resid 140 through 149 Processing helix chain 'C' and resid 167 through 182 Processing helix chain 'C' and resid 199 through 219 Processing helix chain 'C' and resid 232 through 246 Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 259 through 274 Processing helix chain 'C' and resid 284 through 289 removed outlier: 3.553A pdb=" N ARG C 289 " --> pdb=" O ALA C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL C 300 " --> pdb=" O HIS C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 337 Processing helix chain 'C' and resid 369 through 371 No H-bonds generated for 'chain 'C' and resid 369 through 371' Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 398 through 419 Processing helix chain 'C' and resid 422 through 436 removed outlier: 5.850A pdb=" N ARG C 428 " --> pdb=" O LEU C 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 448 Processing helix chain 'D' and resid 13 through 18 Processing helix chain 'D' and resid 42 through 56 Processing helix chain 'D' and resid 62 through 68 Processing helix chain 'D' and resid 69 through 74 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 98 through 107 Processing helix chain 'D' and resid 109 through 113 removed outlier: 3.614A pdb=" N PHE D 113 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 140 through 149 Processing helix chain 'D' and resid 167 through 182 Processing helix chain 'D' and resid 199 through 219 Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 284 through 289 removed outlier: 3.553A pdb=" N ARG D 289 " --> pdb=" O ALA D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL D 300 " --> pdb=" O HIS D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 337 Processing helix chain 'D' and resid 369 through 371 No H-bonds generated for 'chain 'D' and resid 369 through 371' Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 389 through 394 Processing helix chain 'D' and resid 398 through 419 Processing helix chain 'D' and resid 422 through 436 removed outlier: 5.851A pdb=" N ARG D 428 " --> pdb=" O LEU D 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN D 429 " --> pdb=" O ALA D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 448 Processing helix chain 'E' and resid 13 through 18 Processing helix chain 'E' and resid 42 through 56 Processing helix chain 'E' and resid 62 through 68 Processing helix chain 'E' and resid 69 through 74 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 98 through 107 Processing helix chain 'E' and resid 109 through 113 removed outlier: 3.613A pdb=" N PHE E 113 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 132 Processing helix chain 'E' and resid 140 through 149 Processing helix chain 'E' and resid 167 through 182 Processing helix chain 'E' and resid 199 through 219 Processing helix chain 'E' and resid 232 through 246 Processing helix chain 'E' and resid 255 through 259 Processing helix chain 'E' and resid 259 through 274 Processing helix chain 'E' and resid 284 through 289 removed outlier: 3.553A pdb=" N ARG E 289 " --> pdb=" O ALA E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL E 300 " --> pdb=" O HIS E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 337 Processing helix chain 'E' and resid 369 through 371 No H-bonds generated for 'chain 'E' and resid 369 through 371' Processing helix chain 'E' and resid 372 through 381 Processing helix chain 'E' and resid 389 through 394 Processing helix chain 'E' and resid 398 through 419 Processing helix chain 'E' and resid 422 through 436 removed outlier: 5.850A pdb=" N ARG E 428 " --> pdb=" O LEU E 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN E 429 " --> pdb=" O ALA E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 448 Processing helix chain 'F' and resid 13 through 18 Processing helix chain 'F' and resid 42 through 56 Processing helix chain 'F' and resid 62 through 68 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 98 through 107 Processing helix chain 'F' and resid 109 through 113 removed outlier: 3.614A pdb=" N PHE F 113 " --> pdb=" O VAL F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 132 Processing helix chain 'F' and resid 140 through 149 Processing helix chain 'F' and resid 167 through 182 Processing helix chain 'F' and resid 199 through 219 Processing helix chain 'F' and resid 232 through 246 Processing helix chain 'F' and resid 255 through 259 Processing helix chain 'F' and resid 259 through 274 Processing helix chain 'F' and resid 284 through 289 removed outlier: 3.553A pdb=" N ARG F 289 " --> pdb=" O ALA F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL F 300 " --> pdb=" O HIS F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 337 Processing helix chain 'F' and resid 369 through 371 No H-bonds generated for 'chain 'F' and resid 369 through 371' Processing helix chain 'F' and resid 372 through 381 Processing helix chain 'F' and resid 389 through 394 Processing helix chain 'F' and resid 398 through 419 Processing helix chain 'F' and resid 422 through 436 removed outlier: 5.850A pdb=" N ARG F 428 " --> pdb=" O LEU F 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN F 429 " --> pdb=" O ALA F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 448 Processing helix chain 'G' and resid 13 through 18 Processing helix chain 'G' and resid 42 through 56 Processing helix chain 'G' and resid 62 through 68 Processing helix chain 'G' and resid 69 through 74 Processing helix chain 'G' and resid 90 through 94 Processing helix chain 'G' and resid 98 through 107 Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.614A pdb=" N PHE G 113 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 132 Processing helix chain 'G' and resid 140 through 149 Processing helix chain 'G' and resid 167 through 182 Processing helix chain 'G' and resid 199 through 219 Processing helix chain 'G' and resid 232 through 246 Processing helix chain 'G' and resid 255 through 259 Processing helix chain 'G' and resid 259 through 274 Processing helix chain 'G' and resid 284 through 289 removed outlier: 3.553A pdb=" N ARG G 289 " --> pdb=" O ALA G 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL G 300 " --> pdb=" O HIS G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 337 Processing helix chain 'G' and resid 369 through 371 No H-bonds generated for 'chain 'G' and resid 369 through 371' Processing helix chain 'G' and resid 372 through 381 Processing helix chain 'G' and resid 389 through 394 Processing helix chain 'G' and resid 398 through 419 Processing helix chain 'G' and resid 422 through 436 removed outlier: 5.850A pdb=" N ARG G 428 " --> pdb=" O LEU G 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN G 429 " --> pdb=" O ALA G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 448 Processing helix chain 'H' and resid 13 through 18 Processing helix chain 'H' and resid 42 through 56 Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 69 through 74 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 98 through 107 Processing helix chain 'H' and resid 109 through 113 removed outlier: 3.614A pdb=" N PHE H 113 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 140 through 149 Processing helix chain 'H' and resid 167 through 182 Processing helix chain 'H' and resid 199 through 219 Processing helix chain 'H' and resid 232 through 246 Processing helix chain 'H' and resid 255 through 259 Processing helix chain 'H' and resid 259 through 274 Processing helix chain 'H' and resid 284 through 289 removed outlier: 3.553A pdb=" N ARG H 289 " --> pdb=" O ALA H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL H 300 " --> pdb=" O HIS H 296 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 337 Processing helix chain 'H' and resid 369 through 371 No H-bonds generated for 'chain 'H' and resid 369 through 371' Processing helix chain 'H' and resid 372 through 381 Processing helix chain 'H' and resid 389 through 394 Processing helix chain 'H' and resid 398 through 419 Processing helix chain 'H' and resid 422 through 436 removed outlier: 5.850A pdb=" N ARG H 428 " --> pdb=" O LEU H 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN H 429 " --> pdb=" O ALA H 425 " (cutoff:3.500A) Processing helix chain 'H' and resid 438 through 448 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 81 removed outlier: 6.732A pdb=" N TYR A 86 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE A 80 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP A 123 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG A 34 