Starting phenix.real_space_refine on Mon Jul 6 12:52:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eje_48101/07_2026/9eje_48101_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eje_48101/07_2026/9eje_48101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9eje_48101/07_2026/9eje_48101_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eje_48101/07_2026/9eje_48101_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eje_48101/07_2026/9eje_48101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eje_48101/07_2026/9eje_48101.map" } resolution = 4.18 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 S 114 5.16 5 C 11106 2.51 5 N 2992 2.21 5 O 3429 1.98 5 H 16340 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33985 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 5845 Classifications: {'peptide': 393} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 375} Chain: "D" Number of atoms: 5845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 5845 Classifications: {'peptide': 393} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 375} Chain: "G" Number of atoms: 5731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 5731 Classifications: {'peptide': 391} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 373} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 4, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1792 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "I" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1792 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "L" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1709 Classifications: {'peptide': 112} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "M" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1709 Classifications: {'peptide': 112} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "P" Number of atoms: 5845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 5845 Classifications: {'peptide': 393} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 375} Chain: "S" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1792 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "T" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1709 Classifications: {'peptide': 112} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.65, per 1000 atoms: 0.17 Number of scatterers: 33985 At special positions: 0 Unit cell: (146.16, 133.4, 85.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 114 16.00 O 3429 8.00 N 2992 7.00 C 11106 6.00 H 16340 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 46 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 235 " - pdb=" SG CYS A 254 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 46 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 155 " distance=2.04 Simple disulfide: pdb=" SG CYS D 196 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 207 " distance=2.03 Simple disulfide: pdb=" SG CYS D 235 " - pdb=" SG CYS D 254 " distance=2.03 Simple disulfide: pdb=" SG CYS D 343 " - pdb=" SG CYS D 369 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 46 " distance=2.03 Simple disulfide: pdb=" SG CYS G 101 " - pdb=" SG CYS G 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 150 " - pdb=" SG CYS G 155 " distance=2.04 Simple disulfide: pdb=" SG CYS G 196 " - pdb=" SG CYS G 209 " distance=2.03 Simple disulfide: pdb=" SG CYS G 198 " - pdb=" SG CYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS G 235 " - pdb=" SG CYS G 254 " distance=2.03 Simple disulfide: pdb=" SG CYS G 343 " - pdb=" SG CYS G 369 " distance=2.03 Simple disulfide: pdb=" SG CYS H 12 " - pdb=" SG CYS H 87 " distance=2.03 Simple disulfide: pdb=" SG CYS I 12 " - pdb=" SG CYS I 87 " distance=2.03 Simple disulfide: pdb=" SG CYS P 41 " - pdb=" SG CYS P 46 " distance=2.04 Simple disulfide: pdb=" SG CYS P 101 " - pdb=" SG CYS P 148 " distance=2.03 Simple disulfide: pdb=" SG CYS P 150 " - pdb=" SG CYS P 155 " distance=2.04 Simple disulfide: pdb=" SG CYS P 196 " - pdb=" SG CYS P 209 " distance=2.03 Simple disulfide: pdb=" SG CYS P 198 " - pdb=" SG CYS P 207 " distance=2.03 Simple disulfide: pdb=" SG CYS P 235 " - pdb=" SG CYS P 254 " distance=2.04 Simple disulfide: pdb=" SG CYS P 343 " - pdb=" SG CYS P 369 " distance=2.03 Simple disulfide: pdb=" SG CYS S 12 " - pdb=" SG CYS S 87 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A 401 " - " ASN A 3 " " NAG B 1 " - " ASN A 63 " " NAG C 1 " - " ASN D 63 " " NAG D 401 " - " ASN D 3 " " NAG E 1 " - " ASN G 63 " " NAG F 1 " - " ASN P 63 " " NAG G 401 " - " ASN G 3 " " NAG P 401 " - " ASN P 3 " Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 824.6 milliseconds 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4084 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 47 sheets defined 5.5% alpha, 44.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 21 through 27 Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.647A pdb=" N ASN A 63 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 removed outlier: 3.510A pdb=" N THR A 335 " --> pdb=" O PRO A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 392 removed outlier: 3.512A pdb=" N LYS A 392 " --> pdb=" O ASP A 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 27 Processing helix chain 'D' and resid 59 through 63 removed outlier: 3.684A pdb=" N ASN D 63 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 336 removed outlier: 3.653A pdb=" N THR D 335 " --> pdb=" O PRO D 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 27 removed outlier: 3.598A pdb=" N SER G 27 " --> pdb=" O ILE G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 63 Processing helix chain 'G' and resid 331 through 336 removed outlier: 3.646A pdb=" N THR G 335 " --> pdb=" O PRO G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 392 Processing helix chain 'H' and resid 53 through 56 Processing helix chain 'H' and resid 78 through 82 Processing helix chain 'I' and resid 53 through 56 Processing helix chain 'I' and resid 78 through 82 Processing helix chain 'L' and resid 84 through 88 removed outlier: 3.984A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 88 removed outlier: 3.984A pdb=" N VAL M 88 " --> pdb=" O ALA M 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 27 Processing helix chain 'P' and resid 59 through 63 Processing helix chain 'P' and resid 331 through 336 removed outlier: 3.503A pdb=" N THR P 335 " --> pdb=" O PRO P 331 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 Processing helix chain 'S' and resid 78 through 82 Processing helix chain 'T' and resid 84 through 88 removed outlier: 3.966A pdb=" N VAL T 88 " --> pdb=" O ALA T 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 19 removed outlier: 6.862A pdb=" N VAL A 367 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LYS A 19 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N SER A 365 " --> pdb=" O LYS A 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 41 removed outlier: 4.797A pdb=" N PHE A 32 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ALA A 55 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE A 34 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLN A 53 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLU A 36 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 51 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU A 75 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 102 removed outlier: 3.887A pdb=" N SER A 97 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP A 131 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N TYR A 125 " --> pdb=" O PRO A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 143 Processing sheet with id=AA5, first strand: chain 'A' and resid 141 through 143 removed outlier: 4.669A pdb=" N TYR A 170 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N HIS A 176 