Starting phenix.real_space_refine on Sat Feb 7 17:48:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eje_48101/02_2026/9eje_48101_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eje_48101/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9eje_48101/02_2026/9eje_48101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eje_48101/02_2026/9eje_48101.map" model { file = "/net/cci-nas-00/data/ceres_data/9eje_48101/02_2026/9eje_48101_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eje_48101/02_2026/9eje_48101_trim.cif" } 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-2.0-5952/lib/python3.9/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, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 6.57, per 1000 atoms: 0.19 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: 3.23 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.19 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: 9.11 Time building geometry restraints manager: 4.53 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: 2.560 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: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 34.610 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 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 covalent geometry : bond 0.00403 (18081) covalent geometry : angle 0.65056 (24574) SS BOND : bond 0.00324 ( 31) SS BOND : angle 0.97839 ( 62) hydrogen bonds : bond 0.20506 ( 569) hydrogen bonds : angle 9.04554 ( 1611) link_BETA1-4 : bond 0.00666 ( 8) link_BETA1-4 : angle 3.73634 ( 24) link_NAG-ASN : bond 0.00831 ( 8) link_NAG-ASN : angle 3.37831 ( 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 : 0.942 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: symmetry clash REVERT: A 52 THR cc_start: 0.9520 (p) cc_final: 0.9298 (p) REVERT: A 194 GLU cc_start: 0.7171 (tt0) cc_final: 0.6962 (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: 0.6228 (t80) REVERT: A 294 GLU cc_start: 0.7735 (mt-10) cc_final: 0.6906 (mp0) REVERT: A 371 VAL cc_start: 0.8365 (t) cc_final: 0.8023 (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: 0.5882 (pt0) REVERT: G 56 LEU cc_start: 0.8322 (mt) cc_final: 0.8082 (mt) REVERT: G 315 VAL cc_start: 0.7712 (m) cc_final: 0.7328 (m) REVERT: G 316 LEU cc_start: 0.7869 (mt) cc_final: 0.7493 (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: 0.7561 (t) REVERT: I 115 VAL cc_start: 0.6656 (t) cc_final: 0.6368 (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: 0.8794 (m-80) REVERT: P 4 ASN cc_start: 0.8142 (m-40) cc_final: 0.7861 (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: 0.8817 (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: 0.8064 (t) REVERT: P 205 VAL cc_start: 0.8893 (t) cc_final: 0.8579 (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: 0.6252 (tt0) REVERT: P 348 MET cc_start: 0.7187 (mtm) cc_final: 0.6890 (mpp) REVERT: P 349 ILE cc_start: 0.8830 (mt) cc_final: 0.8611 (mm) REVERT: S 74 LEU cc_start: 0.8686 (tp) cc_final: 0.8002 (tp) REVERT: S 85 TYR cc_start: 0.6234 (m-80) cc_final: 0.5513 (m-80) REVERT: S 105 ASP cc_start: 0.8367 (p0) cc_final: 0.8050 (t0) REVERT: T 63 VAL cc_start: 0.8800 (t) cc_final: 0.8424 (p) REVERT: T 76 PHE cc_start: 0.8414 (m-80) cc_final: 0.7888 (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: 0.3513 time to fit residues: 353.8229 Evaluate side-chains 401 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 381 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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: 0.8980 chunk 107 optimal weight: 0.9990 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: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3816 r_free = 0.3816 target = 0.114123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.095683 restraints weight = 136187.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.100043 restraints weight = 58075.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.102793 restraints weight = 31297.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.104488 restraints weight = 19994.