Starting phenix.real_space_refine on Mon Mar 11 00:41:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blf_16109/03_2024/8blf_16109_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blf_16109/03_2024/8blf_16109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blf_16109/03_2024/8blf_16109.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blf_16109/03_2024/8blf_16109.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blf_16109/03_2024/8blf_16109_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blf_16109/03_2024/8blf_16109_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 42 5.49 5 S 280 5.16 5 C 33684 2.51 5 N 9394 2.21 5 O 10976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 523": "OD1" <-> "OD2" Residue "G ASP 5": "OD1" <-> "OD2" Residue "G GLU 76": "OE1" <-> "OE2" Residue "G ASP 121": "OD1" <-> "OD2" Residue "G GLU 408": "OE1" <-> "OE2" Residue "G TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 518": "OE1" <-> "OE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 11": "OD1" <-> "OD2" Residue "B TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 5": "OD1" <-> "OD2" Residue "C GLU 76": "OE1" <-> "OE2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C GLU 461": "OE1" <-> "OE2" Residue "C TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 518": "OE1" <-> "OE2" Residue "D PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 518": "OE1" <-> "OE2" Residue "E ASP 5": "OD1" <-> "OD2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 63": "OE1" <-> "OE2" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 408": "OE1" <-> "OE2" Residue "E GLU 461": "OE1" <-> "OE2" Residue "E TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 518": "OE1" <-> "OE2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 121": "OD1" <-> "OD2" Residue "F TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 5": "OD1" <-> "OD2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H GLU 408": "OE1" <-> "OE2" Residue "H TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 25": "OD1" <-> "OD2" Residue "I PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 523": "OD1" <-> "OD2" Residue "J ASP 5": "OD1" <-> "OD2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J GLU 76": "OE1" <-> "OE2" Residue "J ASP 83": "OD1" <-> "OD2" Residue "J GLU 102": "OE1" <-> "OE2" Residue "J TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 461": "OE1" <-> "OE2" Residue "J TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 518": "OE1" <-> "OE2" Residue "K PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 41": "OD1" <-> "OD2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "K GLU 172": "OE1" <-> "OE2" Residue "K TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 518": "OE1" <-> "OE2" Residue "K ASP 523": "OD1" <-> "OD2" Residue "L ASP 5": "OD1" <-> "OD2" Residue "L PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 63": "OE1" <-> "OE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L ASP 83": "OD1" <-> "OD2" Residue "L GLU 102": "OE1" <-> "OE2" Residue "L ASP 121": "OD1" <-> "OD2" Residue "L PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 386": "OE1" <-> "OE2" Residue "L GLU 408": "OE1" <-> "OE2" Residue "L TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 518": "OE1" <-> "OE2" Residue "M ASP 5": "OD1" <-> "OD2" Residue "M PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 25": "OD1" <-> "OD2" Residue "N GLU 59": "OE1" <-> "OE2" Residue "N GLU 76": "OE1" <-> "OE2" Residue "N ASP 83": "OD1" <-> "OD2" Residue "N GLU 102": "OE1" <-> "OE2" Residue "N GLU 461": "OE1" <-> "OE2" Residue "N TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 518": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 54376 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3846 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3846 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3846 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3846 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3846 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3846 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3846 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.27, per 1000 atoms: 0.37 Number of scatterers: 54376 At special positions: 0 Unit cell: (153.6, 151.68, 162.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 280 16.00 P 42 15.00 O 10976 8.00 N 9394 7.00 C 33684 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: 15.80 Conformation dependent library (CDL) restraints added in 7.5 seconds 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13272 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 275 helices and 99 sheets defined 53.2% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.49 Creating SS restraints... Processing helix chain 'A' and resid 10 through 30 removed outlier: 4.620A pdb=" N THR A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 65 through 85 Processing helix chain 'A' and resid 89 through 108 Processing helix chain 'A' and resid 113 through 134 Processing helix chain 'A' and resid 141 through 151 Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 231 through 243 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 282 through 296 Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 359 through 374 Processing helix chain 'A' and resid 386 through 408 Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 434 through 446 Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 462 through 471 Processing helix chain 'A' and resid 488 through 491 No H-bonds generated for 'chain 'A' and resid 488 through 491' Processing helix chain 'A' and resid 497 through 515 Processing helix chain 'G' and resid 10 through 30 removed outlier: 4.697A pdb=" N THR G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 58 Processing helix chain 'G' and resid 65 through 84 removed outlier: 3.873A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA G 78 " --> pdb=" O VAL G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 108 Processing helix chain 'G' and resid 113 through 134 Processing helix chain 'G' and resid 142 through 151 Processing helix chain 'G' and resid 156 through 169 Processing helix chain 'G' and resid 202 through 204 No H-bonds generated for 'chain 'G' and resid 202 through 204' Processing helix chain 'G' and resid 230 through 242 Proline residue: G 235 - end of helix Processing helix chain 'G' and resid 260 through 266 Processing helix chain 'G' and resid 283 through 296 Processing helix chain 'G' and resid 339 through 355 Processing helix chain 'G' and resid 359 through 374 Processing helix chain 'G' and resid 386 through 408 Processing helix chain 'G' and resid 417 through 426 Processing helix chain 'G' and resid 434 through 458 removed outlier: 3.807A pdb=" N GLU G 448 " --> pdb=" O LEU G 444 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA G 449 " --> pdb=" O ARG G 445 " (cutoff:3.500A) Proline residue: G 450 - end of helix Processing helix chain 'G' and resid 462 through 471 Processing helix chain 'G' and resid 488 through 491 No H-bonds generated for 'chain 'G' and resid 488 through 491' Processing helix chain 'G' and resid 497 through 516 removed outlier: 4.298A pdb=" N THR G 516 " --> pdb=" O GLY G 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 30 removed outlier: 4.638A pdb=" N THR B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 59 removed outlier: 3.668A pdb=" N GLU B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 85 Processing helix chain 'B' and resid 89 through 108 Processing helix chain 'B' and resid 113 through 134 Processing helix chain 'B' and resid 141 through 151 Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 231 through 243 Proline residue: B 235 - end of helix Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 282 through 296 Processing helix chain 'B' and resid 339 through 355 Processing helix chain 'B' and resid 359 through 373 Processing helix chain 'B' and resid 386 through 408 Processing helix chain 'B' and resid 417 through 426 Processing helix chain 'B' and resid 434 through 446 Processing helix chain 'B' and resid 449 through 458 Processing helix chain 'B' and resid 462 through 471 Processing helix chain 'B' and resid 488 through 491 No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 497 through 