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 197 through 201 Processing sheet with id=AA7, first strand: chain 'A' and resid 274 through 275 removed outlier: 7.972A pdb=" N SER A 291 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LEU A 316 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N PHE A 293 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU A 314 " --> pdb=" O PHE A 293 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A 295 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS A 312 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU A 297 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 13 through 19 removed outlier: 6.816A pdb=" N VAL D 367 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS D 19 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER D 365 " --> pdb=" O LYS D 19 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 341 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 32 through 41 removed outlier: 4.765A pdb=" N PHE D 32 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ALA D 55 " --> pdb=" O PHE D 32 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE D 34 " --> pdb=" O GLN D 53 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN D 53 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLU D 36 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU D 51 " --> pdb=" O GLU D 36 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU D 75 " --> pdb=" O GLU D 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 97 through 102 removed outlier: 3.950A pdb=" N SER D 97 " --> pdb=" O ILE D 112 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP D 131 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR D 125 " --> pdb=" O PRO D 129 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 141 through 143 Processing sheet with id=AB3, first strand: chain 'D' and resid 141 through 143 removed outlier: 4.687A pdb=" N TYR D 170 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN D 182 " --> pdb=" O LYS D 174 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N HIS D 176 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL D 180 " --> pdb=" O HIS D 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 197 through 201 Processing sheet with id=AB5, first strand: chain 'D' and resid 274 through 275 removed outlier: 7.982A pdb=" N SER D 291 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LEU D 316 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE D 293 " --> pdb=" O GLU D 314 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU D 314 " --> pdb=" O PHE D 293 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE D 295 " --> pdb=" O LYS D 312 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS D 312 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU D 297 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 13 through 19 removed outlier: 6.802A pdb=" N VAL G 367 " --> pdb=" O VAL G 17 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL G 341 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 32 through 41 removed outlier: 4.954A pdb=" N PHE G 32 " --> pdb=" O ALA G 55 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ALA G 55 " --> pdb=" O PHE G 32 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ILE G 34 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLN G 53 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLU G 36 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU G 51 " --> pdb=" O GLU G 36 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA G 74 " --> pdb=" O THR G 52 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU G 75 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 97 through 102 removed outlier: 4.049A pdb=" N SER G 97 " --> pdb=" O ILE G 112 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA G 121 " --> pdb=" O VAL G 132 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL G 132 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE G 123 " --> pdb=" O THR G 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 142 through 143 removed outlier: 3.927A pdb=" N VAL G 149 " --> pdb=" O TYR G 156 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 142 through 143 removed outlier: 3.517A pdb=" N TRP G 157 " --> pdb=" O PHE G 173 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N HIS G 176 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL G 180 " --> pdb=" O HIS G 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 196 through 201 removed outlier: 3.628A pdb=" N THR G 222 " --> pdb=" O GLU G 230 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 272 through 275 removed outlier: 7.715A pdb=" N ASN G 320 " --> pdb=" O GLY G 292 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N GLU G 294 " --> pdb=" O ASN G 318 " (cutoff:3.500A) removed outlier: 10.917A pdb=" N ASN G 318 " --> pdb=" O GLU G 294 " (cutoff:3.500A) removed outlier: 11.283A pdb=" N LEU G 296 " --> pdb=" O LEU G 316 " (cutoff:3.500A) removed outlier: 13.704A pdb=" N LEU G 316 " --> pdb=" O LEU G 296 " (cutoff:3.500A) removed outlier: 15.491A pdb=" N VAL G 298 " --> pdb=" O GLU G 314 " (cutoff:3.500A) removed outlier: 15.949A pdb=" N GLU G 314 " --> pdb=" O VAL G 298 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 348 through 351 Processing sheet with id=AC5, first strand: chain 'H' and resid 8 through 13 Processing sheet with id=AC6, first strand: chain 'H' and resid 49 through 51 removed outlier: 5.400A pdb=" N TRP H 39 " --> pdb=" O ARG H 30 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG H 30 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY H 41 " --> pdb=" O TRP H 28 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N CYS H 87 " --> pdb=" O VAL H 106 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL H 106 " --> pdb=" O CYS H 87 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG H 89 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU H 104 " --> pdb=" O ARG H 89 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY H 91 " --> pdb=" O PHE H 102 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR H 100 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 49 through 51 removed outlier: 5.400A pdb=" N TRP H 39 " --> pdb=" O ARG H 30 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG H 30 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY H 41 " --> pdb=" O TRP H 28 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 8 through 13 Processing sheet with id=AC9, first strand: chain 'I' and resid 49 through 51 removed outlier: 6.689A pdb=" N TRP I 28 " --> pdb=" O ILE I 40 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASN I 42 " --> pdb=" O TRP I 26 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP I 26 " --> pdb=" O ASN I 42 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N CYS I 87 " --> pdb=" O VAL I 106 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL I 106 " --> pdb=" O CYS I 87 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG I 89 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU I 104 " --> pdb=" O ARG I 89 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY I 91 " --> pdb=" O PHE I 102 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 49 through 51 removed outlier: 6.689A pdb=" N TRP I 28 " --> pdb=" O ILE I 40 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASN I 42 " --> pdb=" O TRP I 26 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP I 26 " --> pdb=" O ASN I 42 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.508A pdb=" N TYR L 75 " --> pdb=" O SER L 72 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.734A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU L 42 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU L 51 " --> pdb=" O LEU L 42 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.734A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR L 102 " --> pdb=" O GLN L 95 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AD6, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.842A pdb=" N GLY M 89 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP M 40 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.842A pdb=" N GLY M 89 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR M 102 " --> pdb=" O GLN M 95 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 13 through 19 removed outlier: 6.829A pdb=" N VAL P 367 " --> pdb=" O VAL P 17 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LYS P 19 " --> pdb=" O SER P 365 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER P 365 " --> pdb=" O LYS P 19 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 32 through 41 removed outlier: 4.835A pdb=" N PHE P 32 " --> pdb=" O ALA P 55 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ALA P 55 " --> pdb=" O PHE P 32 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE P 34 " --> pdb=" O GLN P 53 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLN P 53 " --> pdb=" O ILE P 34 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU P 36 " --> pdb=" O LEU P 51 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU P 51 " --> pdb=" O GLU P 36 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU P 75 " --> pdb=" O GLU P 92 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 97 through 102 removed outlier: 3.915A pdb=" N SER P 97 " --> pdb=" O ILE P 112 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP P 131 " --> pdb=" O ILE P 123 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N TYR P 125 " --> pdb=" O PRO P 129 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 141 through 143 Processing sheet with id=AE3, first strand: chain 'P' and resid 141 through 143 removed outlier: 4.637A pdb=" N TYR P 170 " --> pdb=" O VAL P 186 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N HIS P 176 " --> pdb=" O VAL P 180 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL P 180 " --> pdb=" O HIS P 176 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 197 through 201 Processing sheet with id=AE5, first strand: chain 'P' and resid 274 through 275 removed outlier: 8.039A pdb=" N SER P 291 " --> pdb=" O LEU P 316 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LEU P 316 " --> pdb=" O SER P 291 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N PHE P 293 " --> pdb=" O GLU P 314 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLU P 314 " --> pdb=" O PHE P 293 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE P 295 " --> pdb=" O LYS P 312 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS P 312 " --> pdb=" O ILE P 295 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU P 297 " --> pdb=" O VAL P 310 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 8 through 13 Processing sheet with id=AE7, first strand: chain 'S' and resid 49 through 51 removed outlier: 5.348A pdb=" N TRP S 39 " --> pdb=" O ARG S 30 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG S 30 " --> pdb=" O TRP S 39 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY S 41 " --> pdb=" O TRP S 28 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N CYS S 87 " --> pdb=" O VAL S 106 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL S 106 " --> pdb=" O CYS S 87 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG S 89 " --> pdb=" O LEU S 104 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU S 104 " --> pdb=" O ARG S 89 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY S 91 " --> pdb=" O PHE S 102 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR S 100 " --> pdb=" O SER S 93 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 49 through 51 removed outlier: 5.348A pdb=" N TRP S 39 " --> pdb=" O ARG S 30 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG S 30 " --> pdb=" O TRP S 39 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY S 41 " --> pdb=" O TRP S 28 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'T' and resid 4 through 6 Processing sheet with id=AF1, first strand: chain 'T' and resid 10 through 13 removed outlier: 3.841A pdb=" N GLY T 89 " --> pdb=" O VAL T 109 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP T 40 " --> pdb=" O LEU T 52 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 10 through 13 removed outlier: 3.841A pdb=" N GLY T 89 " --> pdb=" O VAL T 109 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR T 102 " --> pdb=" O GLN T 95 " (cutoff:3.500A) 634 hydrogen bonds defined for protein. 1611 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: 8.67 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 16326 1.03 - 1.23: 131 1.23 - 1.43: 7784 1.43 - 1.63: 10028 1.63 - 1.82: 152 Bond restraints: 34421 Sorted by residual: bond pdb=" N LEU I 1 " pdb=" CA LEU I 1 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.34e+00 bond pdb=" N LEU S 1 " pdb=" CA LEU S 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.19e+00 bond pdb=" N LEU H 1 " pdb=" CA LEU H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N LEU S 1 " pdb=" H LEU S 1 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" N LEU H 1 " pdb=" H LEU H 1 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.33e+00 ... (remaining 34416 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 59847 1.48 - 2.97: 1608 2.97 - 4.45: 140 4.45 - 5.93: 28 5.93 - 7.41: 2 Bond angle restraints: 61625 Sorted by residual: angle pdb=" CA VAL D 78 " pdb=" C VAL D 78 " pdb=" N PRO D 79 " ideal model delta sigma weight residual 116.57 120.71 -4.14 9.80e-01 1.04e+00 1.78e+01 angle pdb=" CA VAL P 78 " pdb=" C VAL P 78 " pdb=" N PRO P 79 " ideal model delta sigma weight residual 116.57 120.57 -4.00 9.80e-01 1.04e+00 1.66e+01 angle pdb=" N VAL P 78 " pdb=" CA VAL P 78 " pdb=" C VAL P 78 " ideal model delta sigma weight residual 109.19 106.36 2.83 8.20e-01 1.49e+00 1.19e+01 angle pdb=" C VAL P 78 " pdb=" CA VAL P 78 " pdb=" CB VAL P 78 " ideal model delta sigma weight residual 109.33 112.66 -3.33 9.80e-01 1.04e+00 1.15e+01 angle pdb=" N GLY A 351 " pdb=" CA GLY A 351 " pdb=" C GLY A 351 " ideal model delta sigma weight residual 110.29 114.34 -4.05 1.28e+00 6.10e-01 9.99e+00 ... (remaining 61620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 15001 16.82 - 33.64: 1113 33.64 - 50.45: 371 50.45 - 67.27: 303 67.27 - 84.09: 24 Dihedral angle restraints: 16812 sinusoidal: 9077 harmonic: 7735 Sorted by residual: dihedral pdb=" CA LYS G 138 " pdb=" C LYS G 138 " pdb=" N GLN G 139 " pdb=" CA GLN G 139 " ideal model delta harmonic sigma weight residual 180.00 152.43 27.57 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA LEU G 227 " pdb=" C LEU G 227 " pdb=" N ASN G 228 " pdb=" CA ASN G 228 " ideal model delta harmonic sigma weight residual 180.00 153.66 26.34 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CB CYS G 235 " pdb=" SG CYS G 235 " pdb=" SG CYS G 254 " pdb=" CB CYS G 254 " ideal model delta sinusoidal sigma weight residual 93.00 135.47 -42.47 1 1.00e+01 1.00e-02 2.52e+01 ... (remaining 16809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2445 0.077 - 0.155: 259 0.155 - 0.232: 1 0.232 - 0.310: 0 0.310 - 0.387: 4 Chirality restraints: 2709 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN G 63 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 63 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN D 63 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 2706 not shown) Planarity restraints: 5286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG G 218 " 0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO G 219 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO G 219 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 219 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL P 78 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.50e+00 