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.105578 restraints weight = 14659.455| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 18128 Z= 0.149 Angle : 0.650 9.228 24684 Z= 0.342 Chirality : 0.050 0.365 2709 Planarity : 0.005 0.057 3136 Dihedral : 7.934 55.379 2774 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % 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: -1.54 (0.17), residues: 2235 helix: -3.15 (0.46), residues: 60 sheet: -0.33 (0.17), residues: 859 loop : -1.42 (0.16), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 98 TYR 0.013 0.002 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 P 192 Details of bonding type rmsd covalent geometry : bond 0.00342 (18081) covalent geometry : angle 0.62792 (24574) SS BOND : bond 0.00312 ( 31) SS BOND : angle 2.09600 ( 62) hydrogen bonds : bond 0.05041 ( 569) hydrogen bonds : angle 6.57623 ( 1611) link_BETA1-4 : bond 0.00686 ( 8) link_BETA1-4 : angle 3.11380 ( 24) link_NAG-ASN : bond 0.00598 ( 8) link_NAG-ASN : angle 3.06544 ( 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 453 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 445 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8836 (m-30) cc_final: 0.8483 (m-30) REVERT: D 35 ARG cc_start: 0.7967 (tpt90) cc_final: 0.7460 (mmm160) REVERT: D 116 ASP cc_start: 0.8075 (m-30) cc_final: 0.7823 (m-30) REVERT: D 182 ASN cc_start: 0.7369 (m-40) cc_final: 0.6998 (m-40) REVERT: G 76 MET cc_start: 0.8182 (mtt) cc_final: 0.7917 (mtp) REVERT: G 128 MET cc_start: 0.7323 (ptp) cc_final: 0.6992 (ptp) REVERT: G 329 THR cc_start: 0.8852 (p) cc_final: 0.8503 (t) REVERT: I 95 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7406 (mt-10) REVERT: I 97 ASP cc_start: 0.6997 (m-30) cc_final: 0.6248 (t0) REVERT: L 2 ILE cc_start: 0.6542 (mt) cc_final: 0.6298 (mm) REVERT: L 42 LEU cc_start: 0.7962 (tp) cc_final: 0.7630 (tp) REVERT: L 76 PHE cc_start: 0.9071 (m-80) cc_final: 0.8739 (m-80) REVERT: L 84 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7525 (mm-30) REVERT: M 53 ILE cc_start: 0.7622 (mp) cc_final: 0.7310 (mm) REVERT: P 4 ASN cc_start: 0.8313 (m-40) cc_final: 0.7786 (m110) REVERT: P 35 ARG cc_start: 0.8124 (tpt90) cc_final: 0.7291 (tpt90) REVERT: P 47 ARG cc_start: 0.7715 (mtt-85) cc_final: 0.7186 (mtt90) REVERT: P 120 TYR cc_start: 0.9028 (p90) cc_final: 0.8562 (p90) REVERT: P 205 VAL cc_start: 0.8782 (t) cc_final: 0.8516 (t) REVERT: S 32 HIS cc_start: 0.5142 (m90) cc_final: 0.4623 (m90) REVERT: S 105 ASP cc_start: 0.8469 (p0) cc_final: 0.8198 (t0) REVERT: T 83 VAL cc_start: 0.7915 (t) cc_final: 0.7099 (t) REVERT: T 92 TYR cc_start: 0.6571 (m-80) cc_final: 0.5448 (m-80) outliers start: 8 outliers final: 5 residues processed: 451 average time/residue: 0.3129 time to fit residues: 212.6935 Evaluate side-chains 357 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 352 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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: 7.9990 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... Flipped N/Q/H residues before XYZ refinement: A 144 GLN ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS G 246 GLN G 317 ASN S 69 GLN T 6 GLN T 33 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.105167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.087204 restraints weight = 134098.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.091210 restraints weight = 56788.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.093757 restraints weight = 30521.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.095329 restraints weight = 19473.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.096367 restraints weight = 14282.557| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 18128 Z= 0.322 Angle : 0.750 10.056 24684 Z= 0.398 Chirality : 0.051 0.479 2709 Planarity : 0.005 0.072 3136 Dihedral : 7.339 58.344 2774 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.31 % Allowed : 3.07 % Favored : 96.62 % 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: -1.95 (0.17), residues: 2235 helix: -2.39 (0.59), residues: 48 sheet: -0.57 (0.17), residues: 895 loop : -1.84 (0.15), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 283 TYR 0.019 0.002 TYR P 72 PHE 0.020 0.002 PHE A 14 TRP 0.013 0.002 TRP G 96 HIS 0.008 0.002 HIS P 61 Details of bonding type rmsd covalent geometry : bond 0.00693 (18081) covalent geometry : angle 0.73279 (24574) SS BOND : bond 0.00436 ( 31) SS BOND : angle 2.08262 ( 62) hydrogen bonds : bond 0.05868 ( 569) hydrogen bonds : angle 6.40813 ( 1611) link_BETA1-4 : bond 0.00577 ( 8) link_BETA1-4 : angle 2.83735 ( 24) link_NAG-ASN : bond 0.00826 ( 8) link_NAG-ASN : angle 3.18212 ( 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 370 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 364 time to evaluate : 0.986 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: A 128 MET cc_start: 0.8022 (ptt) cc_final: 0.7690 (ptm) REVERT: A 151 MET cc_start: 