515 Processing helix chain 'C' and resid 10 through 30 removed outlier: 4.667A pdb=" N THR C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 59 Processing helix chain 'C' and resid 65 through 84 removed outlier: 3.862A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 108 Processing helix chain 'C' and resid 113 through 134 Processing helix chain 'C' and resid 142 through 152 Processing helix chain 'C' and resid 156 through 169 Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 230 through 242 Proline residue: C 235 - end of helix Processing helix chain 'C' and resid 260 through 266 Processing helix chain 'C' and resid 283 through 296 Processing helix chain 'C' and resid 339 through 355 Processing helix chain 'C' and resid 359 through 374 Processing helix chain 'C' and resid 386 through 408 Processing helix chain 'C' and resid 417 through 426 Processing helix chain 'C' and resid 434 through 458 removed outlier: 3.790A pdb=" N GLU C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA C 449 " --> pdb=" O ARG C 445 " (cutoff:3.500A) Proline residue: C 450 - end of helix Processing helix chain 'C' and resid 462 through 471 Processing helix chain 'C' and resid 488 through 491 No H-bonds generated for 'chain 'C' and resid 488 through 491' Processing helix chain 'C' and resid 497 through 516 removed outlier: 4.219A pdb=" N THR C 516 " --> pdb=" O GLY C 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 30 removed outlier: 4.731A pdb=" N THR D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 59 removed outlier: 3.703A pdb=" N GLU D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 85 Processing helix chain 'D' and resid 89 through 108 Processing helix chain 'D' and resid 113 through 134 Processing helix chain 'D' and resid 141 through 151 Processing helix chain 'D' and resid 156 through 169 Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 231 through 243 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 256 through 268 Processing helix chain 'D' and resid 282 through 296 Processing helix chain 'D' and resid 339 through 355 Processing helix chain 'D' and resid 359 through 374 Processing helix chain 'D' and resid 386 through 408 Processing helix chain 'D' and resid 417 through 426 Processing helix chain 'D' and resid 434 through 446 Processing helix chain 'D' and resid 449 through 458 Processing helix chain 'D' and resid 462 through 471 Processing helix chain 'D' and resid 488 through 491 No H-bonds generated for 'chain 'D' and resid 488 through 491' Processing helix chain 'D' and resid 497 through 515 Processing helix chain 'E' and resid 10 through 30 removed outlier: 4.662A pdb=" N THR E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 58 Processing helix chain 'E' and resid 65 through 84 removed outlier: 3.851A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 108 Processing helix chain 'E' and resid 113 through 134 Processing helix chain 'E' and resid 142 through 151 Processing helix chain 'E' and resid 156 through 169 Processing helix chain 'E' and resid 202 through 204 No H-bonds generated for 'chain 'E' and resid 202 through 204' Processing helix chain 'E' and resid 230 through 242 Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 260 through 266 Processing helix chain 'E' and resid 283 through 296 Processing helix chain 'E' and resid 339 through 355 Processing helix chain 'E' and resid 359 through 374 Processing helix chain 'E' and resid 386 through 408 Processing helix chain 'E' and resid 417 through 426 Processing helix chain 'E' and resid 434 through 458 removed outlier: 3.798A pdb=" N GLU E 448 " --> pdb=" O LEU E 444 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA E 449 " --> pdb=" O ARG E 445 " (cutoff:3.500A) Proline residue: E 450 - end of helix Processing helix chain 'E' and resid 462 through 471 Processing helix chain 'E' and resid 488 through 491 No H-bonds generated for 'chain 'E' and resid 488 through 491' Processing helix chain 'E' and resid 497 through 516 removed outlier: 4.357A pdb=" N THR E 516 " --> pdb=" O GLY E 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 30 removed outlier: 4.652A pdb=" N THR F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 59 removed outlier: 3.896A pdb=" N GLU F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 85 Processing helix chain 'F' and resid 89 through 108 Processing helix chain 'F' and resid 113 through 134 Processing helix chain 'F' and resid 141 through 151 Processing helix chain 'F' and resid 156 through 169 Processing helix chain 'F' and resid 202 through 204 No H-bonds generated for 'chain 'F' and resid 202 through 204' Processing helix chain 'F' and resid 231 through 243 Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 256 through 268 Processing helix chain 'F' and resid 282 through 296 Processing helix chain 'F' and resid 339 through 355 Processing helix chain 'F' and resid 359 through 374 Processing helix chain 'F' and resid 386 through 408 Processing helix chain 'F' and resid 417 through 426 Processing helix chain 'F' and resid 434 through 446 Processing helix chain 'F' and resid 449 through 458 Processing helix chain 'F' and resid 462 through 471 Processing helix chain 'F' and resid 497 through 515 Processing helix chain 'H' and resid 10 through 30 removed outlier: 4.770A pdb=" N THR H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 59 Processing helix chain 'H' and resid 65 through 84 removed outlier: 3.800A pdb=" N VAL H 77 " --> pdb=" O MET H 73 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 78 " --> pdb=" O VAL H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 108 Processing helix chain 'H' and resid 113 through 134 Processing helix chain 'H' and resid 142 through 151 Processing helix chain 'H' and resid 156 through 168 Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'H' and resid 231 through 242 Proline residue: H 235 - end of helix Processing helix chain 'H' and resid 260 through 266 Processing helix chain 'H' and resid 283 through 296 Processing helix chain 'H' and resid 339 through 355 Processing helix chain 'H' and resid 359 through 374 Processing helix chain 'H' and resid 386 through 408 Processing helix chain 'H' and resid 417 through 426 Processing helix chain 'H' and resid 434 through 458 removed outlier: 3.852A pdb=" N GLU H 448 " --> pdb=" O LEU H 444 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA H 449 " --> pdb=" O ARG H 445 " (cutoff:3.500A) Proline residue: H 450 - end of helix Processing helix chain 'H' and resid 462 through 471 Processing helix chain 'H' and resid 488 through 491 No H-bonds generated for 'chain 'H' and resid 488 through 491' Processing helix chain 'H' and resid 497 through 516 removed outlier: 4.221A pdb=" N THR H 516 " --> pdb=" O GLY H 512 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 30 removed outlier: 4.664A pdb=" N THR I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 59 removed outlier: 3.666A pdb=" N GLU I 59 " --> pdb=" O SER I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 85 Processing helix chain 'I' and resid 89 through 108 Processing helix chain 'I' and resid 113 through 134 Processing helix chain 'I' and resid 141 through 151 Processing helix chain 'I' and resid 156 through 169 Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'I' and resid 231 through 243 Proline residue: I 235 - end of helix Processing helix chain 'I' and resid 256 through 268 Processing helix chain 'I' and resid 282 through 296 Processing helix chain 'I' and resid 339 through 355 Processing helix chain 'I' and resid 359 through 373 Processing helix chain 'I' and resid 386 through 408 Processing helix chain 'I' and resid 417 through 426 Processing helix chain 'I' and resid 434 through 446 Processing helix chain 'I' and resid 449 through 458 Processing helix chain 'I' and resid 462 through 471 Processing helix chain 'I' and resid 488 through 491 No H-bonds generated for 'chain 'I' and resid 488 through 491' Processing helix chain 'I' and resid 497 through 515 Processing helix chain 'J' and resid 10 through 30 removed outlier: 4.749A pdb=" N THR J 30 " --> pdb=" O ALA J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 59 Processing helix chain 'J' and resid 65 through 84 removed outlier: 3.911A pdb=" N VAL J 77 " --> pdb=" O MET