pdb=" N PRO P 79 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO P 79 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO P 79 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 78 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.98e+00 pdb=" N PRO D 79 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 79 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 79 " -0.020 5.00e-02 4.00e+02 ... (remaining 5283 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 6927 2.31 - 2.88: 75158 2.88 - 3.45: 83236 3.45 - 4.03: 123131 4.03 - 4.60: 183988 Nonbonded interactions: 472440 Sorted by model distance: nonbonded pdb=" HG SER D 97 " pdb="HH21 ARG I 98 " model vdw 1.731 2.100 nonbonded pdb=" H ILE A 385 " pdb=" HE1 HIS D 61 " model vdw 1.781 2.100 nonbonded pdb=" HE1 HIS A 61 " pdb=" H ILE P 385 " model vdw 1.795 2.100 nonbonded pdb=" HG SER A 97 " pdb="HH21 ARG H 98 " model vdw 1.821 2.100 nonbonded pdb=" HZ3 LYS A 19 " pdb=" HD1 TYR D 72 " model vdw 1.832 2.100 ... (remaining 472435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 0 through 34 or (resid 35 through 36 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 37 through 65 \ or (resid 68 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 69 through 144 or (resid 145 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 146 through 193 or (resi \ d 194 through 195 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 196 through 211 or (resid 212 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 213 through 268 or \ (resid 269 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 270 through 402)) selection = (chain 'D' and (resid 0 through 34 or (resid 35 through 36 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 37 through 65 \ or (resid 68 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 69 through 144 or (resid 145 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 146 through 193 or (resi \ d 194 through 195 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 196 through 211 or (resid 212 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 213 through 268 or \ (resid 269 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 270 through 402)) selection = chain 'G' selection = (chain 'P' and (resid 0 through 34 or (resid 35 through 36 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 37 through 65 \ or (resid 68 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 69 through 144 or (resid 145 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 146 through 193 or (resi \ d 194 through 195 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 196 through 211 or (resid 212 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 213 through 268 or \ (resid 269 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 270 through 402)) } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'S' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'T' } 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: 3.080 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: 0.240 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 31.310 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 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 0.035 18128 Z= 0.192 Angle : 0.670 7.413 24684 Z= 0.363 Chirality : 0.046 0.387 2709 Planarity : 0.004 0.059 3136 Dihedral : 11.919 84.088 6674 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.01 % Allowed : 2.60 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.16), residues: 2235 helix: -3.98 (0.37), residues: 48 sheet: -0.52 (0.17), residues: 870 loop : -1.47 (0.15), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 134 TYR 0.015 0.002 TYR P 87 PHE 0.011 0.001 PHE D 271 TRP 0.013 0.001 TRP G 96 HIS 0.004 0.001 HIS D 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (18081) covalent geometry : angle 0.65056 / 0.36 (24574) SS BOND : bond 0.00324 / 0.20 ( 31) SS BOND : angle 0.97839 / 0.61 ( 62) hydrogen bonds : bond 0.20506 / 13.51 ( 569) hydrogen bonds : angle 9.04554 / 6.31 ( 1611) link_BETA1-4 : bond 0.00666 / 0.31 ( 8) link_BETA1-4 : angle 3.73634 / 2.33 ( 24) link_NAG-ASN : bond 0.00831 / 0.43 ( 8) link_NAG-ASN : angle 3.37831 / 1.88 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Evaluate side-chains 720 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 662 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 THR cc_start: 0.9520 (p) cc_final: 0.9299 (p) REVERT: A 194 GLU cc_start: 0.7171 (tt0) cc_final: 0.6964 (tp30) REVERT: A 285 VAL cc_start: 0.8142 (t) cc_final: 0.7770 (p) REVERT: A 293 PHE cc_start: 0.6665 (t80) cc_final: 0.6226 (t80) REVERT: A 294 GLU cc_start: 0.7735 (mt-10) cc_final: 0.6905 (mp0) REVERT: A 371 VAL cc_start: 0.8365 (t) cc_final: 0.8024 (m) REVERT: D 16 ILE cc_start: 0.9101 (tt) cc_final: 0.8851 (tt) REVERT: D 195 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6787 (mt-10) REVERT: D 347 GLU cc_start: 0.6092 (pt0) cc_final: 0.5884 (pt0) REVERT: G 56 LEU cc_start: 0.8322 (mt) cc_final: 0.8080 (mt) REVERT: G 315 VAL cc_start: 0.7712 (m) cc_final: 0.7329 (m) REVERT: G 316 LEU cc_start: 0.7869 (mt) cc_final: 0.7492 (tp) REVERT: I 63 ILE cc_start: 0.7381 (mt) cc_final: 0.7060 (pt) REVERT: I 106 VAL cc_start: 0.7853 (t) cc_final: 0.7562 (t) REVERT: I 115 VAL cc_start: 0.6656 (t) cc_final: 0.6366 (t) REVERT: L 15 PRO cc_start: 0.9292 (Cg_exo) cc_final: 0.8828 (Cg_endo) REVERT: L 76 PHE cc_start: 0.9068 (m-80) cc_final: 0.8793 (m-80) REVERT: P 4 ASN cc_start: 0.8142 (m-40) cc_final: 0.7863 (m110) REVERT: P 35 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6258 (tpt90) REVERT: P 47 ARG cc_start: 0.7755 (mtt-85) cc_final: 0.7383 (mtt90) REVERT: P 120 TYR cc_start: 0.9021 (p90) cc_final: 0.8818 (p90) REVERT: P 149 VAL cc_start: 0.8163 (t) cc_final: 0.7948 (m) REVERT: P 186 VAL cc_start: 0.8295 (t) cc_final: 0.8062 (t) REVERT: P 205 VAL cc_start: 0.8893 (t) cc_final: 0.8582 (t) REVERT: P 238 ILE cc_start: 0.8601 (mm) cc_final: 0.8219 (tt) REVERT: P 314 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6251 (tt0) REVERT: P 348 MET cc_start: 0.7187 (mtm) cc_final: 0.6889 (mpp) REVERT: P 349 ILE cc_start: 0.8830 (mt) cc_final: 0.8612 (mm) REVERT: S 74 LEU cc_start: 0.8686 (tp) cc_final: 0.8016 (tp) REVERT: S 85 TYR cc_start: 0.6234 (m-80) cc_final: 0.5515 (m-80) REVERT: S 105 ASP cc_start: 0.8367 (p0) cc_final: 0.8062 (t0) REVERT: T 63 VAL cc_start: 0.8800 (t) cc_final: 0.8423 (p) REVERT: T 76 PHE cc_start: 0.8414 (m-80) cc_final: 0.7885 (m-80) REVERT: T 83 VAL cc_start: 0.7944 (t) cc_final: 0.6792 (p) outliers start: 58 outliers final: 18 residues processed: 693 average time/residue: 0.3021 time to fit residues: 308.6252 Evaluate side-chains 402 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 382 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 7.9990 chunk 212 optimal weight: 0.0010 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 HIS ** G 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 317 ASN T 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.114244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.095815 restraints weight = 136140.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.100192 restraints weight = 58174.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.102961 restraints weight = 31303.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.104680 restraints weight = 19979.