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU A 121 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU A 36 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU A 119 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 157 removed outlier: 6.394A pdb=" N LEU A 155 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS A 313 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 251 " --> pdb=" O HIS A 278 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N HIS A 280 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL A 253 " --> pdb=" O HIS A 280 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS A 224 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N MET A 252 " --> pdb=" O HIS A 224 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU A 226 " --> pdb=" O MET A 252 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASP A 254 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N THR A 186 " --> pdb=" O TRP A 225 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASN A 227 " --> pdb=" O THR A 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 81 removed outlier: 6.732A pdb=" N TYR B 86 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE B 80 " --> pdb=" O THR B 84 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP B 123 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG B 34 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU B 121 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU B 36 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU B 119 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 155 through 157 removed outlier: 6.394A pdb=" N LEU B 155 " --> pdb=" O PHE B 386 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS B 313 " --> pdb=" O CYS B 279 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 251 " --> pdb=" O HIS B 278 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS B 280 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 253 " --> pdb=" O HIS B 280 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N HIS B 224 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N MET B 252 " --> pdb=" O HIS B 224 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU B 226 " --> pdb=" O MET B 252 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASP B 254 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR B 186 " --> pdb=" O TRP B 225 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASN B 227 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AA7, first strand: chain 'C' and resid 76 through 81 removed outlier: 6.732A pdb=" N TYR C 86 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE C 80 " --> pdb=" O THR C 84 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP C 123 " --> pdb=" O ALA C 32 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG C 34 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU C 121 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU C 36 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU C 119 " --> pdb=" O GLU C 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 155 through 157 removed outlier: 6.395A pdb=" N LEU C 155 " --> pdb=" O PHE C 386 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS C 313 " --> pdb=" O CYS C 279 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE C 251 " --> pdb=" O HIS C 278 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS C 280 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL C 253 " --> pdb=" O HIS C 280 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N HIS C 224 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET C 252 " --> pdb=" O HIS C 224 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU C 226 " --> pdb=" O MET C 252 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASP C 254 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR C 186 " --> pdb=" O TRP C 225 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ASN C 227 " --> pdb=" O THR C 186 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AB1, first strand: chain 'D' and resid 76 through 81 removed outlier: 6.732A pdb=" N TYR D 86 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE D 80 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP D 123 " --> pdb=" O ALA D 32 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG D 34 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU D 121 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLU D 36 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU D 119 " --> pdb=" O GLU D 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 155 through 157 removed outlier: 6.394A pdb=" N LEU D 155 " --> pdb=" O PHE D 386 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS D 313 " --> pdb=" O CYS D 279 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE D 251 " --> pdb=" O HIS D 278 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N HIS D 280 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL D 253 " --> pdb=" O HIS D 280 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS D 224 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET D 252 " --> pdb=" O HIS D 224 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU D 226 " --> pdb=" O MET D 252 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ASP D 254 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N THR D 186 " --> pdb=" O TRP D 225 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASN D 227 " --> pdb=" O THR D 186 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 339 through 340 Processing sheet with id=AB4, first strand: chain 'E' and resid 76 through 81 removed outlier: 6.732A pdb=" N TYR E 86 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE E 80 " --> pdb=" O THR E 84 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP E 123 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG E 34 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU E 121 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU E 36 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU E 119 " --> pdb=" O GLU E 36 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 155 through 157 removed outlier: 6.394A pdb=" N LEU E 155 " --> pdb=" O PHE E 386 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS E 313 " --> pdb=" O CYS E 279 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE E 251 " --> pdb=" O HIS E 278 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS E 280 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL E 253 " --> pdb=" O HIS E 280 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS E 224 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET E 252 " --> pdb=" O HIS E 224 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU E 226 " --> pdb=" O MET E 252 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASP E 254 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR E 186 " --> pdb=" O TRP E 225 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ASN E 227 " --> pdb=" O THR E 186 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 339 through 340 Processing sheet with id=AB7, first strand: chain 'F' and resid 76 through 81 removed outlier: 6.732A pdb=" N TYR F 86 " --> pdb=" O TYR F 78 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE F 80 " --> pdb=" O THR F 84 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP F 123 " --> pdb=" O ALA F 32 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG F 34 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU F 121 " --> pdb=" O ARG F 34 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU F 36 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU F 119 " --> pdb=" O GLU F 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 155 through 157 removed outlier: 6.395A pdb=" N LEU F 155 " --> pdb=" O PHE F 386 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS F 313 " --> pdb=" O CYS F 279 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE F 251 " --> pdb=" O HIS F 278 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS F 280 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL F 253 " --> pdb=" O HIS F 280 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N HIS F 224 " --> pdb=" O TYR F 250 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET F 252 " --> pdb=" O HIS F 224 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU F 226 " --> pdb=" O MET F 252 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ASP F 254 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR F 186 " --> pdb=" O TRP F 225 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASN F 227 " --> pdb=" O THR F 186 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 339 through 340 Processing sheet with id=AC1, first strand: chain 'G' and resid 76 through 81 removed outlier: 6.732A pdb=" N TYR G 86 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE G 80 " --> pdb=" O THR G 84 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP G 123 " --> pdb=" O ALA G 32 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG G 34 " --> pdb=" O LEU G 121 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU G 121 " --> pdb=" O ARG G 34 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU G 36 " --> pdb=" O LEU G 119 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU G 119 " --> pdb=" O GLU G 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 155 through 157 removed outlier: 6.394A pdb=" N LEU G 155 " --> pdb=" O PHE G 386 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS G 313 " --> pdb=" O CYS G 279 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE G 251 " --> pdb=" O HIS G 278 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS G 280 " --> pdb=" O ILE G 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL G 253 " --> pdb=" O HIS G 280 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS G 224 " --> pdb=" O TYR G 250 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET G 252 " --> pdb=" O HIS G 224 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU G 226 " --> pdb=" O MET G 252 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ASP G 254 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR G 186 " --> pdb=" O TRP G 225 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASN G 227 " --> pdb=" O THR G 186 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 339 through 340 Processing sheet with id=AC4, first strand: chain 'H' and resid 76 through 81 removed outlier: 6.731A pdb=" N TYR H 86 " --> pdb=" O TYR H 78 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE H 80 " --> pdb=" O THR H 84 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR H 84 " --> pdb=" O ILE H 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP H 123 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG H 34 " --> pdb=" O LEU H 121 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU H 121 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU H 36 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU H 119 " --> pdb=" O GLU H 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 155 through 157 removed outlier: 6.394A pdb=" N LEU H 155 " --> pdb=" O PHE H 386 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS H 313 " --> pdb=" O CYS H 279 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE H 251 " --> pdb=" O HIS H 278 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS H 280 " --> pdb=" O ILE H 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL H 253 " --> pdb=" O HIS H 280 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS H 224 " --> pdb=" O TYR H 250 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N MET H 252 " --> pdb=" O HIS H 224 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU H 226 " --> pdb=" O MET H 252 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASP H 254 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR H 186 " --> pdb=" O TRP H 225 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ASN H 227 " --> pdb=" O THR H 186 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 339 through 340 1384 hydrogen bonds defined for protein. 3840 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.98 Time building geometry restraints manager: 14.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4693 1.32 - 1.44: 8100 1.44 - 1.56: 16079 1.56 - 1.68: 16 1.68 - 1.81: 208 Bond restraints: 29096 Sorted by residual: bond pdb=" NZ KCX E 187 " pdb=" CX KCX E 187 " ideal model delta sigma weight residual 1.411 1.329 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" NZ KCX F 187 " pdb=" CX KCX F 187 " ideal model delta sigma weight residual 1.411 1.331 0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" NZ KCX D 187 " pdb=" CX KCX D 187 " ideal model delta sigma weight residual 1.411 1.332 0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" NZ KCX H 187 " pdb=" CX KCX H 187 " ideal model delta sigma weight residual 1.411 1.334 0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" NZ KCX C 187 " pdb=" CX KCX C 187 " ideal model delta sigma weight residual 1.411 1.334 0.077 2.00e-02 2.50e+03 1.47e+01 ... (remaining 29091 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.82: 969 106.82 - 113.62: 15435 113.62 - 120.42: 11103 120.42 - 127.21: 11516 127.21 - 134.01: 449 Bond angle restraints: 39472 Sorted by residual: angle pdb=" C3 CAP H 502 " pdb=" C4 CAP H 502 " pdb=" C5 CAP H 502 " ideal model delta sigma weight residual 111.00 124.20 -13.20 3.00e+00 1.11e-01 1.94e+01 angle pdb=" C3 CAP E 502 " pdb=" C4 CAP E 502 " pdb=" C5 CAP E 502 " ideal model delta sigma weight residual 111.00 124.18 -13.18 3.00e+00 1.11e-01 1.93e+01 angle pdb=" C3 CAP G 502 " pdb=" C4 CAP G 502 " pdb=" C5 CAP G 502 " ideal model delta sigma weight residual 111.00 124.18 -13.18 3.00e+00 1.11e-01 1.93e+01 angle pdb=" C3 CAP D 502 " pdb=" C4 CAP D 502 " pdb=" C5 CAP D 502 " ideal model delta sigma weight residual 111.00 124.18 -13.18 3.00e+00 1.11e-01 1.93e+01 angle pdb=" C3 CAP B 502 " pdb=" C4 CAP B 502 " pdb=" C5 CAP B 502 " ideal model delta sigma weight residual 111.00 124.16 -13.16 3.00e+00 1.11e-01 1.92e+01 ... (remaining 39467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.78: 16529 34.78 - 69.56: 507 69.56 - 104.34: 84 104.34 - 139.12: 4 139.12 - 173.90: 4 Dihedral angle restraints: 17128 sinusoidal: 6952 harmonic: 10176 Sorted by residual: dihedral pdb=" C3 CAP H 502 " pdb=" C CAP H 502 " pdb=" C2 CAP H 502 " pdb=" O6 CAP H 502 " ideal model delta sinusoidal sigma weight residual 81.86 -92.04 173.90 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C3 CAP D 502 " pdb=" C CAP D 502 " pdb=" C2 CAP D 502 " pdb=" O6 CAP D 502 " ideal model delta sinusoidal sigma weight residual 81.86 -92.04 173.90 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C3 CAP E 502 " pdb=" C CAP E 502 " pdb=" C2 CAP E 502 " pdb=" O6 CAP E 502 " ideal model delta sinusoidal sigma weight residual 81.86 -92.03 173.89 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 17125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.350: 4144 0.350 - 0.700: 0 0.700 - 1.050: 0 1.050 - 1.400: 0 1.400 - 1.750: 8 Chirality restraints: 4152 Sorted by residual: chirality pdb=" C4 CAP B 502 " pdb=" C3 CAP B 502 " pdb=" C5 CAP B 502 " pdb=" O4 CAP B 502 " both_signs ideal model delta sigma weight residual False -2.47 -0.72 -1.75 2.00e-01 2.50e+01 7.66e+01 chirality pdb=" C4 CAP H 502 " pdb=" C3 CAP H 502 " pdb=" C5 CAP H 502 " pdb=" O4 CAP H 502 " both_signs ideal model delta sigma weight residual False -2.47 -0.72 -1.75 2.00e-01 2.50e+01 7.63e+01 chirality pdb=" C4 CAP G 502 " pdb=" C3 CAP G 502 " pdb=" C5 CAP G 502 " pdb=" O4 CAP G 502 " both_signs ideal model delta sigma weight residual False -2.47 -0.72 -1.75 2.00e-01 2.50e+01 7.63e+01 ... (remaining 4149 not shown) Planarity restraints: 5168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA KCX F 187 " -0.009 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C KCX F 187 " 0.033 2.00e-02 2.50e+03 pdb=" O KCX F 187 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP F 188 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA KCX A 187 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C KCX A 187 " 0.033 2.00e-02 2.50e+03 pdb=" O KCX A 187 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP A 188 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA KCX B 187 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C KCX B 187 " -0.033 2.00e-02 2.50e+03 pdb=" O KCX B 187 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP B 188 " 0.011 2.00e-02 2.50e+03 ... (remaining 5165 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 188 2.48 - 3.08: 21060 3.08 - 3.69: 51577 3.69 - 4.29: 83912 4.29 - 4.90: 129116 Nonbonded interactions: 285853 Sorted by model distance: nonbonded pdb=" OD1 ASP E 189 " pdb="MG MG E 501 " model vdw 1.869 2.170 nonbonded pdb=" OD1 ASP G 189 " pdb="MG MG G 501 " model vdw 1.870 2.170 nonbonded pdb=" OD1 ASP C 189 " pdb="MG MG C 501 " model vdw 1.871 2.170 nonbonded pdb=" OD1 ASP H 189 " pdb="MG MG H 501 " model vdw 1.871 2.170 nonbonded pdb=" OD1 ASP B 189 " pdb="MG MG B 501 " model vdw 1.872 2.170 ... (remaining 285848 