J 73 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 108 Processing helix chain 'J' and resid 113 through 134 Processing helix chain 'J' and resid 142 through 152 Processing helix chain 'J' and resid 156 through 169 Processing helix chain 'J' and resid 202 through 204 No H-bonds generated for 'chain 'J' and resid 202 through 204' Processing helix chain 'J' and resid 230 through 242 Proline residue: J 235 - end of helix Processing helix chain 'J' and resid 260 through 266 Processing helix chain 'J' and resid 283 through 296 Processing helix chain 'J' and resid 309 through 311 No H-bonds generated for 'chain 'J' and resid 309 through 311' Processing helix chain 'J' and resid 339 through 355 Processing helix chain 'J' and resid 359 through 374 Processing helix chain 'J' and resid 386 through 408 Processing helix chain 'J' and resid 417 through 426 Processing helix chain 'J' and resid 434 through 458 removed outlier: 3.776A pdb=" N GLU J 448 " --> pdb=" O LEU J 444 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA J 449 " --> pdb=" O ARG J 445 " (cutoff:3.500A) Proline residue: J 450 - end of helix Processing helix chain 'J' and resid 462 through 471 Processing helix chain 'J' and resid 488 through 491 No H-bonds generated for 'chain 'J' and resid 488 through 491' Processing helix chain 'J' and resid 497 through 516 removed outlier: 4.253A pdb=" N THR J 516 " --> pdb=" O GLY J 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 30 removed outlier: 4.700A pdb=" N THR K 30 " --> pdb=" O ALA K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 59 Processing helix chain 'K' and resid 65 through 85 Processing helix chain 'K' and resid 89 through 108 Processing helix chain 'K' and resid 113 through 134 Processing helix chain 'K' and resid 141 through 151 Processing helix chain 'K' and resid 156 through 169 Processing helix chain 'K' and resid 202 through 204 No H-bonds generated for 'chain 'K' and resid 202 through 204' Processing helix chain 'K' and resid 231 through 243 Proline residue: K 235 - end of helix Processing helix chain 'K' and resid 256 through 268 Processing helix chain 'K' and resid 282 through 296 Processing helix chain 'K' and resid 339 through 355 Processing helix chain 'K' and resid 359 through 374 Processing helix chain 'K' and resid 386 through 408 Processing helix chain 'K' and resid 417 through 426 Processing helix chain 'K' and resid 434 through 446 Processing helix chain 'K' and resid 449 through 458 Processing helix chain 'K' and resid 462 through 471 Processing helix chain 'K' and resid 488 through 491 No H-bonds generated for 'chain 'K' and resid 488 through 491' Processing helix chain 'K' and resid 497 through 515 Processing helix chain 'L' and resid 10 through 30 removed outlier: 4.680A pdb=" N THR L 30 " --> pdb=" O ALA L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 58 Processing helix chain 'L' and resid 65 through 84 removed outlier: 3.916A pdb=" N VAL L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 108 Processing helix chain 'L' and resid 113 through 134 Processing helix chain 'L' and resid 142 through 151 Processing helix chain 'L' and resid 156 through 168 Processing helix chain 'L' and resid 202 through 204 No H-bonds generated for 'chain 'L' and resid 202 through 204' Processing helix chain 'L' and resid 230 through 242 Proline residue: L 235 - end of helix Processing helix chain 'L' and resid 260 through 266 Processing helix chain 'L' and resid 283 through 296 Processing helix chain 'L' and resid 309 through 311 No H-bonds generated for 'chain 'L' and resid 309 through 311' Processing helix chain 'L' and resid 339 through 355 Processing helix chain 'L' and resid 359 through 374 Processing helix chain 'L' and resid 386 through 409 Processing helix chain 'L' and resid 417 through 426 Processing helix chain 'L' and resid 434 through 458 removed outlier: 3.822A pdb=" N GLU L 448 " --> pdb=" O LEU L 444 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA L 449 " --> pdb=" O ARG L 445 " (cutoff:3.500A) Proline residue: L 450 - end of helix Processing helix chain 'L' and resid 462 through 471 Processing helix chain 'L' and resid 488 through 491 No H-bonds generated for 'chain 'L' and resid 488 through 491' Processing helix chain 'L' and resid 497 through 516 removed outlier: 4.341A pdb=" N THR L 516 " --> pdb=" O GLY L 512 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 30 removed outlier: 4.592A pdb=" N THR M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 59 removed outlier: 3.622A pdb=" N GLU M 59 " --> pdb=" O SER M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 85 Processing helix chain 'M' and resid 89 through 108 Processing helix chain 'M' and resid 113 through 134 Processing helix chain 'M' and resid 141 through 151 Processing helix chain 'M' and resid 156 through 169 Processing helix chain 'M' and resid 202 through 204 No H-bonds generated for 'chain 'M' and resid 202 through 204' Processing helix chain 'M' and resid 231 through 243 Proline residue: M 235 - end of helix Processing helix chain 'M' and resid 256 through 268 Processing helix chain 'M' and resid 282 through 296 Processing helix chain 'M' and resid 339 through 355 Processing helix chain 'M' and resid 359 through 374 Processing helix chain 'M' and resid 386 through 408 Processing helix chain 'M' and resid 417 through 426 Processing helix chain 'M' and resid 434 through 446 Processing helix chain 'M' and resid 449 through 458 Processing helix chain 'M' and resid 462 through 471 Processing helix chain 'M' and resid 488 through 491 No H-bonds generated for 'chain 'M' and resid 488 through 491' Processing helix chain 'M' and resid 497 through 515 Processing helix chain 'N' and resid 10 through 30 removed outlier: 4.743A pdb=" N THR N 30 " --> pdb=" O ALA N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 59 Processing helix chain 'N' and resid 65 through 84 removed outlier: 3.896A pdb=" N VAL N 77 " --> pdb=" O MET N 73 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA N 78 " --> pdb=" O VAL N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 108 Processing helix chain 'N' and resid 113 through 134 Processing helix chain 'N' and resid 142 through 151 Processing helix chain 'N' and resid 156 through 168 Processing helix chain 'N' and resid 202 through 204 No H-bonds generated for 'chain 'N' and resid 202 through 204' Processing helix chain 'N' and resid 230 through 242 Proline residue: N 235 - end of helix Processing helix chain 'N' and resid 260 through 266 Processing helix chain 'N' and resid 283 through 296 Processing helix chain 'N' and resid 309 through 311 No H-bonds generated for 'chain 'N' and resid 309 through 311' Processing helix chain 'N' and resid 339 through 355 Processing helix chain 'N' and resid 359 through 374 Processing helix chain 'N' and resid 386 through 409 Processing helix chain 'N' and resid 417 through 425 Processing helix chain 'N' and resid 434 through 458 removed outlier: 3.882A pdb=" N GLU N 448 " --> pdb=" O LEU N 444 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA N 449 " --> pdb=" O ARG N 445 " (cutoff:3.500A) Proline residue: N 450 - end of helix Processing helix chain 'N' and resid 462 through 471 Processing helix chain 'N' and resid 488 through 491 No H-bonds generated for 'chain 'N' and resid 488 through 491' Processing helix chain 'N' and resid 497 through 516 removed outlier: 4.256A pdb=" N THR N 516 " --> pdb=" O GLY N 512 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 4 through 8 Processing sheet with id= B, first strand: chain 'A' and resid 38 through 40 Processing sheet with id= C, first strand: chain 'A' and resid 174 through 179 Processing sheet with id= D, first strand: chain 'A' and resid 192 through 195 Processing sheet with id= E, first strand: chain 'A' and resid 219 through 222 Processing sheet with id= F, first strand: chain 'A' and resid 411 through 413 Processing sheet with id= G, first strand: chain 'A' and resid 476 through 479 Processing sheet with id= H, first strand: chain 'G' and resid 4 through 8 Processing sheet with id= I, first strand: chain 'G' and resid 38 through 40 Processing sheet with id= J, first strand: chain 'G' and resid 174 through 179 Processing sheet with id= K, first strand: chain 'G' and resid 193 