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.105607 restraints weight = 14572.531| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 18128 Z= 0.152 Angle : 0.651 9.029 24684 Z= 0.343 Chirality : 0.050 0.360 2709 Planarity : 0.005 0.056 3136 Dihedral : 7.991 55.711 2774 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.42 % Allowed : 1.56 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.17), residues: 2235 helix: -3.13 (0.46), residues: 60 sheet: -0.32 (0.17), residues: 859 loop : -1.46 (0.15), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 98 TYR 0.014 0.001 TYR G 170 PHE 0.027 0.002 PHE G 188 TRP 0.014 0.001 TRP G 96 HIS 0.005 0.001 HIS G 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (18081) covalent geometry : angle 0.62933 / 0.34 (24574) SS BOND : bond 0.00242 / 0.15 ( 31) SS BOND : angle 2.09860 / 1.55 ( 62) hydrogen bonds : bond 0.05018 / 3.37 ( 569) hydrogen bonds : angle 6.58912 / 4.59 ( 1611) link_BETA1-4 : bond 0.00594 / 0.34 ( 8) link_BETA1-4 : angle 3.08159 / 1.93 ( 24) link_NAG-ASN : bond 0.00562 / 0.29 ( 8) link_NAG-ASN : angle 3.06608 / 1.81 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Evaluate side-chains 455 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 447 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 116 ASP cc_start: 0.8837 (m-30) cc_final: 0.8472 (m-30) REVERT: A 194 GLU cc_start: 0.7442 (tt0) cc_final: 0.7172 (tt0) REVERT: D 35 ARG cc_start: 0.7969 (tpt90) cc_final: 0.7499 (mmm160) REVERT: D 116 ASP cc_start: 0.8073 (m-30) cc_final: 0.7827 (m-30) REVERT: D 182 ASN cc_start: 0.7377 (m-40) cc_final: 0.6987 (m-40) REVERT: D 347 GLU cc_start: 0.6274 (pt0) cc_final: 0.6055 (pt0) REVERT: G 76 MET cc_start: 0.8185 (mtt) cc_final: 0.7930 (mtp) REVERT: G 128 MET cc_start: 0.7026 (ptp) cc_final: 0.6689 (ptp) REVERT: G 329 THR cc_start: 0.8854 (p) cc_final: 0.8507 (t) REVERT: H 28 TRP cc_start: 0.8516 (m100) cc_final: 0.8309 (m100) REVERT: I 95 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7373 (mt-10) REVERT: L 2 ILE cc_start: 0.6500 (mt) cc_final: 0.6252 (mm) REVERT: L 42 LEU cc_start: 0.7957 (tp) cc_final: 0.7630 (tp) REVERT: L 76 PHE cc_start: 0.9078 (m-80) cc_final: 0.8739 (m-80) REVERT: L 84 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7527 (mm-30) REVERT: M 53 ILE cc_start: 0.7628 (mp) cc_final: 0.7324 (mm) REVERT: P 4 ASN cc_start: 0.8301 (m-40) cc_final: 0.7772 (m110) REVERT: P 35 ARG cc_start: 0.8126 (tpt90) cc_final: 0.7493 (tpt90) REVERT: P 47 ARG cc_start: 0.7701 (mtt-85) cc_final: 0.7177 (mtt90) REVERT: P 120 TYR cc_start: 0.9029 (p90) cc_final: 0.8560 (p90) REVERT: P 205 VAL cc_start: 0.8780 (t) cc_final: 0.8513 (t) REVERT: S 32 HIS cc_start: 0.5158 (m90) cc_final: 0.4629 (m90) REVERT: S 59 LEU cc_start: 0.8045 (mt) cc_final: 0.7818 (mt) REVERT: S 105 ASP cc_start: 0.8457 (p0) cc_final: 0.8220 (t0) REVERT: T 83 VAL cc_start: 0.7949 (t) cc_final: 0.7143 (t) REVERT: T 92 TYR cc_start: 0.6592 (m-80) cc_final: 0.5498 (m-80) outliers start: 8 outliers final: 5 residues processed: 453 average time/residue: 0.2796 time to fit residues: 192.7435 Evaluate side-chains 361 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 356 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 159 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 GLN ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 214 ASN S 69 GLN T 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.105633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.087329 restraints weight = 141237.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.091264 restraints weight = 62153.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.093787 restraints weight = 34556.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.095248 restraints weight = 22721.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.096319 restraints weight = 17318.604| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 18128 Z= 0.343 Angle : 0.783 10.248 24684 Z= 0.415 Chirality : 0.051 0.496 2709 Planarity : 0.006 0.079 3136 Dihedral : 7.391 57.325 2774 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.26 % Allowed : 3.43 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.16), residues: 2235 helix: -2.35 (0.62), residues: 48 sheet: -0.60 (0.17), residues: 919 loop : -1.96 (0.15), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 283 TYR 0.018 0.002 TYR S 92 PHE 0.022 0.003 PHE A 14 TRP 0.016 0.002 TRP A 157 HIS 0.008 0.003 HIS P 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00740 / 0.34 (18081) covalent geometry : angle 0.76809 / 0.41 (24574) SS BOND : bond 0.00539 / 0.32 ( 31) SS BOND : angle 1.78431 / 1.20 ( 62) hydrogen bonds : bond 0.06106 / 4.15 ( 569) hydrogen bonds : angle 6.44920 / 4.53 ( 1611) link_BETA1-4 : bond 0.00615 / 0.29 ( 8) link_BETA1-4 : angle 2.93703 / 1.86 ( 24) link_NAG-ASN : bond 0.00874 / 0.52 ( 8) link_NAG-ASN : angle 3.22563 / 1.93 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Evaluate side-chains 364 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 359 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 151 MET cc_start: 0.9010 (mtp) cc_final: 0.8750 (mtp) REVERT: A 263 THR cc_start: 0.8172 (p) cc_final: 0.7970 (p) REVERT: A 347 GLU cc_start: 0.7430 (pt0) cc_final: 0.7078 (pt0) REVERT: D 80 LEU cc_start: 0.7359 (tp) cc_final: 0.6642 (pt) REVERT: D 182 ASN cc_start: 0.7832 (m-40) cc_final: 0.7537 (m-40) REVERT: D 271 PHE cc_start: 0.8055 (p90) cc_final: 0.7805 (p90) REVERT: I 2 VAL cc_start: 0.8095 (m) cc_final: 0.7810 (m) REVERT: I 95 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7347 (mt-10) REVERT: L 42 LEU cc_start: 0.8268 (tp) cc_final: 0.7805 (tp) REVERT: L 84 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7735 (mm-30) REVERT: M 53 ILE cc_start: 0.7729 (mp) cc_final: 0.7339 (mm) REVERT: M 76 PHE cc_start: 0.8457 (m-10) cc_final: 0.8151 (m-10) REVERT: P 20 ASP cc_start: 0.8504 (m-30) cc_final: 0.8260 (m-30) REVERT: P 76 MET cc_start: 0.7609 (mtt) cc_final: 0.7295 (mtp) REVERT: P 205 VAL cc_start: 0.8840 (t) cc_final: 0.8628 (t) REVERT: P 250 PHE cc_start: 0.7026 (t80) cc_final: 0.6670 (t80) REVERT: P 388 PHE cc_start: 0.8565 (m-10) cc_final: 0.8210 (m-80) REVERT: S 59 LEU cc_start: 0.8158 (mt) cc_final: 0.7917 (mt) REVERT: S 105 ASP cc_start: 0.8657 (p0) cc_final: 0.7958 (t0) REVERT: T 13 VAL cc_start: 0.8845 (p) cc_final: 0.8364 (p) REVERT: T 83 VAL cc_start: 0.7809 (t) cc_final: 0.7221 (t) outliers start: 5 outliers final: 3 residues processed: 363 average time/residue: 0.2799 time to fit residues: 154.6614 Evaluate side-chains 289 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 286 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 142 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 150 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 GLN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 69 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.109404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.091143 restraints weight = 137822.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.095219 restraints weight = 59499.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.097820 restraints weight = 32668.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.099284 restraints weight = 21318.