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 83.010 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 : 0.004 0.082 29096 Z= 0.230 Angle : 0.561 13.198 39472 Z= 0.263 Chirality : 0.085 1.750 4152 Planarity : 0.003 0.022 5168 Dihedral : 16.747 173.903 10664 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.28 % Allowed : 11.41 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.15), residues: 3544 helix: 1.76 (0.13), residues: 1664 sheet: 0.50 (0.25), residues: 424 loop : 1.32 (0.18), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 354 HIS 0.003 0.001 HIS E 311 PHE 0.012 0.001 PHE E 297 TYR 0.016 0.001 TYR C 263 ARG 0.001 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 441 time to evaluate : 3.256 Fit side-chains REVERT: A 149 LYS cc_start: 0.8079 (mmtt) cc_final: 0.7795 (mtmt) REVERT: A 208 MET cc_start: 0.8963 (mmm) cc_final: 0.8719 (mmm) REVERT: A 216 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6925 (tm-30) REVERT: A 429 GLN cc_start: 0.6828 (tp-100) cc_final: 0.6564 (tp-100) REVERT: B 208 MET cc_start: 0.8936 (mmm) cc_final: 0.8718 (mmm) REVERT: B 216 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6914 (tm-30) REVERT: B 429 GLN cc_start: 0.6971 (tp-100) cc_final: 0.6697 (tp-100) REVERT: C 23 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7186 (mt-10) REVERT: C 216 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6830 (tm-30) REVERT: C 429 GLN cc_start: 0.6872 (tp-100) cc_final: 0.6455 (tp-100) REVERT: D 23 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7183 (mt-10) REVERT: D 149 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7709 (mtmt) REVERT: D 216 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6866 (tm-30) REVERT: D 217 GLU cc_start: 0.7270 (mt-10) cc_final: 0.7054 (mt-10) REVERT: D 252 MET cc_start: 0.9283 (ptm) cc_final: 0.9025 (ptm) REVERT: D 429 GLN cc_start: 0.6873 (tp-100) cc_final: 0.6535 (tp-100) REVERT: E 65 GLN cc_start: 0.6959 (pt0) cc_final: 0.6626 (pt0) REVERT: E 149 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7789 (mtmt) REVERT: E 208 MET cc_start: 0.8917 (mmm) cc_final: 0.8678 (mmm) REVERT: E 216 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6891 (tm-30) REVERT: E 429 GLN cc_start: 0.6942 (tp-100) cc_final: 0.6679 (tp-100) REVERT: F 149 LYS cc_start: 0.8107 (mmtt) cc_final: 0.7791 (mtmt) REVERT: F 208 MET cc_start: 0.8952 (mmm) cc_final: 0.8727 (mmm) REVERT: F 216 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6851 (tm-30) REVERT: F 429 GLN cc_start: 0.6821 (tp-100) cc_final: 0.6548 (tp-100) REVERT: G 65 GLN cc_start: 0.7020 (pt0) cc_final: 0.6710 (pt0) REVERT: G 149 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7822 (mtmt) REVERT: G 208 MET cc_start: 0.8935 (mmm) cc_final: 0.8726 (mmm) REVERT: G 216 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6933 (tm-30) REVERT: G 429 GLN cc_start: 0.6902 (tp-100) cc_final: 0.6645 (tp-100) REVERT: H 208 MET cc_start: 0.8932 (mmm) cc_final: 0.8729 (mmm) REVERT: H 216 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6932 (tm-30) REVERT: H 429 GLN cc_start: 0.6883 (tp-100) cc_final: 0.6615 (tp-100) outliers start: 8 outliers final: 8 residues processed: 441 average time/residue: 2.1026 time to fit residues: 1035.4363 Evaluate side-chains 411 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 403 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 311 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 1.9990 chunk 266 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 179 optimal weight: 0.0570 chunk 142 optimal weight: 7.9990 chunk 275 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 167 optimal weight: 0.0020 chunk 205 optimal weight: 3.9990 chunk 319 optimal weight: 7.9990 overall best weight: 0.7308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN B 345 GLN C 345 GLN D 109 ASN D 345 GLN E 345 GLN F 345 GLN G 345 GLN H 345 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 29096 Z= 0.168 Angle : 0.503 5.361 39472 Z= 0.267 Chirality : 0.040 0.132 4152 Planarity : 0.004 0.024 5168 Dihedral : 9.391 179.055 4144 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.69 % Allowed : 12.11 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.15), residues: 3544 helix: 1.77 (0.13), residues: 1624 sheet: 0.79 (0.24), residues: 464 loop : 1.20 (0.18), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 354 HIS 0.003 0.001 HIS F 311 PHE 0.015 0.002 PHE G 297 TYR 0.020 0.002 TYR A 263 ARG 0.003 0.000 ARG H 442 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 400 time to evaluate : 3.105 Fit side-chains REVERT: A 208 MET cc_start: 0.8969 (mmm) cc_final: 0.8725 (mmm) REVERT: A 216 GLU cc_start: 0.7257 (tm-30) cc_final: 0.6942 (tm-30) REVERT: A 276 MET cc_start: 0.9120 (mtm) cc_final: 0.8873 (mtm) REVERT: A 397 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7629 (mtm110) REVERT: A 429 GLN cc_start: 0.6920 (tp-100) cc_final: 0.6458 (tp-100) REVERT: A 442 ARG cc_start: 0.7638 (ttm-80) cc_final: 0.7411 (ttm-80) REVERT: B 208 MET cc_start: 0.9003 (mmm) cc_final: 0.8658 (mmm) REVERT: B 216 GLU cc_start: 0.7305 (tm-30) cc_final: 0.6972 (tm-30) REVERT: B 397 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7667 (mtm110) REVERT: B 429 GLN cc_start: 0.6993 (tp-100) cc_final: 0.6450 (tp-100) REVERT: B 446 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7375 (mt-10) REVERT: C 208 MET cc_start: 0.8973 (mmm) cc_final: 0.8493 (mmp) REVERT: C 216 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6875 (tm-30) REVERT: C 429 GLN cc_start: 0.6863 (tp-100) cc_final: 0.6567 (tp-100) REVERT: D 65 GLN cc_start: 0.7023 (pt0) cc_final: 0.6698 (pt0) REVERT: D 149 LYS cc_start: 0.8073 (mmtt) cc_final: 0.7720 (mtmt) REVERT: D 216 GLU cc_start: 0.7271 (tm-30) cc_final: 0.6949 (tm-30) REVERT: D 276 MET cc_start: 0.9078 (mtm) cc_final: 0.8819 (mtm) REVERT: D 397 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7653 (mtm110) REVERT: E 208 MET cc_start: 0.8969 (mmm) cc_final: 0.8739 (mmm) REVERT: E 216 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6959 (tm-30) REVERT: E 397 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7655 (mtm110) REVERT: E 429 GLN cc_start: 0.6972 (tp-100) cc_final: 0.6404 (tp-100) REVERT: F 216 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6964 (tm-30) REVERT: F 276 MET cc_start: 0.9126 (mtm) cc_final: 0.8863 (mtm) REVERT: F 397 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7651 (mtm110) REVERT: F 429 GLN cc_start: 0.6926 (tp-100) cc_final: 0.6483 (tp-100) REVERT: G 65 GLN cc_start: 0.6944 (pt0) cc_final: 0.6587 (pt0) REVERT: G 216 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6999 (tm-30) REVERT: G 276 MET cc_start: 0.9122 (mtm) cc_final: 0.8850 (mtm) REVERT: G 397 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7658 (mtm110) REVERT: G 429 GLN cc_start: 0.6932 (tp-100) cc_final: 0.6400 (tp-100) REVERT: G 442 ARG cc_start: 0.7669 (ttm-80) cc_final: 0.7435 (ttm-80) REVERT: H 208 MET cc_start: 0.9004 (mmm) cc_final: 0.8666 (mmm) REVERT: H 216 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6951 (tm-30) REVERT: H 397 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7653 (mtm110) REVERT: H 429 GLN cc_start: 0.6956 (tp-100) cc_final: 0.6448 (tp-100) REVERT: H 442 ARG cc_start: 0.7745 (ttm-80) cc_final: 0.7540 (ttm-80) REVERT: H 446 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7397 (mt-10) outliers start: 48 outliers final: 17 residues processed: 429 average time/residue: 2.0304 time to fit residues: 977.1077 Evaluate side-chains 404 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 380 time to evaluate : 3.