through 195 removed outlier: 3.518A pdb=" N VAL G 323 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 219 through 222 Processing sheet with id= M, first strand: chain 'G' and resid 411 through 413 Processing sheet with id= N, first strand: chain 'G' and resid 476 through 479 Processing sheet with id= O, first strand: chain 'B' and resid 4 through 8 Processing sheet with id= P, first strand: chain 'B' and resid 38 through 40 Processing sheet with id= Q, first strand: chain 'B' and resid 174 through 179 Processing sheet with id= R, first strand: chain 'B' and resid 192 through 195 Processing sheet with id= S, first strand: chain 'B' and resid 219 through 222 Processing sheet with id= T, first strand: chain 'B' and resid 411 through 413 Processing sheet with id= U, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= V, first strand: chain 'C' and resid 4 through 8 Processing sheet with id= W, first strand: chain 'C' and resid 38 through 40 Processing sheet with id= X, first strand: chain 'C' and resid 174 through 179 Processing sheet with id= Y, first strand: chain 'C' and resid 193 through 195 Processing sheet with id= Z, first strand: chain 'C' and resid 219 through 222 Processing sheet with id= AA, first strand: chain 'C' and resid 411 through 413 Processing sheet with id= AB, first strand: chain 'C' and resid 476 through 479 Processing sheet with id= AC, first strand: chain 'D' and resid 4 through 8 Processing sheet with id= AD, first strand: chain 'D' and resid 38 through 40 Processing sheet with id= AE, first strand: chain 'D' and resid 174 through 179 Processing sheet with id= AF, first strand: chain 'D' and resid 192 through 195 Processing sheet with id= AG, first strand: chain 'D' and resid 219 through 222 Processing sheet with id= AH, first strand: chain 'D' and resid 411 through 413 Processing sheet with id= AI, first strand: chain 'D' and resid 476 through 479 Processing sheet with id= AJ, first strand: chain 'E' and resid 4 through 8 Processing sheet with id= AK, first strand: chain 'E' and resid 38 through 40 Processing sheet with id= AL, first strand: chain 'E' and resid 174 through 179 Processing sheet with id= AM, first strand: chain 'E' and resid 193 through 195 Processing sheet with id= AN, first strand: chain 'E' and resid 219 through 222 Processing sheet with id= AO, first strand: chain 'E' and resid 411 through 413 Processing sheet with id= AP, first strand: chain 'E' and resid 476 through 479 Processing sheet with id= AQ, first strand: chain 'F' and resid 4 through 8 Processing sheet with id= AR, first strand: chain 'F' and resid 38 through 40 Processing sheet with id= AS, first strand: chain 'F' and resid 174 through 179 Processing sheet with id= AT, first strand: chain 'F' and resid 192 through 195 Processing sheet with id= AU, first strand: chain 'F' and resid 219 through 222 Processing sheet with id= AV, first strand: chain 'F' and resid 411 through 413 Processing sheet with id= AW, first strand: chain 'F' and resid 476 through 479 Processing sheet with id= AX, first strand: chain 'H' and resid 4 through 8 Processing sheet with id= AY, first strand: chain 'H' and resid 38 through 40 Processing sheet with id= AZ, first strand: chain 'H' and resid 174 through 179 Processing sheet with id= BA, first strand: chain 'H' and resid 193 through 195 Processing sheet with id= BB, first strand: chain 'H' and resid 219 through 222 Processing sheet with id= BC, first strand: chain 'H' and resid 411 through 413 Processing sheet with id= BD, first strand: chain 'H' and resid 476 through 479 Processing sheet with id= BE, first strand: chain 'I' and resid 4 through 8 Processing sheet with id= BF, first strand: chain 'I' and resid 38 through 40 Processing sheet with id= BG, first strand: chain 'I' and resid 174 through 179 Processing sheet with id= BH, first strand: chain 'I' and resid 192 through 195 Processing sheet with id= BI, first strand: chain 'I' and resid 219 through 222 Processing sheet with id= BJ, first strand: chain 'I' and resid 411 through 413 Processing sheet with id= BK, first strand: chain 'I' and resid 476 through 479 Processing sheet with id= BL, first strand: chain 'J' and resid 4 through 8 Processing sheet with id= BM, first strand: chain 'J' and resid 38 through 40 Processing sheet with id= BN, first strand: chain 'J' and resid 174 through 179 Processing sheet with id= BO, first strand: chain 'J' and resid 193 through 195 removed outlier: 3.504A pdb=" N VAL J 323 " --> pdb=" O LEU J 215 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'J' and resid 219 through 222 Processing sheet with id= BQ, first strand: chain 'J' and resid 411 through 413 Processing sheet with id= BR, first strand: chain 'J' and resid 476 through 479 Processing sheet with id= BS, first strand: chain 'K' and resid 4 through 8 Processing sheet with id= BT, first strand: chain 'K' and resid 38 through 40 Processing sheet with id= BU, first strand: chain 'K' and resid 174 through 179 Processing sheet with id= BV, first strand: chain 'K' and resid 192 through 195 Processing sheet with id= BW, first strand: chain 'K' and resid 219 through 222 Processing sheet with id= BX, first strand: chain 'K' and resid 411 through 413 Processing sheet with id= BY, first strand: chain 'K' and resid 476 through 479 Processing sheet with id= BZ, first strand: chain 'L' and resid 4 through 8 Processing sheet with id= CA, first strand: chain 'L' and resid 38 through 40 Processing sheet with id= CB, first strand: chain 'L' and resid 174 through 179 Processing sheet with id= CC, first strand: chain 'L' and resid 193 through 195 Processing sheet with id= CD, first strand: chain 'L' and resid 219 through 222 Processing sheet with id= CE, first strand: chain 'L' and resid 411 through 413 Processing sheet with id= CF, first strand: chain 'L' and resid 476 through 479 Processing sheet with id= CG, first strand: chain 'M' and resid 4 through 8 Processing sheet with id= CH, first strand: chain 'M' and resid 38 through 40 Processing sheet with id= CI, first strand: chain 'M' and resid 174 through 179 Processing sheet with id= CJ, first strand: chain 'M' and resid 192 through 195 Processing sheet with id= CK, first strand: chain 'M' and resid 219 through 222 Processing sheet with id= CL, first strand: chain 'M' and resid 411 through 413 Processing sheet with id= CM, first strand: chain 'M' and resid 476 through 479 Processing sheet with id= CN, first strand: chain 'N' and resid 4 through 8 Processing sheet with id= CO, first strand: chain 'N' and resid 38 through 40 Processing sheet with id= CP, first strand: chain 'N' and resid 174 through 179 Processing sheet with id= CQ, first strand: chain 'N' and resid 193 through 195 Processing sheet with id= CR, first strand: chain 'N' and resid 213 through 216 Processing sheet with id= CS, first strand: chain 'N' and resid 219 through 222 Processing sheet with id= CT, first strand: chain 'N' and resid 411 through 413 Processing sheet with id= CU, first strand: chain 'N' and resid 476 through 479 3303 hydrogen bonds defined for protein. 9573 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: 18.74 Time building geometry restraints manager: 17.