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.100416 restraints weight = 16171.769| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 18128 Z= 0.135 Angle : 0.600 7.288 24684 Z= 0.318 Chirality : 0.048 0.384 2709 Planarity : 0.005 0.060 3136 Dihedral : 6.992 59.968 2774 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.16 % Allowed : 1.56 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.17), residues: 2235 helix: -2.90 (0.49), residues: 66 sheet: -0.55 (0.17), residues: 911 loop : -1.74 (0.16), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 142 TYR 0.037 0.002 TYR A 170 PHE 0.012 0.001 PHE S 70 TRP 0.011 0.001 TRP G 96 HIS 0.004 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (18081) covalent geometry : angle 0.58561 / 0.31 (24574) SS BOND : bond 0.00288 / 0.21 ( 31) SS BOND : angle 1.54129 / 1.03 ( 62) hydrogen bonds : bond 0.04271 / 2.89 ( 569) hydrogen bonds : angle 6.01262 / 4.20 ( 1611) link_BETA1-4 : bond 0.00365 / 0.17 ( 8) link_BETA1-4 : angle 2.14510 / 1.35 ( 24) link_NAG-ASN : bond 0.00422 / 0.21 ( 8) link_NAG-ASN : angle 2.83316 / 1.74 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Evaluate side-chains 365 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 362 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 116 ASP cc_start: 0.8766 (m-30) cc_final: 0.8473 (m-30) REVERT: A 151 MET cc_start: 0.9030 (mtp) cc_final: 0.8729 (mtp) REVERT: D 91 PHE cc_start: 0.7272 (t80) cc_final: 0.7022 (t80) REVERT: D 182 ASN cc_start: 0.7858 (m-40) cc_final: 0.7478 (m-40) REVERT: D 271 PHE cc_start: 0.7672 (p90) cc_final: 0.7441 (p90) REVERT: G 216 MET cc_start: 0.7527 (ttt) cc_final: 0.7046 (tmm) REVERT: G 329 THR cc_start: 0.8944 (p) cc_final: 0.8546 (t) REVERT: I 2 VAL cc_start: 0.8145 (m) cc_final: 0.7839 (m) REVERT: I 84 VAL cc_start: 0.8500 (t) cc_final: 0.8235 (p) REVERT: L 42 LEU cc_start: 0.8147 (tp) cc_final: 0.7739 (tp) REVERT: L 76 PHE cc_start: 0.9022 (m-80) cc_final: 0.8394 (m-80) REVERT: M 42 LEU cc_start: 0.8528 (mt) cc_final: 0.8215 (mt) REVERT: P 56 LEU cc_start: 0.8887 (mt) cc_final: 0.8557 (mm) REVERT: P 76 MET cc_start: 0.7452 (mtt) cc_final: 0.7088 (mtp) REVERT: P 120 TYR cc_start: 0.8909 (p90) cc_final: 0.8633 (p90) REVERT: P 205 VAL cc_start: 0.8905 (t) cc_final: 0.8693 (t) REVERT: P 250 PHE cc_start: 0.6861 (t80) cc_final: 0.6634 (t80) REVERT: P 388 PHE cc_start: 0.8453 (m-10) cc_final: 0.8132 (m-80) REVERT: S 59 LEU cc_start: 0.8148 (mt) cc_final: 0.7937 (mt) REVERT: S 105 ASP cc_start: 0.8554 (p0) cc_final: 0.7924 (t0) REVERT: T 53 ILE cc_start: 0.8562 (mm) cc_final: 0.8361 (mm) outliers start: 3 outliers final: 3 residues processed: 365 average time/residue: 0.2873 time to fit residues: 157.4481 Evaluate side-chains 309 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 306 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 170 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 216 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.108880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.090468 restraints weight = 138760.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.094511 restraints weight = 60419.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.097124 restraints weight = 33400.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.098741 restraints weight = 21867.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.099668 restraints weight = 16293.560| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18128 Z= 0.160 Angle : 0.590 6.725 24684 Z= 0.312 Chirality : 0.048 0.365 2709 Planarity : 0.005 0.058 3136 Dihedral : 6.741 59.006 2774 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.16 % Allowed : 1.82 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.17), residues: 2235 helix: -2.92 (0.50), residues: 66 sheet: -0.57 (0.17), residues: 919 loop : -1.71 (0.16), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 24 TYR 0.028 0.002 TYR P 72 PHE 0.013 0.002 PHE I 70 TRP 0.024 0.001 TRP I 28 HIS 0.004 0.001 HIS G 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (18081) covalent geometry : angle 0.57763 / 0.31 (24574) SS BOND : bond 0.00528 / 0.29 ( 31) SS BOND : angle 1.40664 / 1.02 ( 62) hydrogen bonds : bond 0.04166 / 2.85 ( 569) hydrogen bonds : angle 5.82123 / 4.06 ( 1611) link_BETA1-4 : bond 0.00434 / 0.22 ( 8) link_BETA1-4 : angle 2.08455 / 1.30 ( 24) link_NAG-ASN : bond 0.00445 / 0.24 ( 8) link_NAG-ASN : angle 2.73303 / 1.66 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Evaluate side-chains 350 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 347 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 116 ASP cc_start: 0.8737 (m-30) cc_final: 0.8367 (m-30) REVERT: A 151 MET cc_start: 0.9046 (mtp) cc_final: 0.8757 (mtp) REVERT: D 182 ASN cc_start: 0.7718 (m-40) cc_final: 0.7373 (m-40) REVERT: G 82 SER cc_start: 0.9266 (m) cc_final: 0.8951 (p) REVERT: G 216 MET cc_start: 0.7729 (ttt) cc_final: 0.7206 (tmm) REVERT: G 320 ASN cc_start: 0.8397 (t0) cc_final: 0.8090 (p0) REVERT: I 2 VAL cc_start: 0.8117 (m) cc_final: 0.7881 (m) REVERT: I 28 TRP cc_start: 0.8662 (m100) cc_final: 0.8451 (m-10) REVERT: I 84 VAL cc_start: 0.8420 (t) cc_final: 0.8111 (p) REVERT: L 6 GLN cc_start: 0.7025 (tt0) cc_final: 0.6808 (tt0) REVERT: L 42 LEU cc_start: 0.8152 (tp) cc_final: 0.7723 (tp) REVERT: L 76 PHE cc_start: 0.9004 (m-80) cc_final: 0.8401 (m-80) REVERT: M 53 ILE cc_start: 0.6246 (mt) cc_final: 0.5972 (mm) REVERT: P 159 MET cc_start: 0.8598 (mtp) cc_final: 0.8218 (mtp) REVERT: P 205 VAL cc_start: 0.8962 (t) cc_final: 0.8744 (t) REVERT: P 388 PHE cc_start: 0.8432 (m-10) cc_final: 0.8113 (m-80) REVERT: S 59 LEU cc_start: 0.8234 (mt) cc_final: 0.8010 (mt) outliers start: 3 outliers final: 3 residues processed: 350 average time/residue: 0.2728 time to fit residues: 145.7694 Evaluate side-chains 295 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 292 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 158 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 184 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 GLN G 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.109019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.090705 restraints weight = 137270.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.094739 restraints weight = 59806.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.097341 restraints weight = 32977.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.098935 restraints weight = 21592.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.099768 restraints weight = 16116.353| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 18128 Z= 0.138 Angle : 0.565 5.585 24684 Z= 0.299 Chirality : 0.047 0.372 2709 Planarity : 0.005 0.064 3136 Dihedral : 6.545 59.360 2774 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.21 % Allowed : 1.35 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.17), residues: 2235 helix: -2.86 (0.49), residues: 66 sheet: -0.48 (0.17), residues: 898 loop : -1.64 (0.16), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 28 TYR 0.026 0.001 TYR M 91 PHE 0.012 0.001 PHE I 70 TRP 0.009 0.001 TRP G 96 HIS 0.004 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (18081) covalent geometry : angle 0.55167 / 0.30 (24574) SS BOND : bond 0.00368 / 0.23 ( 31) SS BOND : angle 1.58680 / 0.99 ( 62) hydrogen bonds : bond 0.03904 / 2.65 ( 569) hydrogen bonds : angle 5.70031 / 3.98 ( 1611) link_BETA1-4 : bond 0.00339 / 0.16 ( 8) link_BETA1-4 : angle 1.93125 / 1.20 ( 24) link_NAG-ASN : bond 0.00370 / 0.20 ( 8) link_NAG-ASN : angle 2.58448 / 1.58 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Evaluate side-chains 349 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 345 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 116 ASP cc_start: 0.8765 (m-30) cc_final: 0.8367 (m-30) REVERT: A 151 MET cc_start: 0.8999 (mtp) cc_final: 0.8715 (mtp) REVERT: A 363 SER cc_start: 0.8648 (t) cc_final: 0.8161 (t) REVERT: D 182 ASN cc_start: 0.7911 (m-40) cc_final: 0.7551 (m-40) REVERT: G 65 THR cc_start: 0.8065 (p) cc_final: 0.7771 (p) REVERT: G 82 SER cc_start: 0.9251 (m) cc_final: 0.8947 (p) REVERT: G 329 THR cc_start: 0.8949 (p) cc_final: 0.8541 (t) REVERT: I 2 VAL cc_start: 0.8144 (m) cc_final: 0.7909 (m) REVERT: I 84 VAL cc_start: 0.8415 (t) cc_final: 0.8101 (p) REVERT: P 35 ARG cc_start: 0.8215 (tpt90) cc_final: 0.7659 (tpt90) REVERT: P 159 MET cc_start: 0.8614 (mtp) cc_final: 0.8171 (mtp) REVERT: P 205 VAL cc_start: 0.8921 (t) cc_final: 0.8692 (t) REVERT: P 388 PHE cc_start: 0.8420 (m-10) cc_final: 0.8098 (m-80) REVERT: S 59 LEU cc_start: 0.8239 (mt) cc_final: 0.8024 (mt) REVERT: T 53 ILE cc_start: 0.8318 (mm) cc_final: 0.8100 (mm) outliers start: 4 outliers final: 3 residues processed: 349 average time/residue: 0.2909 time to fit residues: 153.8770 Evaluate side-chains 299 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 296 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 17 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 185 optimal weight: 0.0030 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 HIS T 50 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.107117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.089434 restraints weight = 131551.