Starting phenix.real_space_refine on Mon Mar 11 00:45:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bld_16107/03_2024/8bld_16107_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bld_16107/03_2024/8bld_16107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bld_16107/03_2024/8bld_16107.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bld_16107/03_2024/8bld_16107.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bld_16107/03_2024/8bld_16107_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bld_16107/03_2024/8bld_16107_updated.pdb" } resolution = 4.4 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= 0.003 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 164": "OE1" <-> "OE2" Residue "A PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 76": "OE1" <-> "OE2" Residue "G ASP 83": "OD1" <-> "OD2" Residue "G ASP 115": "OD1" <-> "OD2" Residue "G ASP 121": "OD1" <-> "OD2" Residue "G ASP 185": "OD1" <-> "OD2" Residue "G ASP 196": "OD1" <-> "OD2" Residue "G TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 495": "OD1" <-> "OD2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "B TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 76": "OE1" <-> "OE2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ASP 185": "OD1" <-> "OD2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 495": "OD1" <-> "OD2" Residue "D PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D ASP 398": "OD1" <-> "OD2" Residue "D GLU 461": "OE1" <-> "OE2" Residue "D TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "E GLU 102": "OE1" <-> "OE2" Residue "E ASP 185": "OD1" <-> "OD2" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 483": "OE1" <-> "OE2" Residue "E TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 164": "OE1" <-> "OE2" Residue "F ASP 328": "OD1" <-> "OD2" Residue "F ASP 398": "OD1" <-> "OD2" Residue "F GLU 408": "OE1" <-> "OE2" Residue "F GLU 461": "OE1" <-> "OE2" Residue "F TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 63": "OE1" <-> "OE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H ASP 83": "OD1" <-> "OD2" Residue "H ASP 196": "OD1" <-> "OD2" Residue "H TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 495": "OD1" <-> "OD2" Residue "I PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 67": "OE1" <-> "OE2" Residue "I GLU 172": "OE1" <-> "OE2" Residue "I ASP 398": "OD1" <-> "OD2" Residue "J PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 76": "OE1" <-> "OE2" Residue "J ASP 83": "OD1" <-> "OD2" Residue "J GLU 102": "OE1" <-> "OE2" Residue "J ASP 115": "OD1" <-> "OD2" Residue "J TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 386": "OE1" <-> "OE2" Residue "J GLU 391": "OE1" <-> "OE2" Residue "J TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 495": "OD1" <-> "OD2" Residue "K PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 67": "OE1" <-> "OE2" Residue "K ASP 398": "OD1" <-> "OD2" Residue "K GLU 461": "OE1" <-> "OE2" Residue "L GLU 63": "OE1" <-> "OE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L ASP 83": "OD1" <-> "OD2" Residue "L ASP 121": "OD1" <-> "OD2" Residue "L TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 461": "OE1" <-> "OE2" Residue "L TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 83": "OD1" <-> "OD2" Residue "M GLU 172": "OE1" <-> "OE2" Residue "M TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 398": "OD1" <-> "OD2" Residue "N GLU 76": "OE1" <-> "OE2" Residue "N ASP 83": "OD1" <-> "OD2" Residue "N ASP 115": "OD1" <-> "OD2" Residue "N ASP 121": "OD1" <-> "OD2" Residue "N ASP 185": "OD1" <-> "OD2" Residue "N TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 391": "OE1" <-> "OE2" Residue "N TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 22.52, per 1000 atoms: 0.41 Number of scatterers: 54376 At special positions: 0 Unit cell: (153.6, 151.68, 163.2, 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: 16.93 Conformation dependent library (CDL) restraints added in 7.6 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: 271 helices and 102 sheets defined 52.4% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.45 Creating SS restraints... Processing helix chain 'A' and resid 10 through 30 removed outlier: 5.115A pdb=" N THR A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 65 through 84 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 409 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 434 through 447 Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 462 through 471 Processing helix chain 'A' and resid 497 through 515 Processing helix chain 'G' and resid 9 through 30 removed outlier: 5.168A 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: 3.976A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.543A 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 168 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 295 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 409 Processing helix chain 'G' and resid 417 through 426 Processing helix chain 'G' and resid 434 through 446 Processing helix chain 'G' and resid 449 through 457 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 514 Processing helix chain 'B' and resid 10 through 30 removed outlier: 5.142A pdb=" N THR B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 65 through 84 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 374 Processing helix chain 'B' and resid 386 through 409 removed outlier: 3.707A pdb=" N GLU B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 425 Processing helix chain 'B' and resid 434 through 458 removed outlier: 3.647A pdb=" N GLU B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) Proline residue: B 450 - end of helix Processing helix chain 'B' and resid 462 through 471 Processing helix chain 'B' and resid 497 through 515 Processing helix chain 'C' and resid 9 through 30 removed outlier: 5.131A 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: 3.881A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.521A 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 151 Processing helix chain 'C' and resid 156 through 168 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 295 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 409 Processing helix chain 'C' and resid 417 through 425 Processing helix chain 'C' and resid 434 through 446 Processing helix chain 'C' and resid 449 through 457 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 515 Processing helix chain 'D' and resid 10 through 30 removed outlier: 5.051A pdb=" N THR D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 58 Processing helix chain 'D' and resid 65 through 84 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 409 removed outlier: 3.884A pdb=" N GLU D 409 " --> pdb=" O ALA D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 426 Processing helix chain 'D' and resid 434 through 447 Processing helix chain 'D' and resid 449 through 458 Processing helix chain 'D' and resid 462 through 471 Processing helix chain 'D' and resid 497 through 515 Processing helix chain 'E' and resid 9 through 30 removed outlier: 5.129A pdb=" N THR E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 59 Processing helix chain 'E' and resid 65 through 84 removed outlier: 3.782A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.547A 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 143 through 151 Processing helix chain 