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 397 ARG Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 397 ARG Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 397 ARG Chi-restraints excluded: chain H residue 254 ASP Chi-restraints excluded: chain H residue 311 HIS Chi-restraints excluded: chain H residue 397 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 266 optimal weight: 7.9990 chunk 217 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 320 optimal weight: 7.9990 chunk 345 optimal weight: 3.9990 chunk 285 optimal weight: 0.9990 chunk 317 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 chunk 256 optimal weight: 0.0070 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 GLN E 193 ASN ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 ASN ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 ASN ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 29096 Z= 0.274 Angle : 0.608 7.463 39472 Z= 0.321 Chirality : 0.043 0.137 4152 Planarity : 0.004 0.028 5168 Dihedral : 9.483 172.961 4144 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.80 % Allowed : 12.29 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.14), residues: 3544 helix: 1.52 (0.13), residues: 1576 sheet: 0.68 (0.22), residues: 512 loop : 1.00 (0.18), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 354 HIS 0.004 0.001 HIS H 393 PHE 0.022 0.003 PHE A 297 TYR 0.029 0.002 TYR B 263 ARG 0.004 0.001 ARG F 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 410 time to evaluate : 3.317 Fit side-chains REVERT: A 65 GLN cc_start: 0.7066 (pt0) cc_final: 0.6796 (pt0) REVERT: A 216 GLU cc_start: 0.7336 (tm-30) cc_final: 0.7046 (tm-30) REVERT: A 429 GLN cc_start: 0.7064 (tp-100) cc_final: 0.6760 (tp-100) REVERT: B 65 GLN cc_start: 0.7058 (pt0) cc_final: 0.6725 (pt0) REVERT: B 216 GLU cc_start: 0.7234 (tm-30) cc_final: 0.6910 (tm-30) REVERT: B 429 GLN cc_start: 0.7111 (tp-100) cc_final: 0.6809 (tp-100) REVERT: C 65 GLN cc_start: 0.7044 (pt0) cc_final: 0.6768 (pt0) REVERT: C 216 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6921 (tm-30) REVERT: C 429 GLN cc_start: 0.7102 (tp-100) cc_final: 0.6779 (tp-100) REVERT: D 65 GLN cc_start: 0.7047 (pt0) cc_final: 0.6761 (pt0) REVERT: D 216 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6941 (tm-30) REVERT: E 65 GLN cc_start: 0.7061 (pt0) cc_final: 0.6725 (pt0) REVERT: E 216 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6939 (tm-30) REVERT: E 429 GLN cc_start: 0.7100 (tp-100) cc_final: 0.6783 (tp-100) REVERT: F 65 GLN cc_start: 0.7066 (pt0) cc_final: 0.6795 (pt0) REVERT: F 216 GLU cc_start: 0.7206 (tm-30) cc_final: 0.6924 (tm-30) REVERT: F 429 GLN cc_start: 0.7077 (tp-100) cc_final: 0.6770 (tp-100) REVERT: G 65 GLN cc_start: 0.7092 (pt0) cc_final: 0.6752 (pt0) REVERT: G 216 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6928 (tm-30) REVERT: G 429 GLN cc_start: 0.7072 (tp-100) cc_final: 0.6765 (tp-100) REVERT: H 65 GLN cc_start: 0.7027 (pt0) cc_final: 0.6760 (pt0) REVERT: H 216 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6922 (tm-30) REVERT: H 429 GLN cc_start: 0.7088 (tp-100) cc_final: 0.6767 (tp-100) outliers start: 51 outliers final: 24 residues processed: 445 average time/residue: 2.2183 time to fit residues: 1096.4485 Evaluate side-chains 419 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 395 time to evaluate : 3.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 311 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 0.6980 chunk 240 optimal weight: 6.9990 chunk 166 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 321 optimal weight: 0.3980 chunk 340 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 304 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 29096 Z= 0.156 Angle : 0.507 5.862 39472 Z= 0.267 Chirality : 0.039 0.127 4152 Planarity : 0.003 0.025 5168 Dihedral : 9.139 171.355 4144 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.94 % Allowed : 12.78 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.14), residues: 3544 helix: 1.65 (0.13), residues: 1576 sheet: 0.59 (0.22), residues: 528 loop : 1.00 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 354 HIS 0.003 0.001 HIS B 311 PHE 0.013 0.002 PHE C 297 TYR 0.020 0.001 TYR G 263 ARG 0.003 0.000 ARG H 442 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 405 time to evaluate : 3.428 Fit side-chains REVERT: A 65 GLN cc_start: 0.7032 (pt0) cc_final: 0.6749 (pt0) REVERT: A 173 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7132 (ttt-90) REVERT: A 216 GLU cc_start: 0.7361 (tm-30) cc_final: 0.7020 (tm-30) REVERT: A 252 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.8643 (ptm) REVERT: A 429 GLN cc_start: 0.6990 (tp-100) cc_final: 0.6663 (tp-100) REVERT: B 65 GLN cc_start: 0.7029 (pt0) cc_final: 0.6748 (pt0) REVERT: B 149 LYS cc_start: 0.8305 (mmtp) cc_final: 0.7983 (mppt) REVERT: B 173 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7100 (ttt-90) REVERT: B 216 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6985 (tm-30) REVERT: B 252 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.8646 (ptm) REVERT: B 429 GLN cc_start: 0.7082 (tp-100) cc_final: 0.6734 (tp-100) REVERT: C 65 GLN cc_start: 0.7039 (pt0) cc_final: 0.6751 (pt0) REVERT: C 173 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7230 (ttt-90) REVERT: C 216 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6989 (tm-30) REVERT: C 252 MET cc_start: 0.9359 (OUTLIER) cc_final: 0.8639 (ptm) REVERT: C 429 GLN cc_start: 0.7071 (tp-100) cc_final: 0.6722 (tp-100) REVERT: D 65 GLN cc_start: 0.7037 (pt0) cc_final: 0.6723 (pt0) REVERT: D 216 GLU cc_start: 0.7352 (tm-30) cc_final: 0.7025 (tm-30) REVERT: D 429 GLN cc_start: 0.6938 (tp40) cc_final: 0.6275 (tp-100) REVERT: E 65 GLN cc_start: 0.7032 (pt0) cc_final: 0.6752 (pt0) REVERT: E 173 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7127 (ttt-90) REVERT: E 216 GLU cc_start: 0.7346 (tm-30) cc_final: 0.7012 (tm-30) REVERT: E 252 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.8635 (ptm) REVERT: E 429 GLN cc_start: 0.7077 (tp-100) cc_final: 0.6730 (tp-100) REVERT: F 65 GLN cc_start: 0.7035 (pt0) cc_final: 0.6747 (pt0) REVERT: F 173 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7260 (ttt-90) REVERT: F 216 GLU cc_start: 0.7341 (tm-30) cc_final: 0.7011 (tm-30) REVERT: F 429 GLN cc_start: 0.7007 (tp-100) cc_final: 0.6680 (tp-100) REVERT: G 65 GLN cc_start: 0.7079 (pt0) cc_final: 0.6771 (pt0) REVERT: G 173 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7258 (ttt-90) REVERT: G 216 GLU cc_start: 0.7341 (tm-30) cc_final: 0.7010 (tm-30) REVERT: G 252 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8646 (ptm) REVERT: G 429 GLN cc_start: 0.7006 (tp-100) cc_final: 0.6681 (tp-100) REVERT: H 65 GLN cc_start: 0.7039 (pt0) cc_final: 0.6753 (pt0) REVERT: H 173 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7292 (ttt-90) REVERT: H 216 GLU cc_start: 0.7342 (tm-30) cc_final: 0.7013 (tm-30) REVERT: H 252 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.8640 (ptm) REVERT: H 429 GLN cc_start: 0.7063 (tp-100) cc_final: 0.6716 (tp-100) outliers start: 55 outliers final: 25 residues processed: 443 average time/residue: 2.2233 time to fit residues: 1093.5324 Evaluate side-chains 441 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 403 time to evaluate : 3.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 252 MET Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain H residue 254 ASP Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 311 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 253 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 290 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 173 optimal weight: 6.9990 chunk 305 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 GLN ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 GLN ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 GLN ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 429 GLN ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 429 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 29096 Z= 0.559 Angle : 0.798 8.346 39472 Z= 0.423 Chirality : 0.053 0.169 4152 Planarity : 0.006 0.056 5168 Dihedral : 10.198 168.307 4144 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.58 % Allowed : 12.68 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.14), residues: 3544 helix: 0.86 (0.12), residues: 1616 sheet: 0.19 (0.22), residues: 512 loop : 0.87 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP G 354 HIS 0.007 0.003 HIS G 224 PHE 0.026 0.004 PHE E 297 TYR 0.038 0.004 TYR B 263 ARG 0.007 0.001 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 434 time to evaluate : 3.109 Fit side-chains REVERT: A 149 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7736 (mppt) REVERT: A 173 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7654 (ttt-90) REVERT: A 216 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6908 (tm-30) REVERT: A 277 ILE cc_start: 0.8714 (mt) cc_final: 0.8462 (mt) REVERT: A 417 TYR cc_start: 0.6761 (t80) cc_final: 0.6442 (t80) REVERT: B 173 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7689 (ttt-90) REVERT: B 216 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6923 (tm-30) REVERT: B 277 ILE cc_start: 0.8716 (mt) cc_final: 0.8462 (mt) REVERT: B 417 TYR cc_start: 0.6757 (t80) cc_final: 0.6482 (t80) REVERT: C 65 GLN cc_start: 0.7097 (pt0) cc_final: 0.6788 (pt0) REVERT: C 173 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7692 (ttt-90) REVERT: C 216 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6921 (tm-30) REVERT: C 252 MET cc_start: 0.9466 (OUTLIER) cc_final: 0.8791 (ptm) REVERT: C 277 ILE cc_start: 0.8721 (mt) cc_final: 0.8456 (mt) REVERT: C 417 TYR cc_start: 0.6754 (t80) cc_final: 0.6454 (t80) REVERT: D 65 GLN cc_start: 0.7094 (pt0) cc_final: 0.6814 (pt0) REVERT: D 149 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7790 (mppt) REVERT: D 173 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7685 (ttt-90) REVERT: D 216 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6901 (tm-30) REVERT: D 277 ILE cc_start: 0.8724 (mt) cc_final: 0.8465 (mt) REVERT: D 417 TYR cc_start: 0.6758 (t80) cc_final: 0.6440 (t80) REVERT: D 429 GLN cc_start: 0.7240 (tp40) cc_final: 0.6910 (tp-100) REVERT: E 149 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7735 (mppt) REVERT: E 173 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7655 (ttt-90) REVERT: E 216 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6922 (tm-30) REVERT: E 252 MET cc_start: 0.9466 (OUTLIER) cc_final: 0.8789 (ptm) REVERT: E 277 ILE cc_start: 0.8713 (mt) cc_final: 0.8460 (mt) REVERT: E 417 TYR cc_start: 0.6764 (t80) cc_final: 0.6441 (t80) REVERT: F 65 GLN cc_start: 0.7092 (pt0) cc_final: 0.6787 (pt0) REVERT: F 149 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7733 (mppt) REVERT: F 173 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7655 (ttt-90) REVERT: F 216 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6921 (tm-30) REVERT: F 277 ILE cc_start: 0.8718 (mt) cc_final: 0.8461 (mt) REVERT: F 417 TYR cc_start: 0.6757 (t80) cc_final: 0.6441 (t80) REVERT: G 149 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7734 (mppt) REVERT: G 173 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7658 (ttt-90) REVERT: G 216 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6918 (tm-30) REVERT: G 277 ILE cc_start: 0.8723 (mt) cc_final: 0.8460 (mt) REVERT: G 417 TYR cc_start: 0.6760 (t80) cc_final: 0.6438 (t80) REVERT: H 173 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7657 (ttt-90) REVERT: H 216 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6925 (tm-30) REVERT: H 252 MET cc_start: 0.9463 (OUTLIER) cc_final: 0.8786 (ptm) REVERT: H 277 ILE cc_start: 0.8720 (mt) cc_final: 0.8456 (mt) REVERT: H 417 TYR cc_start: 0.6758 (t80) cc_final: 0.6434 (t80) outliers start: 73 outliers final: 41 residues processed: 488 average time/residue: 2.1521 time to fit residues: 1169.1404 Evaluate side-chains 471 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 414 time to evaluate : 3.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 378 SER Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain H residue 311 HIS Chi-restraints excluded: chain H residue 378 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 5.9990 chunk 306 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 199 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 340 optimal weight: 0.8980 chunk 282 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 178 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 GLN ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 29096 Z= 0.175 Angle : 0.534 6.056 39472 Z= 0.282 Chirality : 0.040 0.133 4152 Planarity : 0.004 0.030 5168 Dihedral : 9.526 171.417 4144 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.80 % Allowed : 13.24 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.14), residues: 3544 helix: 1.40 (0.13), residues: 1576 sheet: 0.24 (0.22), residues: 528 loop : 0.88 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 354 HIS 0.004 0.001 HIS E 311 PHE 0.014 0.002 PHE C 297 TYR 0.022 0.001 TYR D 263 ARG 0.005 0.000 ARG E 442 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 425 time to evaluate : 3.012 Fit side-chains REVERT: A 173 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7463 (ttt-90) REVERT: A 216 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6899 (tm-30) REVERT: A 417 TYR cc_start: 0.6747 (t80) cc_final: 0.6450 (t80) REVERT: A 429 GLN cc_start: 0.7292 (tp-100) cc_final: 0.6879 (tp-100) REVERT: B 173 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7471 (ttt-90) REVERT: B 216 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6889 (tm-30) REVERT: B 417 TYR cc_start: 0.6750 (t80) cc_final: 0.6448 (t80) REVERT: B 429 GLN cc_start: 0.7332 (tp-100) cc_final: 0.6921 (tp-100) REVERT: C 173 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7473 (ttt-90) REVERT: C 216 GLU cc_start: 0.7213 (tm-30) cc_final: 0.6899 (tm-30) REVERT: C 252 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.8669 (ptm) REVERT: C 417 TYR cc_start: 0.6750 (t80) cc_final: 0.6465 (t80) REVERT: C 429 GLN cc_start: 0.7340 (tp-100) cc_final: 0.6931 (tp-100) REVERT: D 65 GLN cc_start: 0.7076 (pt0) cc_final: 0.6773 (pt0) REVERT: D 117 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7550 (ttp-170) REVERT: D 173 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7366 (ttt-90) REVERT: D 216 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6904 (tm-30) REVERT: D 417 TYR cc_start: 0.6750 (t80) cc_final: 0.6453 (t80) REVERT: D 429 GLN cc_start: 0.7049 (tp40) cc_final: 0.6599 (tp-100) REVERT: E 173 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7465 (ttt-90) REVERT: E 216 GLU cc_start: 0.7224 (tm-30) cc_final: 0.6908 (tm-30) REVERT: E 252 MET cc_start: 0.9386 (OUTLIER) cc_final: 0.8639 (ptm) REVERT: E 417 TYR cc_start: 0.6754 (t80) cc_final: 0.6459 (t80) REVERT: E 429 GLN cc_start: 0.7335 (tp-100) cc_final: 0.6925 (tp-100) REVERT: F 65 GLN cc_start: 0.7202 (pt0) cc_final: 0.6853 (pt0) REVERT: F 173 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7466 (ttt-90) REVERT: F 216 GLU cc_start: 0.7215 (tm-30) cc_final: 0.6900 (tm-30) REVERT: F 417 TYR cc_start: 0.6746 (t80) cc_final: 0.6452 (t80) REVERT: F 429 GLN cc_start: 0.7296 (tp-100) cc_final: 0.6885 (tp-100) REVERT: G 173 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7467 (ttt-90) REVERT: G 216 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6908 (tm-30) REVERT: G 417 TYR cc_start: 0.6748 (t80) cc_final: 0.6449 (t80) REVERT: G 429 GLN cc_start: 0.7294 (tp-100) cc_final: 0.6879 (tp-100) REVERT: H 173 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7468 (ttt-90) REVERT: H 216 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6894 (tm-30) REVERT: H 252 MET cc_start: 0.9382 (OUTLIER) cc_final: 0.8636 (ptm) REVERT: H 417 TYR cc_start: 0.6752 (t80) cc_final: 0.6452 (t80) REVERT: H 429 GLN cc_start: 0.7337 (tp-100) cc_final: 0.6922 (tp-100) outliers start: 51 outliers final: 22 residues processed: 464 average time/residue: 2.2007 time to fit residues: 1133.1706 Evaluate side-chains 455 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 421 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 311 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 192 optimal weight: 0.8980 chunk 286 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 339 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 206 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 29096 Z= 0.433 Angle : 0.716 8.201 39472 Z= 0.378 Chirality : 0.048 0.157 4152 Planarity : 0.006 0.050 5168 Dihedral : 10.050 169.325 4144 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.40 % Allowed : 13.45 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.14), residues: 3544 helix: 1.12 (0.12), residues: 1568 sheet: 0.11 (0.21), residues: 528 loop : 0.80 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 354 HIS 0.006 0.002 HIS E 311 PHE 0.026 0.004 PHE C 297 TYR 0.035 0.003 TYR F 263 ARG 0.005 0.001 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 422 time to evaluate : 3.151 Fit side-chains REVERT: A 173 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7603 (ttt-90) REVERT: A 189 ASP cc_start: 0.8926 (OUTLIER) cc_final: 0.8461 (t0) REVERT: A 216 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6908 (tm-30) REVERT: A 277 ILE cc_start: 0.8671 (mt) cc_final: 0.8363 (mt) REVERT: A 417 TYR cc_start: 0.6802 (t80) cc_final: 0.6565 (t80) REVERT: B 173 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7641 (ttt-90) REVERT: B 189 ASP cc_start: 0.8930 (OUTLIER) cc_final: 0.8442 (t0) REVERT: B 216 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6917 (tm-30) REVERT: B 277 ILE cc_start: 0.8676 (mt) cc_final: 0.8367 (mt) REVERT: B 417 TYR cc_start: 0.6803 (t80) cc_final: 0.6556 (t80) REVERT: C 65 GLN cc_start: 