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.093495 restraints weight = 55714.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.096077 restraints weight = 29873.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.097683 restraints weight = 18999.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.098664 restraints weight = 13768.405| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18128 Z= 0.179 Angle : 0.585 5.423 24684 Z= 0.309 Chirality : 0.048 0.370 2709 Planarity : 0.005 0.067 3136 Dihedral : 6.414 58.495 2774 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.21 % Allowed : 1.04 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.17), residues: 2235 helix: -2.96 (0.48), residues: 66 sheet: -0.48 (0.17), residues: 914 loop : -1.71 (0.16), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 73 TYR 0.026 0.002 TYR A 170 PHE 0.015 0.002 PHE S 44 TRP 0.012 0.001 TRP P 345 HIS 0.005 0.001 HIS G 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (18081) covalent geometry : angle 0.57283 / 0.31 (24574) SS BOND : bond 0.00294 / 0.19 ( 31) SS BOND : angle 1.48810 / 0.92 ( 62) hydrogen bonds : bond 0.04098 / 2.79 ( 569) hydrogen bonds : angle 5.67477 / 3.98 ( 1611) link_BETA1-4 : bond 0.00449 / 0.21 ( 8) link_BETA1-4 : angle 1.92386 / 1.19 ( 24) link_NAG-ASN : bond 0.00469 / 0.26 ( 8) link_NAG-ASN : angle 2.59730 / 1.57 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Evaluate side-chains 330 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 326 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 116 ASP cc_start: 0.8769 (m-30) cc_final: 0.8451 (m-30) REVERT: A 151 MET cc_start: 0.8999 (mtp) cc_final: 0.8721 (mtp) REVERT: A 334 MET cc_start: 0.8390 (tpp) cc_final: 0.8039 (ttm) REVERT: A 363 SER cc_start: 0.8546 (t) cc_final: 0.7972 (t) REVERT: D 73 ARG cc_start: 0.7929 (mmm-85) cc_final: 0.7595 (mmt90) REVERT: D 80 LEU cc_start: 0.7307 (tp) cc_final: 0.6536 (pt) REVERT: D 182 ASN cc_start: 0.7813 (m-40) cc_final: 0.7509 (m-40) REVERT: G 82 SER cc_start: 0.9294 (m) cc_final: 0.9070 (p) REVERT: I 84 VAL cc_start: 0.8311 (t) cc_final: 0.7969 (p) REVERT: I 89 ARG cc_start: 0.7271 (ptt180) cc_final: 0.7009 (ptt180) REVERT: P 35 ARG cc_start: 0.8177 (tpt90) cc_final: 0.7610 (tpt90) REVERT: P 159 MET cc_start: 0.8659 (mtp) cc_final: 0.8313 (mtp) REVERT: P 205 VAL cc_start: 0.8840 (t) cc_final: 0.8633 (t) REVERT: P 348 MET cc_start: 0.6981 (mpp) cc_final: 0.6542 (mpp) REVERT: P 388 PHE cc_start: 0.8436 (m-10) cc_final: 0.8099 (m-80) REVERT: S 59 LEU cc_start: 0.8260 (mt) cc_final: 0.8058 (mt) outliers start: 4 outliers final: 3 residues processed: 330 average time/residue: 0.2859 time to fit residues: 144.2982 Evaluate side-chains 286 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 283 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 149 optimal weight: 4.9990 chunk 197 optimal weight: 0.7980 chunk 221 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN D 124 HIS ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 95 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 = 0.3728 r_free = 0.3728 target = 0.108653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.090955 restraints weight = 130109.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.095082 restraints weight = 55574.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.097699 restraints weight = 29776.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.099205 restraints weight = 18850.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.100314 restraints weight = 13890.814| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.5916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18128 Z= 0.119 Angle : 0.550 6.236 24684 Z= 0.288 Chirality : 0.047 0.345 2709 Planarity : 0.005 0.068 3136 Dihedral : 6.200 57.473 2774 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.26 % Allowed : 0.57 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.17), residues: 2235 helix: -2.91 (0.48), residues: 66 sheet: -0.52 (0.17), residues: 881 loop : -1.60 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 73 TYR 0.029 0.001 TYR A 170 PHE 0.013 0.001 PHE S 70 TRP 0.011 0.001 TRP D 345 HIS 0.004 0.001 HIS D 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (18081) covalent geometry : angle 0.53776 / 0.29 (24574) SS BOND : bond 0.00347 / 0.21 ( 31) SS BOND : angle 1.43941 / 0.82 ( 62) hydrogen bonds : bond 0.03576 / 2.43 ( 569) hydrogen bonds : angle 5.52145 / 3.87 ( 1611) link_BETA1-4 : bond 0.00345 / 0.16 ( 8) link_BETA1-4 : angle 1.84520 / 1.13 ( 24) link_NAG-ASN : bond 0.00343 / 0.17 ( 8) link_NAG-ASN : angle 2.46635 / 1.50 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Evaluate side-chains 339 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 334 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 116 ASP cc_start: 0.8754 (m-30) cc_final: 0.8413 (m-30) REVERT: A 151 MET cc_start: 0.9004 (mtp) cc_final: 0.8708 (mtp) REVERT: A 334 MET cc_start: 0.8408 (tpp) cc_final: 0.8087 (ttm) REVERT: A 363 SER cc_start: 0.8609 (t) cc_final: 0.8097 (t) REVERT: D 73 ARG cc_start: 0.7889 (mmm-85) cc_final: 0.7615 (mmt90) REVERT: D 80 LEU cc_start: 0.7220 (tp) cc_final: 0.6426 (pt) REVERT: D 124 HIS cc_start: 0.7956 (OUTLIER) cc_final: 0.7203 (m-70) REVERT: D 182 ASN cc_start: 0.7903 (m-40) cc_final: 0.7571 (m-40) REVERT: D 347 GLU cc_start: 0.6488 (pt0) cc_final: 0.6175 (pt0) REVERT: G 82 SER cc_start: 0.9303 (m) cc_final: 0.9054 (p) REVERT: G 320 ASN cc_start: 0.8411 (t0) cc_final: 0.8089 (p0) REVERT: G 329 THR cc_start: 0.8970 (p) cc_final: 0.8537 (t) REVERT: I 2 VAL cc_start: 0.8199 (m) cc_final: 0.7997 (m) REVERT: I 84 VAL cc_start: 0.8306 (t) cc_final: 0.7973 (p) REVERT: I 89 ARG cc_start: 0.7259 (ptt180) cc_final: 0.7014 (ptt180) REVERT: L 39 ASP cc_start: 0.7807 (m-30) cc_final: 0.7487 (m-30) REVERT: L 42 LEU cc_start: 0.8033 (tp) cc_final: 0.7580 (tp) REVERT: L 76 PHE cc_start: 0.9005 (m-80) cc_final: 0.8404 (m-80) REVERT: P 35 ARG cc_start: 0.8051 (tpt90) cc_final: 0.7477 (tpt90) REVERT: P 159 MET cc_start: 0.8642 (mtp) cc_final: 0.8247 (mtp) REVERT: P 205 VAL cc_start: 0.8964 (t) cc_final: 0.8741 (t) REVERT: P 348 MET cc_start: 0.7087 (mpp) cc_final: 0.6585 (mpp) REVERT: P 388 PHE cc_start: 0.8401 (m-10) cc_final: 0.8068 (m-80) REVERT: S 68 ASN cc_start: 0.7167 (m-40) cc_final: 0.6965 (m-40) outliers start: 5 outliers final: 3 residues processed: 339 average time/residue: 0.2871 time to fit residues: 148.9663 Evaluate side-chains 286 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 282 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 203 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 chunk 221 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 181 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.109245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.090979 restraints weight = 137734.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.095058 restraints weight = 60186.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.097697 restraints weight = 33185.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.099128 restraints weight = 21656.