'E' and resid 156 through 168 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 295 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 409 Processing helix chain 'E' and resid 417 through 425 Processing helix chain 'E' and resid 434 through 447 Processing helix chain 'E' and resid 449 through 457 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: 3.749A pdb=" N THR E 516 " --> pdb=" O GLY E 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 30 removed outlier: 5.124A pdb=" N THR F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 58 Processing helix chain 'F' and resid 65 through 84 Processing helix chain 'F' and resid 89 through 107 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 373 Processing helix chain 'F' and resid 386 through 409 removed outlier: 3.852A pdb=" N GLU F 409 " --> pdb=" O ALA F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 425 Processing helix chain 'F' and resid 434 through 447 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 9 through 30 removed outlier: 5.059A 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: 3.666A pdb=" N VAL H 77 " --> pdb=" O MET H 73 " (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 143 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 230 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 295 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 409 Processing helix chain 'H' and resid 417 through 426 Processing helix chain 'H' and resid 434 through 457 removed outlier: 3.849A pdb=" N GLU H 448 " --> pdb=" O LEU H 444 " (cutoff:3.500A) removed outlier: 4.710A 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: 3.919A pdb=" N THR H 516 " --> pdb=" O GLY H 512 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 30 removed outlier: 5.091A pdb=" N THR I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 58 Processing helix chain 'I' and resid 65 through 84 Processing helix chain 'I' and resid 89 through 107 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 447 Processing helix chain 'I' and resid 449 through 458 Processing helix chain 'I' and resid 462 through 471 Processing helix chain 'I' and resid 497 through 515 Processing helix chain 'J' and resid 9 through 30 removed outlier: 5.056A pdb=" N THR J 30 " --> pdb=" O ALA J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 58 Processing helix chain 'J' and resid 65 through 84 removed outlier: 3.796A pdb=" N VAL J 77 " --> pdb=" O MET J 73 " (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 151 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 295 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 409 Processing helix chain 'J' and resid 414 through 426 removed outlier: 6.270A pdb=" N ALA J 418 " --> pdb=" O GLY J 415 " (cutoff:3.500A) Processing helix chain 'J' and resid 434 through 457 removed outlier: 3.835A pdb=" N GLU J 448 " --> pdb=" O LEU J 444 " (cutoff:3.500A) removed outlier: 4.844A 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: 3.775A pdb=" N THR J 516 " --> pdb=" O GLY J 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 30 removed outlier: 5.061A pdb=" N THR K 30 " --> pdb=" O ALA K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 59 removed outlier: 4.001A pdb=" N GLU K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 84 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 409 removed outlier: 3.905A pdb=" N GLU K 409 " --> pdb=" O ALA K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 417 through 425 Processing helix chain 'K' and resid 434 through 447 Processing helix chain 'K' and resid 449 through 458 Processing helix chain 'K' and resid 462 through 471 Processing helix chain 'K' and resid 497 through 515 Processing helix chain 'L' and resid 9 through 30 removed outlier: 5.116A pdb=" N THR L 30 " --> pdb=" O ALA L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 59 Processing helix chain 'L' and resid 65 through 84 removed outlier: 3.967A pdb=" N VAL L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) removed outlier: 3.583A 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 143 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 295 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 425 Processing helix chain 'L' and resid 434 through 447 Processing helix chain 'L' and resid 449 through 457 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 514 Processing helix chain 'M' and resid 10 through 30 removed outlier: 5.170A pdb=" N THR M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 59 removed outlier: 4.174A 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 373 Processing helix chain 'M' and resid 386 through 409 removed outlier: 3.521A pdb=" N GLU M 409 " --> pdb=" O ALA M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 417 through 426 Processing helix chain 'M' and resid 434 through 447 Processing helix chain 'M' and resid 449 through 458 Processing helix chain 'M' and resid 462 through 471 Processing helix chain 'M' and resid 497 through 515 Processing helix chain 'N' and resid 9 through 30 removed outlier: 5.107A 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: 4.135A pdb=" N VAL N 77 " --> pdb=" O MET N 73 " (cutoff:3.500A) removed outlier: 3.616A 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 143 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 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 447 Processing helix chain 'N' and resid 449 through 457 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 514 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 180 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: 3.611A 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 removed outlier: 3.579A pdb=" N VAL C 323 " --> pdb=" O LEU C 215 " (cutoff:3.500A) 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 180 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 213 through 216 removed outlier: 3.539A pdb=" N VAL E 323 " --> pdb=" O LEU E 215 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'E' and resid 219 through 222 Processing sheet with id= AP, first strand: chain 'E' and resid 411 through 413 Processing sheet with id= AQ, first strand: chain 'E' and resid 476 through 479 Processing sheet with id= AR, first strand: chain 'F' and resid 4 through 8 Processing sheet with id= AS, first strand: chain 'F' and resid 38 through 40 Processing sheet with id= AT, first strand: chain 'F' and resid 174 through 179 Processing sheet with id= AU, first strand: chain 'F' and resid 192 through 195 Processing sheet with id= AV, first strand: chain 'F' and resid 219 through 222 Processing sheet with id= AW, first strand: chain 'F' and resid 411 through 413 Processing sheet with id= AX, first strand: chain 'F' and resid 476 through 479 Processing sheet with id= AY, first strand: chain 'H' and resid 4 through 8 Processing sheet with id= AZ, first strand: chain 'H' and resid 38 through 40 Processing sheet with id= BA, first strand: chain 'H' and resid 174 through 179 Processing sheet with id= BB, first strand: chain 'H' and resid 193 through 195 removed outlier: 3.501A pdb=" N VAL H 323 " --> pdb=" O LEU H 215 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'H' and resid 219 through 222 Processing sheet with id= BD, first strand: chain 'H' and resid 411 through 413 Processing sheet with id= BE, first strand: chain 'H' and resid 476 through 479 Processing sheet with id= BF, first