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18739 1.34 - 1.46: 8159 1.46 - 1.58: 27345 1.58 - 1.70: 28 1.70 - 1.82: 518 Bond restraints: 54789 Sorted by residual: bond pdb=" CG1 ILE M 100 " pdb=" CD1 ILE M 100 " ideal model delta sigma weight residual 1.513 1.426 0.087 3.90e-02 6.57e+02 4.95e+00 bond pdb=" CB MET M 16 " pdb=" CG MET M 16 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.37e+00 bond pdb=" CB MET B 16 " pdb=" CG MET B 16 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.34e+00 bond pdb=" CB MET D 16 " pdb=" CG MET D 16 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.10e+00 bond pdb=" CB MET A 16 " pdb=" CG MET A 16 " ideal model delta sigma weight residual 1.520 1.468 0.052 3.00e-02 1.11e+03 2.97e+00 ... (remaining 54784 not shown) Histogram of bond angle deviations from ideal: 96.11 - 104.82: 848 104.82 - 113.54: 32379 113.54 - 122.26: 32863 122.26 - 130.97: 7928 130.97 - 139.69: 56 Bond angle restraints: 74074 Sorted by residual: angle pdb=" CB MET B 16 " pdb=" CG MET B 16 " pdb=" SD MET B 16 " ideal model delta sigma weight residual 112.70 96.11 16.59 3.00e+00 1.11e-01 3.06e+01 angle pdb=" CB MET M 16 " pdb=" CG MET M 16 " pdb=" SD MET M 16 " ideal model delta sigma weight residual 112.70 97.88 14.82 3.00e+00 1.11e-01 2.44e+01 angle pdb=" CB MET K 16 " pdb=" CG MET K 16 " pdb=" SD MET K 16 " ideal model delta sigma weight residual 112.70 98.32 14.38 3.00e+00 1.11e-01 2.30e+01 angle pdb=" CB MET D 16 " pdb=" CG MET D 16 " pdb=" SD MET D 16 " ideal model delta sigma weight residual 112.70 98.97 13.73 3.00e+00 1.11e-01 2.10e+01 angle pdb=" CB MET A 16 " pdb=" CG MET A 16 " pdb=" SD MET A 16 " ideal model delta sigma weight residual 112.70 99.27 13.43 3.00e+00 1.11e-01 2.01e+01 ... (remaining 74069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 31148 17.95 - 35.91: 2422 35.91 - 53.86: 503 53.86 - 71.82: 103 71.82 - 89.77: 40 Dihedral angle restraints: 34216 sinusoidal: 13524 harmonic: 20692 Sorted by residual: dihedral pdb=" CA GLU H 61 " pdb=" C GLU H 61 " pdb=" N LEU H 62 " pdb=" CA LEU H 62 " ideal model delta harmonic sigma weight residual -180.00 -161.41 -18.59 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA GLU N 61 " pdb=" C GLU N 61 " pdb=" N LEU N 62 " pdb=" CA LEU N 62 " ideal model delta harmonic sigma weight residual -180.00 -161.60 -18.40 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LEU G 259 " pdb=" C LEU G 259 " pdb=" N ALA G 260 " pdb=" CA ALA G 260 " ideal model delta harmonic sigma weight residual -180.00 -161.82 -18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 34213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 6917 0.050 - 0.100: 1685 0.100 - 0.151: 373 0.151 - 0.201: 7 0.201 - 0.251: 6 Chirality restraints: 8988 Sorted by residual: chirality pdb=" CB ILE D 49 " pdb=" CA ILE D 49 " pdb=" CG1 ILE D 49 " pdb=" CG2 ILE D 49 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB ILE F 49 " pdb=" CA ILE F 49 " pdb=" CG1 ILE F 49 " pdb=" CG2 ILE F 49 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE I 49 " pdb=" CA ILE I 49 " pdb=" CG1 ILE I 49 " pdb=" CG2 ILE I 49 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 8985 not shown) Planarity restraints: 9618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 59 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" CD GLU B 59 " -0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU B 59 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU B 59 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 387 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" C VAL F 387 " 0.027 2.00e-02 2.50e+03 pdb=" O VAL F 387 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU F 388 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 44 " 0.007 2.00e-02 2.50e+03 1.15e-02 2.31e+00 pdb=" CG PHE L 44 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE L 44 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE L 44 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE L 44 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE L 44 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE L 44 " -0.000 2.00e-02 2.50e+03 ... (remaining 9615 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 6373 2.75 - 3.29: 57223 3.29 - 3.82: 96171 3.82 - 4.36: 111657 4.36 - 4.90: 192171 Nonbonded interactions: 463595 Sorted by model distance: nonbonded pdb=" OE2 GLU J 238 " pdb=" OG SER L 228 " model vdw 2.210 2.440 nonbonded pdb=" O LEU N 262 " pdb=" OG1 THR N 266 " model vdw 2.229 2.440 nonbonded pdb=" O LEU C 262 " pdb=" OG1 THR C 266 " model vdw 2.234 2.440 nonbonded pdb=" O LEU H 262 " pdb=" OG1 THR H 266 " model vdw 2.239 2.440 nonbonded pdb=" O LEU G 262 " pdb=" OG1 THR G 266 " model vdw 2.241 2.440 ... (remaining 463590 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 397 or (resid 398 through 399 and (name N or nam \ e CA or name C or name O or name CB )) or resid 400 through 524 or resid 601)) selection = (chain 'B' and (resid 2 through 397 or (resid 398 through 399 and (name N or nam \ e CA or name C or name O or name CB )) or resid 400 through 524 or resid 601)) selection = (chain 'C' and (resid 2 through 433 or (resid 434 and (name N or name CA or name \ C or name O or name CB )) or resid 435 through 524 or resid 601)) selection = (chain 'D' and (resid 2 through 397 or (resid 398 through 399 and (name N or nam \ e CA or name C or name O or name CB )) or resid 400 through 524 or resid 601)) selection = (chain 'E' and (resid 2 through 433 or (resid 434 and (name N or name CA or name \ C or name O or name CB )) or resid 435 through 524 or resid 601)) selection = (chain 'F' and (resid 2 through 397 or (resid 398 through 399 and (name N or nam \ e CA or name C or name O or name CB )) or resid 400 through 524 or resid 601)) selection = (chain 'G' and (resid 2 through 433 or (resid 434 and (name N or name CA or name \ C or name O or name CB )) or resid 435 through 524 or resid 601)) selection = (chain 'H' and (resid 2 through 433 or (resid 434 and (name N or name CA or name \ C or name O or name CB )) or resid 435 through 524 or resid 601)) selection = (chain 'I' and (resid 2 through 397 or (resid 398 through 399 and (name N or nam \ e CA or name C or name O or name CB )) or resid 400 through 524 or resid 601)) selection = (chain 'J' and (resid 2 through 433 or (resid 434 and (name N or name CA or name \ C or name O or name CB )) or resid 435 through 524 or resid 601)) selection = (chain 'K' and (resid 2 through 397 or (resid 398 through 399 and (name N or nam \ e CA or name C or name O or name CB )) or resid 400 through 524 or resid 601)) selection = (chain 'L' and (resid 2 through 433 or (resid 434 and (name N or name CA or name \ C or name O or name CB )) or resid 435 through 524 or resid 601)) selection = (chain 'M' and (resid 2 through 397 or (resid 398 through 399 and (name N or nam \ e CA or name C or name O or name CB )) or resid 400 through 524 or resid 601)) selection = (chain 'N' and (resid 2 through 433 or (resid 434 and (name N or name CA or name \ C or name O or name CB )) or resid 435 through 524 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 13.180 Check model and map are aligned: 0.590 Set scattering table: 0.380 Process input model: 107.650 Find NCS groups from input model: 3.440 Set up NCS constraints: 0.420 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:2.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 0.087 54789 Z= 0.284 Angle : 0.680 16.594 74074 Z= 0.378 Chirality : 0.045 0.251 8988 Planarity : 0.004 0.033 9618 Dihedral : 13.764 89.772 20944 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.09), residues: 7308 helix: 0.87 (0.08), residues: 4095 sheet: -0.39 (0.15), residues: 1015 loop : -0.63 (0.12), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 401 PHE 0.026 0.002 PHE L 44 TYR 0.023 0.001 TYR F 485 ARG 0.007 0.000 ARG I 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 4.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: -0.0990 (mpp) cc_final: -0.1263 (mpp) REVERT: A 389 MET cc_start: 0.3096 (mmt) cc_final: 0.2864 (mmm) REVERT: F 327 LYS cc_start: 0.7731 (mmpt) cc_final: 0.7414 (mmmt) REVERT: H 389 MET cc_start: 0.7019 (tpp) cc_final: 0.6265 (ttm) REVERT: H 488 MET cc_start: 0.8134 (mmt) cc_final: 0.7384 (mmt) REVERT: J 233 MET cc_start: 0.5298 (ppp) cc_final: 0.4235 (ptt) REVERT: K 267 MET cc_start: -0.1583 (mpp) cc_final: -0.1815 (mpp) REVERT: K 327 LYS cc_start: 0.7908 (mmtt) cc_final: 0.7384 (mmmt) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.4733 time to fit residues: 301.5969 Evaluate side-chains 299 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 4.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 5.9990 chunk 551 optimal weight: 50.0000 chunk 306 optimal weight: 0.8980 chunk 188 optimal weight: 0.9990 chunk 372 optimal weight: 6.9990 chunk 294 optimal weight: 5.9990 chunk 570 optimal weight: 0.7980 chunk 220 optimal weight: 7.9990 chunk 346 optimal weight: 30.0000 chunk 424 optimal weight: 5.9990 chunk 661 optimal weight: 20.