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.100262 restraints weight = 16511.233| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.6034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18128 Z= 0.113 Angle : 0.550 12.007 24684 Z= 0.287 Chirality : 0.047 0.339 2709 Planarity : 0.004 0.068 3136 Dihedral : 6.059 56.210 2774 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.21 % Allowed : 0.57 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.17), residues: 2235 helix: -2.78 (0.50), residues: 66 sheet: -0.47 (0.17), residues: 884 loop : -1.55 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 73 TYR 0.029 0.001 TYR A 170 PHE 0.036 0.001 PHE P 250 TRP 0.015 0.001 TRP P 345 HIS 0.005 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (18081) covalent geometry : angle 0.53151 / 0.28 (24574) SS BOND : bond 0.00301 / 0.17 ( 31) SS BOND : angle 2.22186 / 1.30 ( 62) hydrogen bonds : bond 0.03444 / 2.34 ( 569) hydrogen bonds : angle 5.43154 / 3.80 ( 1611) link_BETA1-4 : bond 0.00404 / 0.20 ( 8) link_BETA1-4 : angle 1.84354 / 1.13 ( 24) link_NAG-ASN : bond 0.00335 / 0.17 ( 8) link_NAG-ASN : angle 2.41135 / 1.46 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Evaluate side-chains 329 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 325 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 116 ASP cc_start: 0.8742 (m-30) cc_final: 0.8416 (m-30) REVERT: A 151 MET cc_start: 0.8932 (mtp) cc_final: 0.8651 (mtp) REVERT: A 334 MET cc_start: 0.8379 (tpp) cc_final: 0.8074 (ttm) REVERT: A 348 MET cc_start: 0.7301 (mtp) cc_final: 0.6642 (mtp) REVERT: A 363 SER cc_start: 0.8655 (t) cc_final: 0.8167 (t) REVERT: D 73 ARG cc_start: 0.7870 (mmm-85) cc_final: 0.7609 (mmt90) REVERT: D 80 LEU cc_start: 0.7197 (tp) cc_final: 0.6405 (pt) REVERT: D 182 ASN cc_start: 0.7902 (m-40) cc_final: 0.7576 (m-40) REVERT: G 82 SER cc_start: 0.9293 (m) cc_final: 0.9070 (p) REVERT: G 329 THR cc_start: 0.8931 (p) cc_final: 0.8521 (t) REVERT: I 84 VAL cc_start: 0.8327 (t) cc_final: 0.7985 (p) REVERT: I 89 ARG cc_start: 0.7287 (ptt180) cc_final: 0.7039 (ptt180) REVERT: L 6 GLN cc_start: 0.7001 (tt0) cc_final: 0.6777 (tt0) REVERT: L 39 ASP cc_start: 0.7709 (m-30) cc_final: 0.7443 (m-30) REVERT: L 76 PHE cc_start: 0.9003 (m-80) cc_final: 0.8431 (m-80) REVERT: P 35 ARG cc_start: 0.8014 (tpt90) cc_final: 0.7424 (tpt90) REVERT: P 128 MET cc_start: 0.8374 (ptp) cc_final: 0.8148 (ptp) REVERT: P 205 VAL cc_start: 0.8932 (t) cc_final: 0.8695 (t) REVERT: P 388 PHE cc_start: 0.8351 (m-10) cc_final: 0.7992 (m-80) REVERT: S 68 ASN cc_start: 0.7135 (m-40) cc_final: 0.6911 (m-40) REVERT: T 83 VAL cc_start: 0.7901 (t) cc_final: 0.7206 (m) outliers start: 4 outliers final: 3 residues processed: 329 average time/residue: 0.2631 time to fit residues: 132.7768 Evaluate side-chains 285 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 282 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 46 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 79 optimal weight: 0.0770 chunk 45 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 183 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN D 124 HIS ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 317 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.107386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.089144 restraints weight = 139847.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.093129 restraints weight = 61534.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.095702 restraints weight = 34214.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.097200 restraints weight = 22483.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.098285 restraints weight = 17030.321| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.6182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18128 Z= 0.177 Angle : 0.585 8.732 24684 Z= 0.307 Chirality : 0.047 0.359 2709 Planarity : 0.005 0.073 3136 Dihedral : 6.089 53.841 2774 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.26 % Allowed : 0.42 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.17), residues: 2235 helix: -2.86 (0.49), residues: 66 sheet: -0.49 (0.17), residues: 878 loop : -1.62 (0.16), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 73 TYR 0.030 0.001 TYR A 170 PHE 0.019 0.002 PHE P 250 TRP 0.015 0.001 TRP D 345 HIS 0.006 0.001 HIS G 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (18081) covalent geometry : angle 0.57009 / 0.30 (24574) SS BOND : bond 0.00327 / 0.19 ( 31) SS BOND : angle 1.94965 / 1.16 ( 62) hydrogen bonds : bond 0.03886 / 2.66 ( 569) hydrogen bonds : angle 5.49985 / 3.87 ( 1611) link_BETA1-4 : bond 0.00448 / 0.22 ( 8) link_BETA1-4 : angle 1.84592 / 1.13 ( 24) link_NAG-ASN : bond 0.00427 / 0.24 ( 8) link_NAG-ASN : angle 2.41376 / 1.46 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue ILE 251 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Evaluate side-chains 318 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 313 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 334 MET cc_start: 0.8479 (tpp) cc_final: 0.8116 (ttm) REVERT: A 363 SER cc_start: 0.8753 (t) cc_final: 0.8225 (t) REVERT: D 80 LEU cc_start: 0.7321 (tp) cc_final: 0.6466 (pt) REVERT: D 182 ASN cc_start: 0.7834 (m-40) cc_final: 0.7556 (m-40) REVERT: G 82 SER cc_start: 0.9347 (m) cc_final: 0.9131 (p) REVERT: I 84 VAL cc_start: 0.8319 (t) cc_final: 0.7963 (p) REVERT: I 89 ARG cc_start: 0.7432 (ptt180) cc_final: 0.7180 (ptt180) REVERT: L 42 LEU cc_start: 0.8046 (tp) cc_final: 0.7577 (tp) REVERT: L 95 GLN cc_start: 0.8688 (pp30) cc_final: 0.8285 (pp30) REVERT: P 35 ARG cc_start: 0.8131 (tpt90) cc_final: 0.7617 (tpt90) REVERT: P 165 ASN cc_start: 0.8745 (m-40) cc_final: 0.8328 (m-40) REVERT: P 205 VAL cc_start: 0.8852 (t) cc_final: 0.8640 (t) REVERT: P 348 MET cc_start: 0.7114 (mpp) cc_final: 0.6678 (mpp) REVERT: P 388 PHE cc_start: 0.8367 (m-10) cc_final: 0.8029 (m-80) REVERT: S 68 ASN cc_start: 0.7168 (m-40) cc_final: 0.6968 (m-40) outliers start: 5 outliers final: 3 residues processed: 318 average time/residue: 0.2760 time to fit residues: 136.2123 Evaluate side-chains 273 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 270 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 161 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 143 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN D 144 GLN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 95 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 = 0.3728 r_free = 0.3728 target = 0.108910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.090868 restraints weight = 138096.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.094877 restraints weight = 60153.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.097420 restraints weight = 33217.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.099007 restraints weight = 21772.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.099908 restraints weight = 16220.453| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.6266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 18128 Z= 0.106 Angle : 0.540 7.148 24684 Z= 0.282 Chirality : 0.047 0.326 2709 Planarity : 0.004 0.070 3136 Dihedral : 5.916 54.055 2774 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.21 % Allowed : 0.21 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.17), residues: 2235 helix: -2.72 (0.52), residues: 66 sheet: -0.49 (0.17), residues: 875 loop : -1.53 (0.16), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 73 TYR 0.015 0.001 TYR D 170 PHE 0.021 0.001 PHE P 250 TRP 0.015 0.001 TRP P 345 HIS 0.003 0.001 HIS D 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (18081) covalent geometry : angle 0.52806 / 0.28 (24574) SS BOND : bond 0.00296 / 0.19 ( 31) SS BOND : angle 1.51891 / 0.93 ( 62) hydrogen bonds : bond 0.03370 / 2.30 ( 569) hydrogen bonds : angle 5.40391 / 3.79 ( 1611) link_BETA1-4 : bond 0.00345 / 0.17 ( 8) link_BETA1-4 : angle 1.84333 / 1.12 ( 24) link_NAG-ASN : bond 0.00326 / 0.15 ( 8) link_NAG-ASN : angle 2.31621 / 1.40 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5304.71 seconds wall clock time: 91 minutes 22.29 seconds (5482.29 seconds total)