strand: chain 'I' and resid 4 through 8 Processing sheet with id= BG, first strand: chain 'I' and resid 38 through 40 Processing sheet with id= BH, first strand: chain 'I' and resid 174 through 179 Processing sheet with id= BI, first strand: chain 'I' and resid 192 through 195 Processing sheet with id= BJ, first strand: chain 'I' and resid 219 through 222 Processing sheet with id= BK, first strand: chain 'I' and resid 411 through 413 Processing sheet with id= BL, first strand: chain 'I' and resid 476 through 479 Processing sheet with id= BM, first strand: chain 'J' and resid 4 through 8 Processing sheet with id= BN, first strand: chain 'J' and resid 38 through 40 Processing sheet with id= BO, first strand: chain 'J' and resid 174 through 179 Processing sheet with id= BP, first strand: chain 'J' and resid 193 through 195 Processing sheet with id= BQ, first strand: chain 'J' and resid 213 through 216 Processing sheet with id= BR, first strand: chain 'J' and resid 219 through 222 Processing sheet with id= BS, first strand: chain 'J' and resid 411 through 413 Processing sheet with id= BT, first strand: chain 'J' and resid 476 through 479 Processing sheet with id= BU, first strand: chain 'K' and resid 4 through 8 Processing sheet with id= BV, first strand: chain 'K' and resid 38 through 40 Processing sheet with id= BW, first strand: chain 'K' and resid 174 through 180 Processing sheet with id= BX, first strand: chain 'K' and resid 192 through 195 removed outlier: 3.629A pdb=" N THR K 329 " --> pdb=" O ASN K 326 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'K' and resid 219 through 222 Processing sheet with id= BZ, first strand: chain 'K' and resid 411 through 413 Processing sheet with id= CA, first strand: chain 'K' and resid 476 through 479 Processing sheet with id= CB, first strand: chain 'L' and resid 4 through 8 Processing sheet with id= CC, first strand: chain 'L' and resid 38 through 40 Processing sheet with id= CD, first strand: chain 'L' and resid 174 through 179 Processing sheet with id= CE, first strand: chain 'L' and resid 193 through 195 Processing sheet with id= CF, first strand: chain 'L' and resid 213 through 216 Processing sheet with id= CG, first strand: chain 'L' and resid 219 through 222 Processing sheet with id= CH, first strand: chain 'L' and resid 411 through 413 Processing sheet with id= CI, first strand: chain 'L' and resid 476 through 479 Processing sheet with id= CJ, first strand: chain 'M' and resid 4 through 8 Processing sheet with id= CK, first strand: chain 'M' and resid 38 through 40 Processing sheet with id= CL, first strand: chain 'M' and resid 174 through 180 Processing sheet with id= CM, first strand: chain 'M' and resid 192 through 195 Processing sheet with id= CN, first strand: chain 'M' and resid 219 through 222 Processing sheet with id= CO, first strand: chain 'M' and resid 411 through 413 Processing sheet with id= CP, first strand: chain 'M' and resid 476 through 479 Processing sheet with id= CQ, first strand: chain 'N' and resid 5 through 8 Processing sheet with id= CR, first strand: chain 'N' and resid 38 through 40 Processing sheet with id= CS, first strand: chain 'N' and resid 174 through 179 Processing sheet with id= CT, first strand: chain 'N' and resid 193 through 195 Processing sheet with id= CU, first strand: chain 'N' and resid 213 through 216 Processing sheet with id= CV, first strand: chain 'N' and resid 219 through 222 Processing sheet with id= CW, first strand: chain 'N' and resid 411 through 413 Processing sheet with id= CX, first strand: chain 'N' and resid 476 through 479 3283 hydrogen bonds defined for protein. 9486 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: 20.52 Time building geometry restraints manager: 18.48 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: 18624 1.34 - 1.46: 6685 1.46 - 1.58: 28907 1.58 - 1.70: 55 1.70 - 1.82: 518 Bond restraints: 54789 Sorted by residual: bond pdb=" CG1 ILE H 60 " pdb=" CD1 ILE H 60 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.71e+00 bond pdb=" CA ASP K 328 " pdb=" CB ASP K 328 " ideal model delta sigma weight residual 1.526 1.562 -0.036 1.68e-02 3.54e+03 4.57e+00 bond pdb=" CG1 ILE N 60 " pdb=" CD1 ILE N 60 " ideal model delta sigma weight residual 1.513 1.435 0.078 3.90e-02 6.57e+02 3.95e+00 bond pdb=" CB PRO M 525 " pdb=" CG PRO M 525 " ideal model delta sigma weight residual 1.492 1.590 -0.098 5.00e-02 4.00e+02 3.81e+00 bond pdb=" CG ARG K 404 " pdb=" CD ARG K 404 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.30e+00 ... (remaining 54784 not shown) Histogram of bond angle deviations from ideal: 94.95 - 103.94: 718 103.94 - 112.93: 31388 112.93 - 121.92: 31303 121.92 - 130.91: 10604 130.91 - 139.90: 61 Bond angle restraints: 74074 Sorted by residual: angle pdb=" CB MET M 16 " pdb=" CG MET M 16 " pdb=" SD MET M 16 " ideal model delta sigma weight residual 112.70 128.84 -16.14 3.00e+00 1.11e-01 2.89e+01 angle pdb=" C ARG H 58 " pdb=" N GLU H 59 " pdb=" CA GLU H 59 " ideal model delta sigma weight residual 121.14 113.00 8.14 1.75e+00 3.27e-01 2.16e+01 angle pdb=" CA PRO M 525 " pdb=" N PRO M 525 " pdb=" CD PRO M 525 " ideal model delta sigma weight residual 112.00 105.51 6.49 1.40e+00 5.10e-01 2.15e+01 angle pdb=" CA MET M 16 " pdb=" CB MET M 16 " pdb=" CG MET M 16 " ideal model delta sigma weight residual 114.10 123.36 -9.26 2.00e+00 2.50e-01 2.14e+01 angle pdb=" N MET M 16 " pdb=" CA MET M 16 " pdb=" CB MET M 16 " ideal model delta sigma weight residual 110.39 118.02 -7.63 1.66e+00 3.63e-01 2.11e+01 ... (remaining 74069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.37: 30789 16.37 - 32.73: 2580 32.73 - 49.10: 701 49.10 - 65.46: 98 65.46 - 81.83: 48 Dihedral angle restraints: 34216 sinusoidal: 13524 harmonic: 20692 Sorted by residual: dihedral pdb=" CA ASP B 41 " pdb=" C ASP B 41 " pdb=" N LYS B 42 " pdb=" CA LYS B 42 " ideal model delta harmonic sigma weight residual 180.00 151.18 28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ASP D 41 " pdb=" C ASP D 41 " pdb=" N LYS D 42 " pdb=" CA LYS D 42 " ideal model delta harmonic sigma weight residual 180.00 151.23 28.77 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA LEU H 40 " pdb=" C LEU H 40 " pdb=" N ASP H 41 " pdb=" CA ASP H 41 " ideal model delta harmonic sigma weight residual 180.00 157.19 22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 34213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 7754 0.069 - 0.137: 1166 0.137 - 0.206: 58 0.206 - 0.275: 8 0.275 - 0.343: 2 Chirality restraints: 8988 Sorted by residual: chirality pdb=" CG LEU E 40 " pdb=" CB LEU E 40 " pdb=" CD1 LEU E 40 " pdb=" CD2 LEU E 40 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CB ILE I 379 " pdb=" CA ILE I 379 " pdb=" CG1 ILE I 379 " pdb=" CG2 ILE I 379 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB ILE A 379 " pdb=" CA ILE A 379 " pdb=" CG1 ILE A 379 " pdb=" CG2 ILE A 379 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 8985 not shown) Planarity restraints: 9618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU M 524 " -0.080 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO M 525 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO M 525 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO M 525 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP K 328 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C ASP K 328 