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 GLN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 453 GLN ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 437 ASN K 437 ASN ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 437 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 54789 Z= 0.316 Angle : 0.567 13.128 74074 Z= 0.302 Chirality : 0.043 0.141 8988 Planarity : 0.003 0.029 9618 Dihedral : 7.928 73.024 8204 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.53 % Allowed : 7.07 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.10), residues: 7308 helix: 1.22 (0.08), residues: 4137 sheet: -0.46 (0.15), residues: 1015 loop : -0.60 (0.12), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 401 PHE 0.024 0.002 PHE I 195 TYR 0.022 0.002 TYR F 360 ARG 0.003 0.000 ARG I 58 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 321 time to evaluate : 4.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 267 MET cc_start: -0.2612 (OUTLIER) cc_final: -0.2907 (mpp) REVERT: B 193 MET cc_start: 0.6923 (tpt) cc_final: 0.6388 (tpp) REVERT: D 193 MET cc_start: 0.6946 (tpt) cc_final: 0.6154 (tpp) REVERT: H 267 MET cc_start: 0.0737 (ptt) cc_final: -0.0169 (mpp) REVERT: H 389 MET cc_start: 0.7064 (tpp) cc_final: 0.6294 (ttm) REVERT: I 193 MET cc_start: 0.6666 (tpt) cc_final: 0.5931 (tpp) REVERT: J 233 MET cc_start: 0.5287 (ppp) cc_final: 0.4430 (ptt) REVERT: L 288 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7211 (mmt) REVERT: M 16 MET cc_start: 0.8611 (ttp) cc_final: 0.8357 (ttp) REVERT: M 69 MET cc_start: 0.6621 (tpp) cc_final: 0.6360 (tpp) REVERT: M 193 MET cc_start: 0.7017 (tpt) cc_final: 0.6192 (tpp) outliers start: 30 outliers final: 11 residues processed: 338 average time/residue: 0.4744 time to fit residues: 281.7962 Evaluate side-chains 302 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 289 time to evaluate : 4.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 327 LYS Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain N residue 327 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 550 optimal weight: 9.9990 chunk 450 optimal weight: 7.9990 chunk 182 optimal weight: 3.9990 chunk 662 optimal weight: 0.9990 chunk 715 optimal weight: 5.9990 chunk 589 optimal weight: 10.0000 chunk 656 optimal weight: 10.0000 chunk 225 optimal weight: 8.9990 chunk 531 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 GLN ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 GLN ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 54789 Z= 0.223 Angle : 0.516 12.318 74074 Z= 0.272 Chirality : 0.041 0.141 8988 Planarity : 0.003 0.028 9618 Dihedral : 7.555 72.334 8204 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.76 % Allowed : 9.78 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.10), residues: 7308 helix: 1.48 (0.08), residues: 4095 sheet: -0.36 (0.15), residues: 1015 loop : -0.50 (0.12), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS J 401 PHE 0.012 0.001 PHE L 195 TYR 0.011 0.001 TYR M 485 ARG 0.004 0.000 ARG L 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 318 time to evaluate : 4.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 267 MET cc_start: -0.2629 (OUTLIER) cc_final: -0.2934 (mpp) REVERT: C 447 MET cc_start: 0.8635 (mtp) cc_final: 0.8405 (mtm) REVERT: F 488 MET cc_start: 0.9121 (mmm) cc_final: 0.8431 (mmm) REVERT: H 267 MET cc_start: 0.0645 (ptt) cc_final: -0.0090 (mpp) REVERT: H 288 MET cc_start: 0.7402 (mpp) cc_final: 0.7194 (ptp) REVERT: H 389 MET cc_start: 0.7087 (tpp) cc_final: 0.6280 (ttm) REVERT: J 233 MET cc_start: 0.5265 (ppp) cc_final: 0.4455 (ptt) REVERT: K 267 MET cc_start: -0.0740 (OUTLIER) cc_final: -0.1095 (mtp) REVERT: K 327 LYS cc_start: 0.7908 (mmtt) cc_final: 0.7375 (mmmt) REVERT: K 363 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7915 (pm20) REVERT: L 288 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7591 (ptp) outliers start: 43 outliers final: 14 residues processed: 349 average time/residue: 0.4743 time to fit residues: 290.7288 Evaluate side-chains 311 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 293 time to evaluate : 4.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 327 LYS Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain K residue 363 GLU Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain N residue 327 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 5.9990 chunk 497 optimal weight: 40.0000 chunk 343 optimal weight: 50.0000 chunk 73 optimal weight: 7.9990 chunk 316 optimal weight: 3.9990 chunk 444 optimal weight: 6.9990 chunk 664 optimal weight: 6.9990 chunk 703 optimal weight: 9.9990 chunk 347 optimal weight: 30.0000 chunk 629 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN F 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 54789 Z= 0.475 Angle : 0.642 13.133 74074 Z= 0.339 Chirality : 0.045 0.170 8988 Planarity : 0.004 0.039 9618 Dihedral : 7.669 74.741 8204 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.77 % Allowed : 11.33 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.09), residues: 7308 helix: 1.13 (0.08), residues: 4116 sheet: -0.43 (0.16), residues: 1008 loop : -0.71 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS J 401 PHE 0.014 0.002 PHE C 8 TYR 0.023 0.002 TYR C 485 ARG 0.004 0.001 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 295 time to evaluate : 4.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 267 MET cc_start: -0.2632 (OUTLIER) cc_final: -0.2883 (mpp) REVERT: B 267 MET cc_start: 0.0124 (OUTLIER) cc_final: -0.0395 (mtp) REVERT: B 519 CYS cc_start: 0.8489 (m) cc_final: 0.8254 (t) REVERT: F 389 MET cc_start: 0.3265 (mmm) cc_final: 0.3035 (mmm) REVERT: F 488 MET cc_start: 0.9151 (mmm) cc_final: 0.8494 (mmm) REVERT: H 267 MET cc_start: 0.0755 (ptt) cc_final: -0.0028 (mpp) REVERT: H 288 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.7005 (mmt) REVERT: I 8 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7648 (p90) REVERT: J 233 MET cc_start: 0.5266 (ppp) cc_final: 0.4349 (ptt) REVERT: K 267 MET cc_start: -0.1093 (OUTLIER) cc_final: -0.1401 (mtp) REVERT: K 514 MET cc_start: 0.8538 (ttt) cc_final: 0.8299 (ttp) REVERT: M 69 MET cc_start: 0.7662 (tpp) cc_final: 0.7084 (tpp) REVERT: N 61 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8155 (pt0) REVERT: N 288 MET cc_start: 0.7026 (ptp) cc_final: 0.6810 (ptp) outliers start: 100 outliers final: 46 residues processed: 371 average time/residue: 0.4793 time to fit residues: 314.4358 Evaluate side-chains 334 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 282 time to evaluate : 4.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 327 LYS Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain I residue 8 PHE Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 485 TYR Chi-restraints excluded: chain N residue 61 GLU Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 213 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 2.9990 chunk 399 optimal weight: 50.0000 chunk 10 optimal weight: 0.9980 chunk 523 optimal weight: 0.9980 chunk 290 optimal weight: 0.0010 chunk 600 optimal weight: 50.0000 chunk 486 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 359 optimal weight: 1.9990 chunk 631 optimal weight: 1.9990 chunk 177 optimal weight: 7.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 194 GLN B 437 ASN ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 GLN ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 GLN I 437 ASN ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 54789 Z= 0.169 Angle : 0.511 10.463 74074 Z= 0.268 Chirality : 0.041 0.143 8988 Planarity : 0.003 0.030 9618 Dihedral : 7.232 71.999 8204 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.22 % Allowed : 12.73 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.10), residues: 7308 helix: 1.47 (0.08), residues: 4109 sheet: -0.35 (0.16), residues: 1008 loop : -0.55 (0.12), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 401 PHE 0.019 0.001 PHE D 219 TYR 0.019 0.001 TYR M 485 ARG 0.003 0.000 ARG F 268 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 319 time to evaluate : 4.