0.7004 (pt0) cc_final: 0.6737 (pt0) REVERT: C 173 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7520 (ttt-90) REVERT: C 189 ASP cc_start: 0.8928 (OUTLIER) cc_final: 0.8438 (t0) REVERT: C 216 GLU cc_start: 0.7234 (tm-30) cc_final: 0.6916 (tm-30) REVERT: C 277 ILE cc_start: 0.8677 (mt) cc_final: 0.8358 (mt) REVERT: C 417 TYR cc_start: 0.6803 (t80) cc_final: 0.6522 (t80) REVERT: D 65 GLN cc_start: 0.7137 (pt0) cc_final: 0.6755 (pt0) REVERT: D 173 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7661 (ttt-90) REVERT: D 189 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8448 (t0) REVERT: D 216 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6947 (tm-30) REVERT: D 277 ILE cc_start: 0.8683 (mt) cc_final: 0.8393 (mt) REVERT: D 417 TYR cc_start: 0.6803 (t80) cc_final: 0.6569 (t80) REVERT: D 429 GLN cc_start: 0.7269 (tp40) cc_final: 0.6938 (tp-100) REVERT: E 173 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7604 (ttt-90) REVERT: E 189 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8438 (t0) REVERT: E 216 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6918 (tm-30) REVERT: E 277 ILE cc_start: 0.8670 (mt) cc_final: 0.8363 (mt) REVERT: E 417 TYR cc_start: 0.6807 (t80) cc_final: 0.6564 (t80) REVERT: F 65 GLN cc_start: 0.7131 (pt0) cc_final: 0.6744 (pt0) REVERT: F 173 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7606 (ttt-90) REVERT: F 189 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8458 (t0) REVERT: F 216 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6918 (tm-30) REVERT: F 277 ILE cc_start: 0.8679 (mt) cc_final: 0.8363 (mt) REVERT: F 417 TYR cc_start: 0.6800 (t80) cc_final: 0.6563 (t80) REVERT: G 173 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7604 (ttt-90) REVERT: G 189 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8437 (t0) REVERT: G 216 GLU cc_start: 0.7234 (tm-30) cc_final: 0.6916 (tm-30) REVERT: G 277 ILE cc_start: 0.8679 (mt) cc_final: 0.8361 (mt) REVERT: G 417 TYR cc_start: 0.6802 (t80) cc_final: 0.6561 (t80) REVERT: H 173 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7604 (ttt-90) REVERT: H 189 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8433 (t0) REVERT: H 216 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6940 (tm-30) REVERT: H 277 ILE cc_start: 0.8675 (mt) cc_final: 0.8359 (mt) REVERT: H 417 TYR cc_start: 0.6805 (t80) cc_final: 0.6559 (t80) outliers start: 68 outliers final: 33 residues processed: 477 average time/residue: 2.1547 time to fit residues: 1150.0977 Evaluate side-chains 470 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 421 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain E residue 14 ARG Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 378 SER Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 189 ASP Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 311 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 231 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 266 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 29096 Z= 0.173 Angle : 0.540 6.050 39472 Z= 0.286 Chirality : 0.040 0.130 4152 Planarity : 0.004 0.031 5168 Dihedral : 9.517 171.058 4144 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.12 % Allowed : 13.74 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.14), residues: 3544 helix: 1.42 (0.13), residues: 1576 sheet: 0.22 (0.21), residues: 528 loop : 0.87 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 354 HIS 0.003 0.001 HIS H 311 PHE 0.015 0.002 PHE C 297 TYR 0.022 0.001 TYR A 263 ARG 0.007 0.000 ARG F 442 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 424 time to evaluate : 3.303 Fit side-chains REVERT: A 173 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7473 (ttt-90) REVERT: A 216 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6917 (tm-30) REVERT: A 417 TYR cc_start: 0.6754 (t80) cc_final: 0.6439 (t80) REVERT: A 429 GLN cc_start: 0.7309 (tp-100) cc_final: 0.6890 (tp-100) REVERT: B 173 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7481 (ttt-90) REVERT: B 189 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8435 (t0) REVERT: B 216 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6938 (tm-30) REVERT: B 417 TYR cc_start: 0.6756 (t80) cc_final: 0.6430 (t80) REVERT: B 429 GLN cc_start: 0.7343 (tp-100) cc_final: 0.6927 (tp-100) REVERT: C 65 GLN cc_start: 0.6930 (pt0) cc_final: 0.6643 (pt0) REVERT: C 173 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7466 (ttt-90) REVERT: C 189 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8435 (t0) REVERT: C 216 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6929 (tm-30) REVERT: C 417 TYR cc_start: 0.6756 (t80) cc_final: 0.6446 (t80) REVERT: C 429 GLN cc_start: 0.7354 (tp-100) cc_final: 0.6938 (tp-100) REVERT: D 65 GLN cc_start: 0.7205 (pt0) cc_final: 0.6845 (pt0) REVERT: D 117 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7542 (ttp-170) REVERT: D 173 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7376 (ttt-90) REVERT: D 216 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6931 (tm-30) REVERT: D 417 TYR cc_start: 0.6757 (t80) cc_final: 0.6442 (t80) REVERT: D 429 GLN cc_start: 0.7058 (tp40) cc_final: 0.6611 (tp-100) REVERT: E 173 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7474 (ttt-90) REVERT: E 189 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8444 (t0) REVERT: E 216 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6940 (tm-30) REVERT: E 417 TYR cc_start: 0.6760 (t80) cc_final: 0.6436 (t80) REVERT: E 429 GLN cc_start: 0.7311 (tp-100) cc_final: 0.6893 (tp-100) REVERT: F 173 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7475 (ttt-90) REVERT: F 216 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6928 (tm-30) REVERT: F 417 TYR cc_start: 0.6753 (t80) cc_final: 0.6438 (t80) REVERT: F 429 GLN cc_start: 0.7312 (tp-100) cc_final: 0.6894 (tp-100) REVERT: G 173 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7475 (ttt-90) REVERT: G 189 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8434 (t0) REVERT: G 216 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6938 (tm-30) REVERT: G 417 TYR cc_start: 0.6758 (t80) cc_final: 0.6442 (t80) REVERT: G 429 GLN cc_start: 0.7313 (tp-100) cc_final: 0.6894 (tp-100) REVERT: H 173 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7476 (ttt-90) REVERT: H 189 ASP cc_start: 0.8925 (OUTLIER) cc_final: 0.8458 (t0) REVERT: H 216 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6910 (tm-30) REVERT: H 417 TYR cc_start: 0.6760 (t80) cc_final: 0.6433 (t80) REVERT: H 429 GLN cc_start: 0.7316 (tp-100) cc_final: 0.6895 (tp-100) outliers start: 60 outliers final: 33 residues processed: 470 average time/residue: 2.1761 time to fit residues: 1137.2237 Evaluate side-chains 460 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 413 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 14 ARG Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 189 ASP Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 311 HIS Chi-restraints excluded: chain H residue 378 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 5.9990 chunk 325 optimal weight: 6.9990 chunk 296 optimal weight: 6.9990 chunk 316 optimal weight: 0.1980 chunk 324 optimal weight: 0.8980 chunk 190 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 285 optimal weight: 9.9990 chunk 299 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 29096 Z= 0.309 Angle : 0.635 7.394 39472 Z= 0.335 Chirality : 0.044 0.143 4152 Planarity : 0.005 0.042 5168 Dihedral : 9.799 169.844 4144 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.22 % Allowed : 14.09 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.14), residues: 3544 helix: 1.28 (0.13), residues: 1576 sheet: 0.19 (0.21), residues: 528 loop : 0.86 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 354 HIS 0.005 0.002 HIS E 311 PHE 0.023 0.003 PHE D 297 TYR 0.031 0.003 TYR F 263 ARG 0.007 0.001 ARG E 442 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 424 time to evaluate : 3.443 Fit side-chains REVERT: A 173 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7545 (ttt-90) REVERT: A 189 ASP cc_start: 0.8934 (OUTLIER) cc_final: 0.8458 (t0) REVERT: A 216 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6867 (tm-30) REVERT: A 277 ILE cc_start: 0.8613 (mt) cc_final: 0.8227 (mt) REVERT: A 417 TYR cc_start: 0.6776 (t80) cc_final: 0.6492 (t80) REVERT: B 173 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7567 (ttt-90) REVERT: B 189 ASP cc_start: 0.8935 (OUTLIER) cc_final: 0.8469 (t0) REVERT: B 216 GLU cc_start: 0.7233 (tm-30) cc_final: 0.6897 (tm-30) REVERT: B 277 ILE cc_start: 0.8674 (mt) cc_final: 0.8231 (mt) REVERT: B 417 TYR cc_start: 0.6773 (t80) cc_final: 0.6481 (t80) REVERT: C 65 GLN cc_start: 0.6957 (pt0) cc_final: 0.6675 (pt0) REVERT: C 173 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7580 (ttt-90) REVERT: C 189 ASP cc_start: 0.8934 (OUTLIER) cc_final: 0.8466 (t0) REVERT: C 216 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6877 (tm-30) REVERT: C 277 ILE cc_start: 0.8616 (mt) cc_final: 0.8217 (mt) REVERT: C 417 TYR cc_start: 0.6775 (t80) cc_final: 0.6494 (t80) REVERT: D 65 GLN cc_start: 0.7118 (pt0) cc_final: 0.6815 (pt0) REVERT: D 117 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7581 (ttp-170) REVERT: D 173 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7474 (ttt-90) REVERT: D 189 ASP cc_start: 0.8922 (OUTLIER) cc_final: 0.8446 (t0) REVERT: D 216 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6883 (tm-30) REVERT: D 277 ILE cc_start: 0.8680 (mt) cc_final: 0.8231 (mt) REVERT: D 417 TYR cc_start: 0.6776 (t80) cc_final: 0.6494 (t80) REVERT: D 429 GLN cc_start: 0.7116 (tp40) cc_final: 0.6730 (tp-100) REVERT: E 173 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7548 (ttt-90) REVERT: E 189 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8447 (t0) REVERT: E 216 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6879 (tm-30) REVERT: E 277 ILE cc_start: 0.8612 (mt) cc_final: 0.8224 (mt) REVERT: E 417 TYR cc_start: 0.6777 (t80) cc_final: 0.6487 (t80) REVERT: F 65 GLN cc_start: 0.6984 (pt0) cc_final: 0.6728 (pt0) REVERT: F 173 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7551 (ttt-90) REVERT: F 189 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8451 (t0) REVERT: F 216 GLU cc_start: 0.7234 (tm-30) cc_final: 0.6875 (tm-30) REVERT: F 277 ILE cc_start: 0.8680 (mt) cc_final: 0.8233 (mt) REVERT: F 417 TYR cc_start: 0.6772 (t80) cc_final: 0.6487 (t80) REVERT: G 173 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7549 (ttt-90) REVERT: G 189 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8466 (t0) REVERT: G 216 GLU cc_start: 0.7234 (tm-30) cc_final: 0.6875 (tm-30) REVERT: G 277 ILE cc_start: 0.8619 (mt) cc_final: 0.8221 (mt) REVERT: G 417 TYR cc_start: 0.6775 (t80) cc_final: 0.6488 (t80) REVERT: H 173 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7549 (ttt-90) REVERT: H 189 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8463 (t0) REVERT: H 216 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6879 (tm-30) REVERT: H 277 ILE cc_start: 0.8617 (mt) cc_final: 0.8219 (mt) REVERT: H 417 TYR cc_start: 0.6778 (t80) cc_final: 0.6485 (t80) outliers start: 63 outliers final: 39 residues processed: 474 average time/residue: 2.1567 time to fit residues: 1139.5543 Evaluate side-chains 481 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 425 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 14 ARG Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 14 ARG Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 14 ARG Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 189 ASP Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 311 HIS Chi-restraints excluded: chain H residue 378 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 334 optimal weight: 0.8980 chunk 204 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 350 optimal weight: 2.9990 chunk 322 optimal weight: 0.9980 chunk 279 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 29096 Z= 0.183 Angle : 0.547 6.038 39472 Z= 0.289 Chirality : 0.040 0.129 4152 Planarity : 0.004 0.031 5168 Dihedral : 9.475 170.297 4144 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.91 % Allowed : 14.55 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.14), residues: 3544 helix: 1.28 (0.13), residues: 1624 sheet: 0.69 (0.25), residues: 384 loop : 0.34 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 354 HIS 0.004 0.001 HIS G 224 PHE 0.015 0.002 PHE B 297 TYR 0.022 0.002 TYR G 263 ARG 0.008 0.000 ARG C 442 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 420 time to evaluate : 3.202 Fit side-chains REVERT: A 173 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7462 (ttt-90) REVERT: A 216 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6911 (tm-30) REVERT: A 417 TYR cc_start: 0.6752 (t80) cc_final: 0.6435 (t80) REVERT: A 429 GLN cc_start: 0.7315 (tp-100) cc_final: 0.6919 (tp-100) REVERT: B 173 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7470 (ttt-90) REVERT: B 189 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8440 (t0) REVERT: B 216 GLU cc_start: 0.7216 (tm-30) cc_final: 0.6897 (tm-30) REVERT: B 429 GLN cc_start: 0.7312 (tp-100) cc_final: 0.6915 (tp-100) REVERT: C 65 GLN cc_start: 0.6933 (pt0) cc_final: 0.6624 (pt0) REVERT: C 173 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7478 (ttt-90) REVERT: C 189 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8439 (t0) REVERT: C 216 GLU cc_start: 0.7216 (tm-30) cc_final: 0.6893 (tm-30) REVERT: C 417 TYR cc_start: 0.6754 (t80) cc_final: 0.6439 (t80) REVERT: C 429 GLN cc_start: 0.7324 (tp-100) cc_final: 0.6926 (tp-100) REVERT: D 65 GLN cc_start: 0.7069 (pt0) cc_final: 0.6742 (pt0) REVERT: D 117 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7536 (ttp-170) REVERT: D 173 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7475 (ttt-90) REVERT: D 216 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6907 (tm-30) REVERT: D 417 TYR cc_start: 0.6755 (t80) cc_final: 0.6438 (t80) REVERT: D 429 GLN cc_start: 0.7054 (tp40) cc_final: 0.6546 (tp-100) REVERT: E 173 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7430 (ttt-90) REVERT: E 189 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.8445 (t0) REVERT: E 216 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6900 (tm-30) REVERT: E 429 GLN cc_start: 0.7318 (tp-100) cc_final: 0.6919 (tp-100) REVERT: F 173 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7464 (ttt-90) REVERT: F 216 GLU cc_start: 0.7214 (tm-30) cc_final: 0.6896 (tm-30) REVERT: F 417 TYR cc_start: 0.6751 (t80) cc_final: 0.6432 (t80) REVERT: F 429 GLN cc_start: 0.7318 (tp-100) cc_final: 0.6923 (tp-100) REVERT: G 173 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7431 (ttt-90) REVERT: G 189 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8437 (t0) REVERT: G 216 GLU cc_start: 0.7215 (tm-30) cc_final: 0.6898 (tm-30) REVERT: G 417 TYR cc_start: 0.6757 (t80) cc_final: 0.6436 (t80) REVERT: G 429 GLN cc_start: 0.7281 (tp-100) cc_final: 0.6881 (tp-100) REVERT: H 173 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7446 (ttt-90) REVERT: H 216 GLU cc_start: 0.7216 (tm-30) cc_final: 0.6899 (tm-30) REVERT: H 429 GLN cc_start: 0.7303 (tp-100) cc_final: 0.6901 (tp-100) outliers start: 54 outliers final: 39 residues processed: 461 average time/residue: 2.2029 time to fit residues: 1129.1687 Evaluate side-chains 470 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 418 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 14 ARG Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 14 ARG Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 14 ARG Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 311 HIS Chi-restraints excluded: chain H residue 378 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 5.9990 chunk 221 optimal weight: 0.9990 chunk 297 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 257 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 77 optimal weight: 0.9990 chunk 279 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 287 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.130188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.116912 restraints weight = 26360.162| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 0.80 r_work: 0.3241 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 29096 Z= 0.169 Angle : 0.529 5.918 39472 Z= 0.278 Chirality : 0.040 0.129 4152 Planarity : 0.004 0.031 5168 Dihedral : 9.282 169.027 4144 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.05 % Allowed : 14.62 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.14), residues: 3544 helix: 1.25 (0.13), residues: 1672 sheet: 0.93 (0.26), residues: 368 loop : 0.39 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 354 HIS 0.003 0.001 HIS C 224 PHE 0.015 0.002 PHE C 297 TYR 0.022 0.001 TYR G 263 ARG 0.008 0.000 ARG E 442 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14687.43 seconds wall clock time: 255 minutes 50.94 seconds (15350.94 seconds total)