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP K 328 " 0.016 2.00e-02 2.50e+03 pdb=" N THR K 329 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA N 96 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.50e+00 pdb=" C ALA N 96 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA N 96 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN N 97 " 0.014 2.00e-02 2.50e+03 ... (remaining 9615 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 2940 2.72 - 3.26: 59389 3.26 - 3.81: 97677 3.81 - 4.35: 114461 4.35 - 4.90: 190691 Nonbonded interactions: 465158 Sorted by model distance: nonbonded pdb=" ND2 ASN G 112 " pdb=" OD1 ASP G 115 " model vdw 2.174 2.520 nonbonded pdb=" ND2 ASN E 112 " pdb=" OD2 ASP E 115 " model vdw 2.175 2.520 nonbonded pdb=" OG1 THR J 90 " pdb=" O1G ATP J 601 " model vdw 2.197 2.440 nonbonded pdb=" OG1 THR N 90 " pdb=" O1G ATP N 601 " model vdw 2.201 2.440 nonbonded pdb=" O ARG F 421 " pdb=" OG SER F 424 " model vdw 2.209 2.440 ... (remaining 465153 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.090 Check model and map are aligned: 0.590 Set scattering table: 0.360 Process input model: 113.010 Find NCS groups from input model: 3.400 Set up NCS constraints: 0.430 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 0.098 54789 Z= 0.297 Angle : 0.765 16.140 74074 Z= 0.418 Chirality : 0.047 0.343 8988 Planarity : 0.005 0.117 9618 Dihedral : 13.605 81.827 20944 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: 0.34 (0.09), residues: 7308 helix: 0.89 (0.08), residues: 4025 sheet: -0.26 (0.15), residues: 1064 loop : -0.57 (0.12), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS K 401 PHE 0.029 0.002 PHE A 44 TYR 0.012 0.001 TYR L 478 ARG 0.020 0.001 ARG I 445 *********************** 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 554 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 554 time to evaluate : 4.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8797 (pmm) cc_final: 0.7813 (pmm) REVERT: A 100 ILE cc_start: 0.9133 (tp) cc_final: 0.8908 (tp) REVERT: G 49 ILE cc_start: 0.9038 (mt) cc_final: 0.8827 (mt) REVERT: G 69 MET cc_start: 0.7795 (mtt) cc_final: 0.7505 (mtt) REVERT: G 419 LEU cc_start: 0.8776 (tp) cc_final: 0.8528 (tt) REVERT: B 69 MET cc_start: 0.7599 (mtm) cc_final: 0.7375 (mtt) REVERT: B 120 ILE cc_start: 0.9383 (mt) cc_final: 0.9155 (tp) REVERT: B 447 MET cc_start: 0.8035 (ptm) cc_final: 0.7813 (ptm) REVERT: B 520 MET cc_start: 0.7713 (tpp) cc_final: 0.7398 (tpp) REVERT: C 390 LYS cc_start: 0.8661 (pttp) cc_final: 0.7475 (pttm) REVERT: C 478 TYR cc_start: 0.7718 (t80) cc_final: 0.7430 (t80) REVERT: D 100 ILE cc_start: 0.9081 (tp) cc_final: 0.8842 (tp) REVERT: D 513 LEU cc_start: 0.8631 (mm) cc_final: 0.7884 (tp) REVERT: E 162 ILE cc_start: 0.9488 (mm) cc_final: 0.9178 (tt) REVERT: I 111 MET cc_start: 0.7100 (ptp) cc_final: 0.6813 (mpp) REVERT: I 307 MET cc_start: 0.5589 (tmm) cc_final: 0.4870 (tpp) REVERT: I 524 LEU cc_start: 0.8499 (tp) cc_final: 0.8187 (tp) REVERT: J 162 ILE cc_start: 0.9202 (mm) cc_final: 0.8912 (tt) REVERT: J 389 MET cc_start: 0.7066 (mmt) cc_final: 0.6623 (mmm) REVERT: K 16 MET cc_start: 0.8513 (ptp) cc_final: 0.7850 (ptp) REVERT: K 100 ILE cc_start: 0.9224 (tp) cc_final: 0.8981 (tp) REVERT: K 267 MET cc_start: 0.1188 (ptt) cc_final: 0.0913 (ppp) REVERT: K 520 MET cc_start: 0.7873 (ttt) cc_final: 0.7286 (ttt) REVERT: L 49 ILE cc_start: 0.8791 (mt) cc_final: 0.8450 (mt) REVERT: L 97 GLN cc_start: 0.8858 (tt0) cc_final: 0.8528 (tt0) REVERT: L 389 MET cc_start: 0.6886 (mmm) cc_final: 0.6119 (mmm) REVERT: L 390 LYS cc_start: 0.7775 (pttp) cc_final: 0.7567 (mmtt) REVERT: M 69 MET cc_start: 0.8123 (ttp) cc_final: 0.7868 (ttp) REVERT: M 100 ILE cc_start: 0.9211 (tp) cc_final: 0.8874 (tp) REVERT: M 401 HIS cc_start: 0.8808 (t-90) cc_final: 0.8421 (t70) REVERT: N 111 MET cc_start: 0.7799 (tpt) cc_final: 0.7124 (tpt) REVERT: N 193 MET cc_start: 0.5989 (mmp) cc_final: 0.5464 (mmm) REVERT: N 390 LYS cc_start: 0.8160 (pttm) cc_final: 0.7664 (pttm) outliers start: 0 outliers final: 0 residues processed: 554 average time/residue: 0.4786 time to fit residues: 464.2444 Evaluate side-chains 450 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 450 time to evaluate : 4.553 ------------------------------------------------------------------------------- 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: 5.9990 chunk 188 optimal weight: 4.9990 chunk 372 optimal weight: 0.9990 chunk 294 optimal weight: 20.0000 chunk 570 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 chunk 346 optimal weight: 50.0000 chunk 424 optimal weight: 1.9990 chunk 661 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 GLN ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 290 GLN ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 457 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: 0.7869 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 54789 Z= 0.243 Angle : 0.552 11.377 74074 Z= 0.296 Chirality : 0.041 0.158 8988 Planarity : 0.003 0.061 9618 Dihedral : 7.757 86.091 8204 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.18 % Allowed : 4.93 % Favored : 94.90 % 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: 0.74 (0.10), residues: 7308 helix: 1.33 (0.08), residues: 3997 sheet: -0.18 (0.15), residues: 1190 loop : -0.58 (0.12), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 401 PHE 0.010 0.001 PHE D 66 TYR 0.011 0.001 TYR L 478 ARG 0.006 0.000 ARG L 452 *********************** 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 532 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 522 time to evaluate : 4.559 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 16 MET cc_start: 0.8859 (pmm) cc_final: 0.8368 (pmm) REVERT: B 17 LEU cc_start: 0.9252 (tp) cc_final: 0.9032 (tp) REVERT: B 69 MET cc_start: 0.7473 (mtm) cc_final: 0.7228 (mtt) REVERT: C 111 MET cc_start: 0.7211 (tpt) cc_final: 0.6970 (tpp) REVERT: C 513 LEU cc_start: 0.8866 (tp) cc_final: 0.8646 (tp) REVERT: D 100 ILE cc_start: 0.8898 (tp) cc_final: 0.8595 (tp) REVERT: D 447 MET cc_start: 0.8418 (ptm) cc_final: 0.8111 (ptp) REVERT: D 513 LEU cc_start: 0.8689 (mm) cc_final: 0.7861 (tp) REVERT: E 111 MET cc_start: 0.7552 (tpp) cc_final: 0.7323 (tpp) REVERT: H 389 MET cc_start: 0.7612 (mmm) cc_final: 0.7325 (mmm) REVERT: H 390 LYS cc_start: 0.8457 (pttt) cc_final: 0.8211 (pttp) REVERT: I 17 LEU cc_start: 0.9404 (tp) cc_final: 0.9186 (tp) REVERT: I 73 MET cc_start: 0.7476 (mtm) cc_final: 0.7258 (mtm) REVERT: I 307 MET cc_start: 0.5461 (tmm) cc_final: 0.4766 (tpp) REVERT: J 73 MET cc_start: 0.7643 (mtp) cc_final: 0.7374 (mtt) REVERT: J 162 ILE cc_start: 0.9262 (mm) cc_final: 0.8914 (tt) REVERT: J 389 MET cc_start: 0.7045 (mmt) cc_final: 0.6803 (mmm) REVERT: K 16 MET cc_start: 0.8530 (ptp) cc_final: 0.7869 (ptp) REVERT: K 17 LEU cc_start: 0.9408 (tp) cc_final: 0.9170 (tp) REVERT: K 100 ILE cc_start: 0.9204 (tp) cc_final: 0.8901 (tp) REVERT: K 520 MET cc_start: 0.7471 (ttt) cc_final: 0.7268 (ttt) REVERT: L 69 MET cc_start: 0.8388 (ttm) cc_final: 0.7770 (mtm) REVERT: L 97 GLN cc_start: 0.8939 (tt0) cc_final: 0.8624 (tt0) REVERT: L 193 MET cc_start: 0.6711 (tpt) cc_final: 0.5248 (mmm) REVERT: L 389 MET cc_start: 0.7073 (mmm) cc_final: 0.6721 (mmm) REVERT: L 390 LYS cc_start: 0.7763 (pttp) cc_final: 0.7478 (mmtt) REVERT: M 61 GLU cc_start: 0.7566 (pt0) cc_final: 0.7252 (pt0) REVERT: M 100 ILE cc_start: 0.9265 (tp) cc_final: 0.8979 (tp) REVERT: M 401 HIS cc_start: 0.8903 (t-90) cc_final: 0.8582 (t-170) REVERT: N 193 MET cc_start: 0.5985 (mmp) cc_final: 0.5453 (mmm) REVERT: N 390 LYS cc_start: 0.8176 (pttm) cc_final: 0.7713 (pttm) REVERT: N 488 MET cc_start: 0.7879 (mmp) cc_final: 0.7358 (mmt) outliers start: 10 outliers final: 0 residues processed: 531 average time/residue: 0.4818 time to fit residues: 452.1283 Evaluate side-chains 441 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 4.