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 267 MET cc_start: -0.2665 (OUTLIER) cc_final: -0.2933 (mpp) REVERT: B 267 MET cc_start: 0.0274 (OUTLIER) cc_final: -0.0240 (mtp) REVERT: F 389 MET cc_start: 0.3242 (mmm) cc_final: 0.3016 (mmm) REVERT: F 488 MET cc_start: 0.8997 (mmm) cc_final: 0.8329 (mmm) REVERT: H 267 MET cc_start: 0.1009 (ptt) cc_final: 0.0212 (mpp) REVERT: H 288 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6855 (mmt) REVERT: H 389 MET cc_start: 0.7040 (tpp) cc_final: 0.5976 (ttp) REVERT: J 233 MET cc_start: 0.5111 (ppp) cc_final: 0.4206 (ptt) REVERT: K 267 MET cc_start: -0.0622 (OUTLIER) cc_final: -0.1017 (mtp) REVERT: K 327 LYS cc_start: 0.7982 (mmtt) cc_final: 0.7435 (mmmt) REVERT: L 447 MET cc_start: 0.8775 (mtm) cc_final: 0.8535 (mtm) REVERT: M 69 MET cc_start: 0.7068 (tpp) cc_final: 0.6484 (tpp) REVERT: M 514 MET cc_start: 0.8575 (ttp) cc_final: 0.8341 (ttp) outliers start: 69 outliers final: 32 residues processed: 376 average time/residue: 0.4804 time to fit residues: 317.6933 Evaluate side-chains 337 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 301 time to evaluate : 4.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 327 LYS Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain H residue 422 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 327 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 6.9990 chunk 633 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 413 optimal weight: 3.9990 chunk 173 optimal weight: 20.0000 chunk 704 optimal weight: 5.9990 chunk 584 optimal weight: 0.9980 chunk 326 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 232 optimal weight: 30.0000 chunk 369 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 194 GLN ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 GLN F 37 ASN I 37 ASN I 194 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 54789 Z= 0.352 Angle : 0.574 13.561 74074 Z= 0.301 Chirality : 0.043 0.182 8988 Planarity : 0.003 0.030 9618 Dihedral : 7.142 72.037 8204 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.61 % Allowed : 13.20 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.10), residues: 7308 helix: 1.39 (0.08), residues: 4109 sheet: -0.38 (0.16), residues: 1008 loop : -0.66 (0.12), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 401 PHE 0.023 0.001 PHE M 195 TYR 0.015 0.001 TYR M 485 ARG 0.006 0.000 ARG M 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 303 time to evaluate : 4.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 267 MET cc_start: -0.2631 (OUTLIER) cc_final: -0.2918 (mpp) REVERT: B 267 MET cc_start: 0.0312 (OUTLIER) cc_final: -0.0221 (mtp) REVERT: F 195 PHE cc_start: 0.7306 (p90) cc_final: 0.6866 (p90) REVERT: F 488 MET cc_start: 0.9049 (mmm) cc_final: 0.8400 (mmm) REVERT: H 267 MET cc_start: 0.1084 (ptt) cc_final: 0.0256 (mpp) REVERT: H 288 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.6962 (mmt) REVERT: H 389 MET cc_start: 0.7176 (tpp) cc_final: 0.6020 (ttp) REVERT: J 233 MET cc_start: 0.4767 (ppp) cc_final: 0.3811 (ptt) REVERT: K 267 MET cc_start: -0.0567 (OUTLIER) cc_final: -0.0987 (mtp) REVERT: K 519 CYS cc_start: 0.8130 (m) cc_final: 0.7854 (t) REVERT: M 69 MET cc_start: 0.7236 (tpp) cc_final: 0.6732 (tpp) REVERT: M 514 MET cc_start: 0.8616 (ttp) cc_final: 0.8395 (ttp) outliers start: 91 outliers final: 58 residues processed: 376 average time/residue: 0.4937 time to fit residues: 327.5904 Evaluate side-chains 359 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 297 time to evaluate : 4.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 327 LYS Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 8 PHE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 435 ASP Chi-restraints excluded: chain N residue 213 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 0.0770 chunk 79 optimal weight: 20.0000 chunk 401 optimal weight: 10.0000 chunk 514 optimal weight: 1.9990 chunk 398 optimal weight: 20.0000 chunk 592 optimal weight: 0.0970 chunk 393 optimal weight: 8.9990 chunk 701 optimal weight: 0.9990 chunk 439 optimal weight: 8.9990 chunk 427 optimal weight: 3.9990 chunk 323 optimal weight: 1.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 ASN ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 54789 Z= 0.170 Angle : 0.521 16.720 74074 Z= 0.270 Chirality : 0.041 0.208 8988 Planarity : 0.003 0.029 9618 Dihedral : 6.880 71.818 8204 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.13 % Allowed : 14.23 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.10), residues: 7308 helix: 1.57 (0.08), residues: 4123 sheet: -0.32 (0.16), residues: 1015 loop : -0.58 (0.12), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS L 401 PHE 0.016 0.001 PHE M 195 TYR 0.017 0.001 TYR F 485 ARG 0.002 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 321 time to evaluate : 4.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 267 MET cc_start: -0.2775 (OUTLIER) cc_final: -0.3063 (mpp) REVERT: B 267 MET cc_start: 0.0233 (OUTLIER) cc_final: -0.0277 (mtp) REVERT: F 389 MET cc_start: 0.3481 (mmm) cc_final: 0.3105 (mmm) REVERT: F 488 MET cc_start: 0.8942 (mmm) cc_final: 0.8326 (mmm) REVERT: H 267 MET cc_start: 0.0932 (ptt) cc_final: 0.0155 (mpp) REVERT: H 288 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.6894 (mmt) REVERT: H 389 MET cc_start: 0.7045 (tpp) cc_final: 0.5989 (ttp) REVERT: J 233 MET cc_start: 0.4617 (ppp) cc_final: 0.3441 (ptt) REVERT: K 267 MET cc_start: -0.0560 (OUTLIER) cc_final: -0.1009 (mtp) REVERT: K 327 LYS cc_start: 0.7988 (mmtt) cc_final: 0.7498 (mmmt) REVERT: M 69 MET cc_start: 0.6778 (tpp) cc_final: 0.6175 (tpp) REVERT: M 195 PHE cc_start: 0.7431 (p90) cc_final: 0.7119 (p90) outliers start: 64 outliers final: 46 residues processed: 372 average time/residue: 0.4693 time to fit residues: 308.0548 Evaluate side-chains 358 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 308 time to evaluate : 4.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 327 LYS Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 519 CYS Chi-restraints excluded: chain E residue 520 MET Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 435 ASP Chi-restraints excluded: chain N residue 213 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 9.9990 chunk 280 optimal weight: 1.9990 chunk 419 optimal weight: 4.9990 chunk 211 optimal weight: 0.4980 chunk 137 optimal weight: 20.0000 chunk 135 optimal weight: 50.0000 chunk 446 optimal weight: 0.1980 chunk 478 optimal weight: 0.0050 chunk 346 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 551 optimal weight: 50.0000 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 GLN ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 54789 Z= 0.207 Angle : 0.540 28.514 74074 Z= 0.277 Chirality : 0.041 0.209 8988 Planarity : 0.003 0.029 9618 Dihedral : 6.666 71.940 8204 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.40 % Allowed : 14.14 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.10), residues: 7308 helix: 1.61 (0.08), residues: 4116 sheet: -0.31 (0.16), residues: 1015 loop : -0.56 (0.12), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 401 PHE 0.029 0.001 PHE F 195 TYR 0.019 0.001 TYR M 485 ARG 0.002 0.000 ARG M 395 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 318 time to evaluate : 4.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 267 MET cc_start: -0.2768 (OUTLIER) cc_final: -0.3070 (mpp) REVERT: B 90 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8489 (m) REVERT: B 267 MET cc_start: 0.0238 (OUTLIER) cc_final: -0.0310 (mtp) REVERT: D 519 CYS cc_start: 0.8296 (m) cc_final: 0.7921 (t) REVERT: F 488 MET cc_start: 0.8944 (mmm) cc_final: 0.7816 (mmm) REVERT: H 267 MET cc_start: 0.0922 (ptt) cc_final: 0.0112 (mpp) REVERT: H 288 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.6927 (mmt) REVERT: H 389 MET cc_start: 0.7063 (tpp) cc_final: 0.6220 (ttm) REVERT: J 233 MET cc_start: 0.4624 (ppp) cc_final: 0.3478 (ptt) REVERT: K 90 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8669 (m) REVERT: K 267 MET cc_start: -0.0430 (OUTLIER) cc_final: -0.0901 (mtp) REVERT: K 327 LYS cc_start: 0.8007 (mmtt) cc_final: 0.7508 (mmmt) REVERT: K 363 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8108 (pm20) REVERT: M 69 MET cc_start: 0.6693 (tpp) cc_final: 0.6258 (tpp) REVERT: M 193 MET cc_start: 0.6566 (tpp) cc_final: 0.5943 (tmm) outliers start: 79 outliers final: 52 residues processed: 378 average time/residue: 0.4717 time to fit residues: 315.7519 Evaluate side-chains 364 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 305 time to evaluate : 4.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 327 LYS Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 8 PHE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 519 CYS Chi-restraints excluded: chain E residue 520 MET Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain K residue 363 GLU Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain M residue 8 PHE Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 435 ASP Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 327 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 6.9990 chunk 672 optimal weight: 3.9990 chunk 613 optimal weight: 0.8980 chunk 653 optimal weight: 30.0000 chunk 393 optimal weight: 20.0000 chunk 284 optimal weight: 50.0000 chunk 513 optimal weight: 0.8980 chunk 200 optimal weight: 0.8980 chunk 590 optimal weight: 4.9990 chunk 618 optimal weight: 0.9990 chunk 651 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 GLN ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 54789 Z= 0.210 Angle : 0.543 14.119 74074 Z= 0.279 Chirality : 0.041 0.225 8988 Planarity : 0.003 0.028 9618 Dihedral : 6.602 71.937 8204 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.28 % Allowed : 14.43 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.10), residues: 7308 helix: 1.64 (0.08), residues: 4109 sheet: -0.32 (0.16), residues: 1015 loop : -0.55 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS L 401 PHE 0.035 0.001 PHE M 195 TYR 0.017 0.001 TYR M 485 ARG 0.002 0.000 ARG M 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 320 time to evaluate : 4.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 267 MET cc_start: -0.3108 (OUTLIER) cc_final: -0.3416 (mpp) REVERT: B 90 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8506 (m) REVERT: B 195 PHE cc_start: 0.7326 (p90) cc_final: 0.6706 (p90) REVERT: B 267 MET cc_start: 0.0374 (OUTLIER) cc_final: -0.0149 (mtp) REVERT: B 520 MET cc_start: 0.8622 (mtp) cc_final: 0.8342 (mtt) REVERT: C 233 MET cc_start: 0.4832 (ppp) cc_final: 0.4612 (ppp) REVERT: E 134 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8855 (tt) REVERT: E 288 MET cc_start: 0.7413 (mpp) cc_final: 0.7081 (pmm) REVERT: F 389 MET cc_start: 0.3441 (mmm) cc_final: 0.3059 (mmm) REVERT: F 488 MET cc_start: 0.8931 (mmm) cc_final: 0.7803 (mmm) REVERT: H 267 MET cc_start: 0.0939 (ptt) cc_final: 0.0270 (mpp) REVERT: H 288 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6915 (mmt) REVERT: H 389 MET cc_start: 0.7072 (tpp) cc_final: 0.6232 (ttm) REVERT: I 195 PHE cc_start: 0.7276 (p90) cc_final: 0.6619 (p90) REVERT: J 233 MET cc_start: 0.4358 (ppp) cc_final: 0.3248 (ptt) REVERT: K 90 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8678 (m) REVERT: K 267 MET cc_start: -0.0430 (OUTLIER) cc_final: -0.0904 (mtp) REVERT: K 327 LYS cc_start: 0.8012 (mmtt) cc_final: 0.7515 (mmmt) REVERT: K 363 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8102 (pm20) REVERT: L 447 MET cc_start: 0.8587 (mtm) cc_final: 0.8356 (mtm) REVERT: M 69 MET cc_start: 0.6703 (tpp) cc_final: 0.6278 (tpp) outliers start: 72 outliers final: 54 residues processed: 374 average time/residue: 0.4699 time to fit residues: 310.5541 Evaluate side-chains 371 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 309 time to evaluate : 5.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 327 LYS Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 519 CYS Chi-restraints excluded: chain E residue 520 MET Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain I residue 8 PHE Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain K residue 363 GLU Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain M residue 8 PHE Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 435 ASP Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 327 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 9.9990 chunk 691 optimal weight: 0.2980 chunk 422 optimal weight: 3.9990 chunk 328 optimal weight: 20.0000 chunk 480 optimal weight: 0.9990 chunk 725 optimal weight: 0.9990 chunk 667 optimal weight: 0.9990 chunk 577 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 446 optimal weight: 3.9990 chunk 354 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 ASN ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 54789 Z= 0.159 Angle : 0.532 12.277 74074 Z= 0.272 Chirality : 0.040 0.211 8988 Planarity : 0.003 0.028 9618 Dihedral : 6.373 72.211 8204 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.08 % Allowed : 14.71 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.10), residues: 7308 helix: 1.76 (0.08), residues: 4060 sheet: -0.36 (0.16), residues: 1029 loop : -0.50 (0.12), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 401 PHE 0.038 0.001 PHE M 195 TYR 0.015 0.001 TYR F 485 ARG 0.005 0.000 ARG M 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 338 time to evaluate : 4.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 267 MET cc_start: -0.3071 (OUTLIER) cc_final: -0.3419 (mpp) REVERT: G 288 MET cc_start: 0.7657 (mpp) cc_final: 0.7147 (pmm) REVERT: B 90 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8435 (m) REVERT: B 195 PHE cc_start: 0.7286 (p90) cc_final: 0.6729 (p90) REVERT: B 267 MET cc_start: 0.0342 (OUTLIER) cc_final: -0.0183 (mtp) REVERT: C 288 MET cc_start: 0.7474 (mpp) cc_final: 0.7259 (pmm) REVERT: D 195 PHE cc_start: 0.7342 (p90) cc_final: 0.6603 (p90) REVERT: E 288 MET cc_start: 0.7445 (mpp) cc_final: 0.7107 (pmm) REVERT: F 195 PHE cc_start: 0.7431 (p90) cc_final: 0.7076 (p90) REVERT: F 389 MET cc_start: 0.3394 (mmm) cc_final: 0.3017 (mmm) REVERT: F 488 MET cc_start: 0.8855 (mmm) cc_final: 0.8201 (mmm) REVERT: H 267 MET cc_start: 0.0950 (ptt) cc_final: 0.0276 (mpp) REVERT: H 288 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6878 (mmt) REVERT: H 389 MET cc_start: 0.6999 (tpp) cc_final: 0.6173 (ttm) REVERT: I 69 MET cc_start: 0.7114 (tpp) cc_final: 0.6842 (tpp) REVERT: I 195 PHE cc_start: 0.7210 (p90) cc_final: 0.6655 (p90) REVERT: J 233 MET cc_start: 0.4043 (ppp) cc_final: 0.2942 (ptt) REVERT: K 90 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8641 (m) REVERT: K 267 MET cc_start: -0.0444 (OUTLIER) cc_final: -0.0918 (mtp) REVERT: K 327 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7497 (mmmt) REVERT: K 363 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8104 (pm20) REVERT: L 193 MET cc_start: 0.6954 (ppp) cc_final: 0.4204 (tpt) REVERT: L 447 MET cc_start: 0.8593 (mtm) cc_final: 0.8339 (mtm) REVERT: M 69 MET cc_start: 0.6501 (tpp) cc_final: 0.6081 (tpp) REVERT: M 195 PHE cc_start: 0.7697 (p90) cc_final: 0.7381 (p90) REVERT: M 491 MET cc_start: 0.7926 (ptp) cc_final: 0.7399 (ptp) outliers start: 61 outliers final: 48 residues processed: 382 average time/residue: 0.4789 time to fit residues: 322.0358 Evaluate side-chains 370 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 315 time to evaluate : 4.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 327 LYS Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 8 PHE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 520 MET Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain K residue 363 GLU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain M residue 8 PHE Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 327 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 9.9990 chunk 615 optimal weight: 7.9990 chunk 176 optimal weight: 0.5980 chunk 532 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 578 optimal weight: 0.0060 chunk 242 optimal weight: 20.0000 chunk 593 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 GLN ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.122953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.089212 restraints weight = 137826.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.089018 restraints weight = 132258.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.086167 restraints weight = 83486.351| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 54789 Z= 0.166 Angle : 0.534 12.818 74074 Z= 0.273 Chirality : 0.041 0.205 8988 Planarity : 0.003 0.028 9618 Dihedral : 6.213 72.187 8204 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.10 % Allowed : 15.05 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.10), residues: 7308 helix: 1.82 (0.08), residues: 4053 sheet: -0.34 (0.16), residues: 1029 loop : -0.48 (0.12), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 401 PHE 0.024 0.001 PHE D 66 TYR 0.014 0.001 TYR M 485 ARG 0.003 0.000 ARG J 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6990.86 seconds wall clock time: 127 minutes 35.09 seconds (7655.09 seconds total)