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 0.9980 chunk 205 optimal weight: 10.0000 chunk 550 optimal weight: 20.0000 chunk 450 optimal weight: 20.0000 chunk 182 optimal weight: 6.9990 chunk 662 optimal weight: 1.9990 chunk 715 optimal weight: 5.9990 chunk 589 optimal weight: 7.9990 chunk 656 optimal weight: 4.9990 chunk 225 optimal weight: 30.0000 chunk 531 optimal weight: 0.8980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 GLN ** I 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 457 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: 0.7881 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 54789 Z= 0.247 Angle : 0.557 9.979 74074 Z= 0.297 Chirality : 0.042 0.187 8988 Planarity : 0.003 0.061 9618 Dihedral : 7.532 87.096 8204 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.11 % Allowed : 4.31 % Favored : 95.59 % 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: 0.78 (0.10), residues: 7308 helix: 1.39 (0.08), residues: 3983 sheet: -0.19 (0.15), residues: 1190 loop : -0.59 (0.12), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 401 PHE 0.012 0.001 PHE C 195 TYR 0.009 0.001 TYR D 506 ARG 0.009 0.000 ARG B 445 *********************** 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 521 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 515 time to evaluate : 4.616 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 16 MET cc_start: 0.8750 (pmm) cc_final: 0.8303 (pmm) REVERT: G 111 MET cc_start: 0.7400 (tpt) cc_final: 0.7050 (tpp) REVERT: B 17 LEU cc_start: 0.9284 (tp) cc_final: 0.9066 (tp) REVERT: B 524 LEU cc_start: 0.8164 (tp) cc_final: 0.7963 (tp) REVERT: C 111 MET cc_start: 0.7191 (tpt) cc_final: 0.6962 (tpp) REVERT: D 69 MET cc_start: 0.7876 (ttm) cc_final: 0.7639 (ttm) REVERT: D 100 ILE cc_start: 0.9040 (tp) cc_final: 0.8641 (tp) REVERT: D 447 MET cc_start: 0.8421 (ptm) cc_final: 0.7946 (ptp) REVERT: D 513 LEU cc_start: 0.8716 (mm) cc_final: 0.7909 (tp) REVERT: E 166 MET cc_start: 0.9147 (tmm) cc_final: 0.8900 (tmm) REVERT: F 100 ILE cc_start: 0.9357 (tp) cc_final: 0.8974 (tt) REVERT: H 389 MET cc_start: 0.7762 (mmm) cc_final: 0.7541 (mmm) REVERT: I 307 MET cc_start: 0.5332 (tmm) cc_final: 0.4654 (tpp) REVERT: J 162 ILE cc_start: 0.9270 (mm) cc_final: 0.8905 (tt) REVERT: K 16 MET cc_start: 0.8494 (ptp) cc_final: 0.7696 (ptp) REVERT: K 17 LEU cc_start: 0.9432 (tp) cc_final: 0.9221 (tp) REVERT: K 100 ILE cc_start: 0.9178 (tp) cc_final: 0.8902 (tp) REVERT: K 267 MET cc_start: 0.0915 (ptt) cc_final: 0.0629 (ppp) REVERT: K 520 MET cc_start: 0.7611 (ttt) cc_final: 0.7317 (ttt) REVERT: L 97 GLN cc_start: 0.8960 (tt0) cc_final: 0.8702 (tt0) REVERT: L 111 MET cc_start: 0.7154 (tpt) cc_final: 0.6925 (tpp) REVERT: L 193 MET cc_start: 0.6631 (tpt) cc_final: 0.5455 (mmm) REVERT: L 390 LYS cc_start: 0.7852 (pttp) cc_final: 0.7529 (mmtt) REVERT: L 514 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8080 (tmm) REVERT: M 16 MET cc_start: 0.8927 (pmm) cc_final: 0.8662 (pmm) REVERT: M 100 ILE cc_start: 0.9261 (tp) cc_final: 0.9003 (tp) REVERT: M 401 HIS cc_start: 0.8908 (t-90) cc_final: 0.8537 (t-170) REVERT: M 447 MET cc_start: 0.8215 (ppp) cc_final: 0.7263 (ppp) REVERT: N 193 MET cc_start: 0.6150 (mmp) cc_final: 0.5595 (mmm) REVERT: N 488 MET cc_start: 0.8026 (mmp) cc_final: 0.7405 (mmp) outliers start: 6 outliers final: 0 residues processed: 518 average time/residue: 0.4851 time to fit residues: 443.5528 Evaluate side-chains 442 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 441 time to evaluate : 4.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 50.0000 chunk 497 optimal weight: 20.0000 chunk 343 optimal weight: 50.0000 chunk 73 optimal weight: 7.9990 chunk 316 optimal weight: 0.9990 chunk 444 optimal weight: 6.9990 chunk 664 optimal weight: 7.9990 chunk 703 optimal weight: 5.9990 chunk 347 optimal weight: 40.0000 chunk 629 optimal weight: 4.9990 chunk 189 optimal weight: 0.0770 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 ASN ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 GLN ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 GLN ** F 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 194 GLN ** N 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 : 0.004 0.051 54789 Z= 0.285 Angle : 0.577 10.530 74074 Z= 0.309 Chirality : 0.042 0.220 8988 Planarity : 0.004 0.067 9618 Dihedral : 7.304 87.545 8204 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.24 % 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: 1.38 (0.08), residues: 4032 sheet: -0.23 (0.15), residues: 1190 loop : -0.64 (0.12), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 401 PHE 0.010 0.001 PHE B 66 TYR 0.011 0.001 TYR K 506 ARG 0.013 0.001 ARG M 445 *********************** 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 499 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 497 time to evaluate : 4.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 MET cc_start: 0.8428 (ptm) cc_final: 0.8169 (ptm) REVERT: G 111 MET cc_start: 0.7438 (tpt) cc_final: 0.7233 (tpp) REVERT: G 115 ASP cc_start: 0.7735 (m-30) cc_final: 0.7424 (m-30) REVERT: B 17 LEU cc_start: 0.9300 (tp) cc_final: 0.9094 (tp) REVERT: B 69 MET cc_start: 0.7535 (mtm) cc_final: 0.7317 (mtt) REVERT: B 111 MET cc_start: 0.7389 (mpp) cc_final: 0.7154 (mpp) REVERT: B 447 MET cc_start: 0.8344 (ptm) cc_final: 0.8046 (ptm) REVERT: B 524 LEU cc_start: 0.8241 (tp) cc_final: 0.7973 (tp) REVERT: C 111 MET cc_start: 0.7079 (tpt) cc_final: 0.6856 (tpp) REVERT: D 513 LEU cc_start: 0.8777 (mm) cc_final: 0.8017 (tp) REVERT: E 111 MET cc_start: 0.7487 (tpp) cc_final: 0.7262 (tpp) REVERT: E 166 MET cc_start: 0.9196 (tmm) cc_final: 0.8944 (tmm) REVERT: F 16 MET cc_start: 0.8345 (ppp) cc_final: 0.8128 (ppp) REVERT: F 67 GLU cc_start: 0.8453 (mp0) cc_final: 0.8116 (mp0) REVERT: H 389 MET cc_start: 0.7889 (mmm) cc_final: 0.7623 (mmm) REVERT: I 307 MET cc_start: 0.5337 (tmm) cc_final: 0.4668 (tpp) REVERT: I 389 MET cc_start: 0.2491 (tpp) cc_final: 0.2280 (mmm) REVERT: K 16 MET cc_start: 0.8488 (ptp) cc_final: 0.7222 (ptp) REVERT: K 17 LEU cc_start: 0.9485 (tp) cc_final: 0.9264 (tp) REVERT: K 100 ILE cc_start: 0.9149 (tp) cc_final: 0.8917 (tp) REVERT: K 520 MET cc_start: 0.7177 (ttt) cc_final: 0.6587 (ttt) REVERT: L 193 MET cc_start: 0.6924 (tpt) cc_final: 0.6332 (tpp) REVERT: L 389 MET cc_start: 0.7016 (mmm) cc_final: 0.5906 (mmm) REVERT: L 390 LYS cc_start: 0.7926 (pttp) cc_final: 0.7627 (mmtt) REVERT: M 100 ILE cc_start: 0.9298 (tp) cc_final: 0.9030 (tp) REVERT: M 401 HIS cc_start: 0.8917 (t-90) cc_final: 0.8459 (t-170) REVERT: N 111 MET cc_start: 0.7717 (tpt) cc_final: 0.7469 (tpp) REVERT: N 193 MET cc_start: 0.6383 (mmp) cc_final: 0.6159 (mmm) REVERT: N 390 LYS cc_start: 0.8180 (pttm) cc_final: 0.7779 (pttm) REVERT: N 488 MET cc_start: 0.8151 (mmp) cc_final: 0.7628 (mmp) outliers start: 2 outliers final: 1 residues processed: 499 average time/residue: 0.4766 time to fit residues: 420.0905 Evaluate side-chains 439 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 438 time to evaluate : 4.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 10.0000 chunk 399 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 523 optimal weight: 3.9990 chunk 290 optimal weight: 1.9990 chunk 600 optimal weight: 2.9990 chunk 486 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 359 optimal weight: 2.9990 chunk 631 optimal weight: 1.9990 chunk 177 optimal weight: 50.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 194 GLN ** N 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 54789 Z= 0.225 Angle : 0.541 10.069 74074 Z= 0.288 Chirality : 0.042 0.204 8988 Planarity : 0.003 0.063 9618 Dihedral : 7.166 88.762 8204 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.02 % Allowed : 2.50 % Favored : 97.48 % 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: 0.93 (0.10), residues: 7308 helix: 1.52 (0.08), residues: 3990 sheet: -0.18 (0.15), residues: 1204 loop : -0.50 (0.12), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 401 PHE 0.008 0.001 PHE C 195 TYR 0.008 0.001 TYR K 506 ARG 0.013 0.000 ARG D 445 *********************** 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 513 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 512 time to evaluate : 4.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8734 (pmm) cc_final: 0.8123 (pmm) REVERT: A 67 GLU cc_start: 0.8497 (mp0) cc_final: 0.8251 (mp0) REVERT: G 288 MET cc_start: 0.4577 (mmt) cc_final: 0.4268 (mmt) REVERT: B 16 MET cc_start: 0.8652 (ppp) cc_final: 0.8414 (ppp) REVERT: B 17 LEU cc_start: 0.9291 (tp) cc_final: 0.9038 (tp) REVERT: C 513 LEU cc_start: 0.8828 (tp) cc_final: 0.8606 (tp) REVERT: D 513 LEU cc_start: 0.8743 (mm) cc_final: 0.7955 (tp) REVERT: E 111 MET cc_start: 0.7492 (tpp) cc_final: 0.7192 (tpp) REVERT: E 166 MET cc_start: 0.9181 (tmm) cc_final: 0.8953 (tmm) REVERT: F 16 MET cc_start: 0.8395 (ppp) cc_final: 0.7852 (ppp) REVERT: F 67 GLU cc_start: 0.8366 (mp0) cc_final: 0.7958 (mp0) REVERT: H 389 MET cc_start: 0.7816 (mmm) cc_final: 0.7521 (mmm) REVERT: I 307 MET cc_start: 0.5342 (tmm) cc_final: 0.4705 (tpp) REVERT: I 447 MET cc_start: 0.8719 (ptm) cc_final: 0.8427 (ptm) REVERT: J 40 LEU cc_start: 0.8703 (mm) cc_final: 0.8335 (mm) REVERT: K 16 MET cc_start: 0.8551 (ptp) cc_final: 0.7337 (ptp) REVERT: K 17 LEU cc_start: 0.9483 (tp) cc_final: 0.9270 (tp) REVERT: K 100 ILE cc_start: 0.9153 (tp) cc_final: 0.8855 (tp) REVERT: K 267 MET cc_start: 0.1375 (ptt) cc_final: 0.1066 (ppp) REVERT: L 16 MET cc_start: 0.8453 (ttp) cc_final: 0.8235 (ttm) REVERT: L 111 MET cc_start: 0.7279 (tpt) cc_final: 0.6895 (tpp) REVERT: L 166 MET cc_start: 0.8834 (mmm) cc_final: 0.8437 (mmm) REVERT: L 193 MET cc_start: 0.6967 (tpt) cc_final: 0.6428 (tpp) REVERT: L 385 THR cc_start: 0.8177 (p) cc_final: 0.7845 (p) REVERT: L 389 MET cc_start: 0.6977 (mmm) cc_final: 0.5849 (mmm) REVERT: L 390 LYS cc_start: 0.7933 (pttp) cc_final: 0.7639 (mmtt) REVERT: L 488 MET cc_start: 0.8353 (mmp) cc_final: 0.7997 (mmt) REVERT: M 100 ILE cc_start: 0.9235 (tp) cc_final: 0.8883 (tp) REVERT: M 401 HIS cc_start: 0.8907 (t-90) cc_final: 0.8394 (t-170) REVERT: M 447 MET cc_start: 0.8391 (ptm) cc_final: 0.7531 (ptm) REVERT: N 193 MET cc_start: 0.6318 (mmp) cc_final: 0.6011 (mmm) REVERT: N 194 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7779 (pm20) REVERT: N 390 LYS cc_start: 0.8126 (pttm) cc_final: 0.7608 (pttm) outliers start: 1 outliers final: 0 residues processed: 512 average time/residue: 0.4820 time to fit residues: 435.1983 Evaluate side-chains 443 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 442 time to evaluate : 4.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 1.9990 chunk 633 optimal weight: 0.8980 chunk 139 optimal weight: 40.0000 chunk 413 optimal weight: 6.9990 chunk 173 optimal weight: 20.0000 chunk 704 optimal weight: 6.9990 chunk 584 optimal weight: 0.7980 chunk 326 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 369 optimal weight: 2.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 194 GLN ** N 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 54789 Z= 0.234 Angle : 0.551 8.788 74074 Z= 0.293 Chirality : 0.042 0.180 8988 Planarity : 0.003 0.063 9618 Dihedral : 7.072 89.470 8204 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.02 % Allowed : 1.99 % Favored : 98.00 % 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: 0.94 (0.10), residues: 7308 helix: 1.51 (0.08), residues: 3990 sheet: -0.18 (0.15), residues: 1204 loop : -0.48 (0.12), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 401 PHE 0.011 0.001 PHE D 66 TYR 0.008 0.001 TYR D 506 ARG 0.007 0.000 ARG D 445 *********************** 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 513 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 512 time to evaluate : 5.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8663 (pmm) cc_final: 0.8101 (pmm) REVERT: A 67 GLU cc_start: 0.8483 (mp0) cc_final: 0.8207 (mp0) REVERT: G 111 MET cc_start: 0.7226 (tpt) cc_final: 0.6963 (tpp) REVERT: G 288 MET cc_start: 0.4302 (mmt) cc_final: 0.4014 (mmt) REVERT: C 513 LEU cc_start: 0.8759 (tp) cc_final: 0.8502 (tp) REVERT: D 100 ILE cc_start: 0.9030 (tp) cc_final: 0.8695 (tp) REVERT: D 513 LEU cc_start: 0.8764 (mm) cc_final: 0.7984 (tp) REVERT: E 111 MET cc_start: 0.7645 (tpp) cc_final: 0.7321 (tpp) REVERT: E 166 MET cc_start: 0.9199 (tmm) cc_final: 0.8993 (tmm) REVERT: F 67 GLU cc_start: 0.8286 (mp0) cc_final: 0.7869 (mp0) REVERT: F 447 MET cc_start: 0.8240 (ptt) cc_final: 0.7861 (ppp) REVERT: H 389 MET cc_start: 0.7733 (mmm) cc_final: 0.7429 (mmm) REVERT: H 513 LEU cc_start: 0.9032 (tp) cc_final: 0.8713 (tp) REVERT: I 307 MET cc_start: 0.5249 (tmm) cc_final: 0.4654 (tpp) REVERT: I 447 MET cc_start: 0.8677 (ptm) cc_final: 0.8441 (ptp) REVERT: J 115 ASP cc_start: 0.7519 (m-30) cc_final: 0.7080 (m-30) REVERT: K 16 MET cc_start: 0.8576 (ptp) cc_final: 0.7834 (ptp) REVERT: K 17 LEU cc_start: 0.9492 (tp) cc_final: 0.9285 (tp) REVERT: K 100 ILE cc_start: 0.9198 (tp) cc_final: 0.8979 (tp) REVERT: K 267 MET cc_start: 0.1277 (ptt) cc_final: 0.0972 (ppp) REVERT: K 520 MET cc_start: 0.7473 (ttt) cc_final: 0.6806 (ttt) REVERT: L 97 GLN cc_start: 0.8875 (tt0) cc_final: 0.8666 (tt0) REVERT: L 111 MET cc_start: 0.7282 (tpt) cc_final: 0.6951 (tpp) REVERT: L 166 MET cc_start: 0.8782 (mmm) cc_final: 0.8482 (mmm) REVERT: L 193 MET cc_start: 0.6920 (tpt) cc_final: 0.6352 (tpp) REVERT: L 389 MET cc_start: 0.6950 (mmm) cc_final: 0.6727 (mmm) REVERT: M 401 HIS cc_start: 0.8899 (t-90) cc_final: 0.8541 (t70) REVERT: N 193 MET cc_start: 0.6401 (mmp) cc_final: 0.6021 (mmm) REVERT: N 194 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7825 (pm20) REVERT: N 390 LYS cc_start: 0.8165 (pttm) cc_final: 0.7785 (pttp) outliers start: 1 outliers final: 0 residues processed: 513 average time/residue: 0.4787 time to fit residues: 431.4706 Evaluate side-chains 441 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 440 time to evaluate : 4.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 0.8980 chunk 79 optimal weight: 30.0000 chunk 401 optimal weight: 0.2980 chunk 514 optimal weight: 6.9990 chunk 398 optimal weight: 5.9990 chunk 592 optimal weight: 0.0870 chunk 393 optimal weight: 9.9990 chunk 701 optimal weight: 8.9990 chunk 439 optimal weight: 6.9990 chunk 427 optimal weight: 2.9990 chunk 323 optimal weight: 0.9980 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** D 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 146 GLN N 194 GLN ** N 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 54789 Z= 0.168 Angle : 0.538 11.949 74074 Z= 0.282 Chirality : 0.041 0.151 8988 Planarity : 0.003 0.059 9618 Dihedral : 6.956 89.964 8204 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.02 % Allowed : 1.28 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.10), residues: 7308 helix: 1.56 (0.08), residues: 3997 sheet: -0.13 (0.15), residues: 1204 loop : -0.43 (0.13), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 401 PHE 0.009 0.001 PHE K 195 TYR 0.007 0.001 TYR L 478 ARG 0.019 0.000 ARG D 445 *********************** 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 520 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 519 time to evaluate : 4.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8576 (mp0) cc_final: 0.8170 (mp0) REVERT: A 447 MET cc_start: 0.8316 (ptm) cc_final: 0.7833 (ptm) REVERT: G 40 LEU cc_start: 0.8870 (mt) cc_final: 0.8630 (tt) REVERT: C 513 LEU cc_start: 0.8691 (tp) cc_final: 0.8425 (tp) REVERT: D 513 LEU cc_start: 0.8602 (mm) cc_final: 0.7847 (tp) REVERT: E 69 MET cc_start: 0.7478 (mtm) cc_final: 0.7193 (mtm) REVERT: E 111 MET cc_start: 0.7631 (tpp) cc_final: 0.7365 (tpp) REVERT: E 488 MET cc_start: 0.8526 (mmm) cc_final: 0.8144 (mmm) REVERT: F 67 GLU cc_start: 0.8298 (mp0) cc_final: 0.7974 (mp0) REVERT: F 447 MET cc_start: 0.8133 (ptt) cc_final: 0.7822 (ppp) REVERT: H 389 MET cc_start: 0.7730 (mmm) cc_final: 0.7057 (mmm) REVERT: H 488 MET cc_start: 0.7492 (mmt) cc_final: 0.7240 (mmt) REVERT: I 307 MET cc_start: 0.5181 (tmm) cc_final: 0.4557 (tpp) REVERT: I 447 MET cc_start: 0.8555 (ptm) cc_final: 0.8136 (ptm) REVERT: J 111 MET cc_start: 0.7284 (tpt) cc_final: 0.6923 (tpp) REVERT: J 115 ASP cc_start: 0.7458 (m-30) cc_final: 0.7127 (m-30) REVERT: K 16 MET cc_start: 0.8572 (ptp) cc_final: 0.7800 (ptp) REVERT: K 100 ILE cc_start: 0.9216 (tp) cc_final: 0.8849 (tp) REVERT: K 520 MET cc_start: 0.7719 (ttt) cc_final: 0.7196 (ttt) REVERT: L 111 MET cc_start: 0.7225 (tpt) cc_final: 0.7021 (tpp) REVERT: L 166 MET cc_start: 0.8855 (mmm) cc_final: 0.8507 (mmm) REVERT: L 193 MET cc_start: 0.6827 (tpt) cc_final: 0.6292 (tpp) REVERT: L 390 LYS cc_start: 0.7847 (pttp) cc_final: 0.7638 (mmtt) REVERT: L 488 MET cc_start: 0.8137 (mmp) cc_final: 0.7780 (mmt) REVERT: M 61 GLU cc_start: 0.7327 (pt0) cc_final: 0.7018 (pt0) REVERT: M 401 HIS cc_start: 0.8874 (t-90) cc_final: 0.8327 (t-90) REVERT: M 447 MET cc_start: 0.8074 (ptm) cc_final: 0.6790 (ppp) REVERT: N 114 MET cc_start: 0.8439 (pmm) cc_final: 0.8221 (pmm) REVERT: N 390 LYS cc_start: 0.8154 (pttm) cc_final: 0.7734 (pttp) outliers start: 1 outliers final: 0 residues processed: 520 average time/residue: 0.4767 time to fit residues: 435.0804 Evaluate side-chains 439 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 439 time to evaluate : 4.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 5.9990 chunk 280 optimal weight: 7.9990 chunk 419 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 137 optimal weight: 40.0000 chunk 135 optimal weight: 3.9990 chunk 446 optimal weight: 10.0000 chunk 478 optimal weight: 0.9980 chunk 346 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 551 optimal weight: 30.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 ASN ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 505 GLN N 194 GLN ** 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: 0.7894 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 54789 Z= 0.234 Angle : 0.556 9.409 74074 Z= 0.293 Chirality : 0.042 0.169 8988 Planarity : 0.003 0.060 9618 Dihedral : 6.881 89.510 8204 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.10), residues: 7308 helix: 1.59 (0.08), residues: 4004 sheet: -0.14 (0.15), residues: 1204 loop : -0.40 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS K 401 PHE 0.009 0.001 PHE D 66 TYR 0.009 0.001 TYR D 506 ARG 0.018 0.000 ARG D 445 *********************** 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 505 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 4.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8562 (mp0) cc_final: 0.8148 (mp0) REVERT: A 447 MET cc_start: 0.8447 (ptm) cc_final: 0.7707 (ptm) REVERT: G 111 MET cc_start: 0.7383 (tpt) cc_final: 0.7137 (tpp) REVERT: C 111 MET cc_start: 0.6936 (tpt) cc_final: 0.6657 (tpp) REVERT: C 513 LEU cc_start: 0.8655 (tp) cc_final: 0.8379 (tp) REVERT: D 447 MET cc_start: 0.8384 (ptm) cc_final: 0.7289 (ttp) REVERT: D 513 LEU cc_start: 0.8578 (mm) cc_final: 0.7916 (tp) REVERT: E 111 MET cc_start: 0.7594 (tpp) cc_final: 0.7362 (tpp) REVERT: E 488 MET cc_start: 0.8441 (mmm) cc_final: 0.8130 (mmm) REVERT: F 16 MET cc_start: 0.7818 (ppp) cc_final: 0.7422 (ppp) REVERT: F 67 GLU cc_start: 0.8362 (mp0) cc_final: 0.7819 (mp0) REVERT: H 389 MET cc_start: 0.7680 (mmm) cc_final: 0.7340 (mmm) REVERT: H 488 MET cc_start: 0.7559 (mmt) cc_final: 0.7258 (mmt) REVERT: I 307 MET cc_start: 0.5238 (tmm) cc_final: 0.4625 (tpp) REVERT: I 447 MET cc_start: 0.8630 (ptm) cc_final: 0.8236 (ptm) REVERT: J 40 LEU cc_start: 0.8763 (mt) cc_final: 0.8260 (mt) REVERT: J 115 ASP cc_start: 0.7523 (m-30) cc_final: 0.7285 (m-30) REVERT: K 16 MET cc_start: 0.8538 (ptp) cc_final: 0.7761 (ptp) REVERT: K 17 LEU cc_start: 0.9460 (tp) cc_final: 0.9254 (tp) REVERT: K 267 MET cc_start: 0.1490 (ptt) cc_final: 0.1206 (ppp) REVERT: K 520 MET cc_start: 0.7387 (ttt) cc_final: 0.6704 (ttt) REVERT: L 115 ASP cc_start: 0.7567 (m-30) cc_final: 0.7309 (m-30) REVERT: L 166 MET cc_start: 0.8825 (mmm) cc_final: 0.8534 (mmm) REVERT: L 193 MET cc_start: 0.6942 (tpt) cc_final: 0.6420 (tpp) REVERT: M 100 ILE cc_start: 0.9227 (tp) cc_final: 0.8800 (tp) REVERT: M 401 HIS cc_start: 0.8899 (t-90) cc_final: 0.8407 (t70) REVERT: M 447 MET cc_start: 0.8252 (ptm) cc_final: 0.6909 (ppp) REVERT: N 111 MET cc_start: 0.7755 (tpt) cc_final: 0.7236 (tpt) REVERT: N 193 MET cc_start: 0.7116 (mmm) cc_final: 0.6576 (mmm) REVERT: N 390 LYS cc_start: 0.8149 (pttm) cc_final: 0.7790 (pttp) REVERT: N 523 ASP cc_start: 0.6676 (m-30) cc_final: 0.6164 (t70) outliers start: 0 outliers final: 0 residues processed: 505 average time/residue: 0.4809 time to fit residues: 426.1606 Evaluate side-chains 439 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 439 time to evaluate : 4.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 10.0000 chunk 672 optimal weight: 3.9990 chunk 613 optimal weight: 0.9990 chunk 653 optimal weight: 50.0000 chunk 393 optimal weight: 50.0000 chunk 284 optimal weight: 30.0000 chunk 513 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 590 optimal weight: 6.9990 chunk 618 optimal weight: 2.9990 chunk 651 optimal weight: 30.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 505 GLN N 194 GLN ** 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: 0.7884 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 54789 Z= 0.215 Angle : 0.566 13.099 74074 Z= 0.299 Chirality : 0.042 0.247 8988 Planarity : 0.003 0.058 9618 Dihedral : 6.846 89.989 8204 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.02 % Allowed : 0.74 % Favored : 99.24 % 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: 1.02 (0.10), residues: 7308 helix: 1.54 (0.08), residues: 4004 sheet: -0.15 (0.15), residues: 1204 loop : -0.38 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 401 PHE 0.009 0.001 PHE D 66 TYR 0.009 0.001 TYR L 478 ARG 0.022 0.000 ARG M 445 *********************** 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 499 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 498 time to evaluate : 4.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8784 (pmm) cc_final: 0.7822 (pmm) REVERT: A 67 GLU cc_start: 0.8601 (mp0) cc_final: 0.8140 (mp0) REVERT: A 447 MET cc_start: 0.8376 (ptm) cc_final: 0.7722 (ptm) REVERT: G 111 MET cc_start: 0.7445 (tpt) cc_final: 0.7146 (tpp) REVERT: C 111 MET cc_start: 0.6911 (tpt) cc_final: 0.6706 (tpp) REVERT: C 513 LEU cc_start: 0.8644 (tp) cc_final: 0.8394 (tp) REVERT: D 447 MET cc_start: 0.8405 (ptm) cc_final: 0.7325 (ttp) REVERT: D 513 LEU cc_start: 0.8443 (mm) cc_final: 0.7868 (tp) REVERT: E 111 MET cc_start: 0.7617 (tpp) cc_final: 0.7414 (tpp) REVERT: E 488 MET cc_start: 0.8362 (mmm) cc_final: 0.8073 (mmm) REVERT: F 67 GLU cc_start: 0.8291 (mp0) cc_final: 0.7822 (mp0) REVERT: H 389 MET cc_start: 0.7704 (mmm) cc_final: 0.7363 (mmm) REVERT: I 288 MET cc_start: 0.9082 (ppp) cc_final: 0.8873 (ppp) REVERT: I 307 MET cc_start: 0.5223 (tmm) cc_final: 0.4580 (tpp) REVERT: I 447 MET cc_start: 0.8590 (ptm) cc_final: 0.8176 (ptm) REVERT: J 111 MET cc_start: 0.7261 (tpt) cc_final: 0.7038 (tpp) REVERT: K 16 MET cc_start: 0.8637 (ptp) cc_final: 0.7942 (ptp) REVERT: K 267 MET cc_start: 0.1380 (ptt) cc_final: 0.1074 (ppp) REVERT: K 520 MET cc_start: 0.7696 (ttt) cc_final: 0.7115 (ttt) REVERT: L 73 MET cc_start: 0.8114 (mtm) cc_final: 0.7737 (mtm) REVERT: L 111 MET cc_start: 0.7433 (tpt) cc_final: 0.6908 (tpp) REVERT: L 166 MET cc_start: 0.8841 (mmm) cc_final: 0.8603 (mmm) REVERT: L 193 MET cc_start: 0.6941 (tpt) cc_final: 0.6404 (tpp) REVERT: M 100 ILE cc_start: 0.9161 (tp) cc_final: 0.8919 (tp) REVERT: M 401 HIS cc_start: 0.8892 (t-90) cc_final: 0.8510 (t70) REVERT: M 447 MET cc_start: 0.8004 (ptm) cc_final: 0.6667 (ppp) REVERT: N 59 GLU cc_start: 0.7762 (mp0) cc_final: 0.7516 (mp0) REVERT: N 111 MET cc_start: 0.7743 (tpt) cc_final: 0.7449 (tpp) REVERT: N 193 MET cc_start: 0.7178 (mmm) cc_final: 0.6894 (mmm) REVERT: N 390 LYS cc_start: 0.8154 (pttm) cc_final: 0.7804 (pttp) REVERT: N 523 ASP cc_start: 0.6716 (m-30) cc_final: 0.6267 (t70) outliers start: 1 outliers final: 0 residues processed: 499 average time/residue: 0.4809 time to fit residues: 421.9822 Evaluate side-chains 434 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 434 time to evaluate : 4.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 422 optimal weight: 0.9980 chunk 328 optimal weight: 9.9990 chunk 480 optimal weight: 2.9990 chunk 725 optimal weight: 0.4980 chunk 667 optimal weight: 5.9990 chunk 577 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 446 optimal weight: 6.9990 chunk 354 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 505 GLN N 194 GLN ** 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: 0.7880 moved from start: 0.2180 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= 0.204 Angle : 0.562 13.540 74074 Z= 0.296 Chirality : 0.042 0.246 8988 Planarity : 0.003 0.059 9618 Dihedral : 6.767 89.341 8204 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: 1.05 (0.10), residues: 7308 helix: 1.56 (0.08), residues: 4004 sheet: -0.11 (0.15), residues: 1204 loop : -0.36 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 401 PHE 0.008 0.001 PHE E 66 TYR 0.011 0.001 TYR J 203 ARG 0.012 0.000 ARG M 445 ********************** 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 500 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 500 time to evaluate : 4.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8662 (mp0) cc_final: 0.8014 (mp0) REVERT: A 447 MET cc_start: 0.8355 (ptm) cc_final: 0.7704 (ptm) REVERT: A 491 MET cc_start: 0.8455 (pmm) cc_final: 0.8110 (pmm) REVERT: G 111 MET cc_start: 0.7546 (tpt) cc_final: 0.7186 (tpp) REVERT: D 69 MET cc_start: 0.7705 (mtm) cc_final: 0.7245 (mtp) REVERT: D 447 MET cc_start: 0.8371 (ptm) cc_final: 0.7285 (ttp) REVERT: D 513 LEU cc_start: 0.8449 (mm) cc_final: 0.7834 (tp) REVERT: E 488 MET cc_start: 0.8318 (mmm) cc_final: 0.7961 (mmm) REVERT: F 67 GLU cc_start: 0.8293 (mp0) cc_final: 0.7863 (mp0) REVERT: H 389 MET cc_start: 0.7630 (mmm) cc_final: 0.7288 (mmm) REVERT: I 307 MET cc_start: 0.5218 (tmm) cc_final: 0.4564 (tpp) REVERT: I 447 MET cc_start: 0.8572 (ptm) cc_final: 0.8293 (ptm) REVERT: J 16 MET cc_start: 0.8486 (ttm) cc_final: 0.8155 (ttm) REVERT: K 16 MET cc_start: 0.8616 (ptp) cc_final: 0.7540 (ptp) REVERT: K 267 MET cc_start: 0.1227 (ptt) cc_final: 0.1017 (ppp) REVERT: K 520 MET cc_start: 0.7306 (ttt) cc_final: 0.6574 (ttt) REVERT: L 73 MET cc_start: 0.8167 (mtm) cc_final: 0.7802 (mtm) REVERT: L 111 MET cc_start: 0.7518 (tpt) cc_final: 0.6901 (tpp) REVERT: L 166 MET cc_start: 0.8857 (mmm) cc_final: 0.8644 (mmm) REVERT: L 193 MET cc_start: 0.6895 (tpt) cc_final: 0.6378 (tpp) REVERT: L 390 LYS cc_start: 0.7896 (pttp) cc_final: 0.7591 (mmtt) REVERT: M 61 GLU cc_start: 0.7261 (pt0) cc_final: 0.6927 (pt0) REVERT: M 67 GLU cc_start: 0.8468 (mp0) cc_final: 0.8153 (mp0) REVERT: M 100 ILE cc_start: 0.9154 (tp) cc_final: 0.8928 (tp) REVERT: M 389 MET cc_start: 0.3789 (tpp) cc_final: 0.3503 (mmm) REVERT: M 401 HIS cc_start: 0.8891 (t-90) cc_final: 0.8506 (t70) REVERT: M 447 MET cc_start: 0.8004 (ptm) cc_final: 0.6665 (ppp) REVERT: N 111 MET cc_start: 0.7787 (tpt) cc_final: 0.7517 (tpp) REVERT: N 193 MET cc_start: 0.7244 (mmm) cc_final: 0.6893 (mmm) REVERT: N 390 LYS cc_start: 0.8145 (pttm) cc_final: 0.7723 (pttp) REVERT: N 523 ASP cc_start: 0.6744 (m-30) cc_final: 0.6309 (t70) outliers start: 0 outliers final: 0 residues processed: 500 average time/residue: 0.4823 time to fit residues: 424.7744 Evaluate side-chains 433 residues out of total 5663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 4.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 8.9990 chunk 615 optimal weight: 7.9990 chunk 176 optimal weight: 0.7980 chunk 532 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 chunk 160 optimal weight: 10.0000 chunk 578 optimal weight: 3.9990 chunk 242 optimal weight: 6.9990 chunk 593 optimal weight: 40.0000 chunk 73 optimal weight: 0.0980 chunk 106 optimal weight: 0.8980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 505 GLN N 194 GLN ** N 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.092706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.057467 restraints weight = 250401.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.059416 restraints weight = 142780.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.060679 restraints weight = 97276.357| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 54789 Z= 0.212 Angle : 0.564 9.965 74074 Z= 0.298 Chirality : 0.042 0.251 8988 Planarity : 0.003 0.060 9618 Dihedral : 6.711 89.959 8204 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.02 % Allowed : 0.18 % Favored : 99.81 % 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: 1.05 (0.10), residues: 7308 helix: 1.57 (0.08), residues: 4004 sheet: -0.13 (0.15), residues: 1204 loop : -0.34 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 401 PHE 0.008 0.001 PHE N 44 TYR 0.008 0.001 TYR L 478 ARG 0.015 0.000 ARG D 445 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8671.43 seconds wall clock time: 156 minutes 4.06 seconds (9364.06 seconds total)