0.9072 (mtp) cc_final: 0.8765 (mtp) REVERT: A 263 THR cc_start: 0.7870 (p) cc_final: 0.7514 (t) REVERT: A 347 GLU cc_start: 0.7429 (pt0) cc_final: 0.7047 (pt0) REVERT: D 80 LEU cc_start: 0.7299 (tp) cc_final: 0.6601 (pt) REVERT: D 182 ASN cc_start: 0.7767 (m-40) cc_final: 0.7459 (m-40) REVERT: D 271 PHE cc_start: 0.8009 (p90) cc_final: 0.7780 (p90) REVERT: G 76 MET cc_start: 0.8229 (mtt) cc_final: 0.8020 (mtp) REVERT: G 320 ASN cc_start: 0.8415 (t0) cc_final: 0.8079 (p0) REVERT: I 2 VAL cc_start: 0.8089 (m) cc_final: 0.7809 (m) REVERT: L 42 LEU cc_start: 0.8250 (tp) cc_final: 0.7806 (tp) REVERT: L 84 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7725 (mm-30) REVERT: M 53 ILE cc_start: 0.7679 (mp) cc_final: 0.7285 (mm) REVERT: M 76 PHE cc_start: 0.8405 (m-10) cc_final: 0.8169 (m-10) REVERT: P 20 ASP cc_start: 0.8520 (m-30) cc_final: 0.8294 (m-30) REVERT: P 76 MET cc_start: 0.7541 (mtt) cc_final: 0.7240 (mtp) REVERT: P 205 VAL cc_start: 0.8843 (t) cc_final: 0.8642 (t) REVERT: P 250 PHE cc_start: 0.6993 (t80) cc_final: 0.6738 (t80) REVERT: P 388 PHE cc_start: 0.8568 (m-10) cc_final: 0.8197 (m-80) REVERT: S 59 LEU cc_start: 0.8142 (mt) cc_final: 0.7907 (mt) REVERT: S 64 ASP cc_start: 0.6982 (t0) cc_final: 0.6775 (t0) REVERT: S 105 ASP cc_start: 0.8712 (p0) cc_final: 0.7679 (t0) REVERT: T 13 VAL cc_start: 0.8858 (p) cc_final: 0.8380 (p) REVERT: T 53 ILE cc_start: 0.8580 (mm) cc_final: 0.8319 (mm) outliers start: 6 outliers final: 3 residues processed: 369 average time/residue: 0.3130 time to fit residues: 174.1662 Evaluate side-chains 291 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 288 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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: 5.9990 chunk 1 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 150 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 63 optimal weight: 0.0170 overall best weight: 2.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 214 ASN S 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.107724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.089427 restraints weight = 138753.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.093419 restraints weight = 60519.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.095972 restraints weight = 33583.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.097474 restraints weight = 22048.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.098558 restraints weight = 16667.423| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 18128 Z= 0.200 Angle : 0.633 7.156 24684 Z= 0.336 Chirality : 0.048 0.398 2709 Planarity : 0.005 0.066 3136 Dihedral : 7.072 58.480 2774 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.16 % Allowed : 2.03 % Favored : 97.82 % 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: -1.94 (0.17), residues: 2235 helix: -2.98 (0.49), residues: 66 sheet: -0.57 (0.17), residues: 899 loop : -1.77 (0.16), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG T 66 TYR 0.038 0.002 TYR A 170 PHE 0.012 0.002 PHE D 223 TRP 0.011 0.001 TRP G 96 HIS 0.005 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00441 (18081) covalent geometry : angle 0.61601 (24574) SS BOND : bond 0.00674 ( 31) SS BOND : angle 2.02336 ( 62) hydrogen bonds : bond 0.04677 ( 569) hydrogen bonds : angle 6.08802 ( 1611) link_BETA1-4 : bond 0.00421 ( 8) link_BETA1-4 : angle 2.20858 ( 24) link_NAG-ASN : bond 0.00488 ( 8) link_NAG-ASN : angle 2.87721 ( 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 351 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 348 time to evaluate : 0.926 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: 0.8783 (m-30) cc_final: 0.8464 (m-30) REVERT: A 151 MET cc_start: 0.9099 (mtp) cc_final: 0.8788 (mtp) REVERT: A 263 THR cc_start: 0.7791 (p) cc_final: 0.7581 (p) REVERT: A 347 GLU cc_start: 0.7260 (pt0) cc_final: 0.7026 (pt0) REVERT: D 80 LEU cc_start: 0.7258 (tp) cc_final: 0.6603 (pt) REVERT: D 182 ASN cc_start: 0.7682 (m-40) cc_final: 0.7378 (m-40) REVERT: G 320 ASN cc_start: 0.8289 (t0) cc_final: 0.8007 (p0) REVERT: I 2 VAL cc_start: 0.8096 (m) cc_final: 0.7777 (m) REVERT: I 28 TRP cc_start: 0.8816 (m100) cc_final: 0.8612 (m100) REVERT: I 84 VAL cc_start: 0.8500 (t) cc_final: 0.8227 (p) REVERT: I 95 GLU cc_start: 0.7786 (mp0) cc_final: 0.7154 (mt-10) REVERT: L 42 LEU cc_start: 0.8179 (tp) cc_final: 0.7753 (tp) REVERT: L 76 PHE cc_start: 0.9025 (m-80) cc_final: 0.8412 (m-80) REVERT: M 42 LEU cc_start: 0.8463 (mt) cc_final: 0.8117 (mt) REVERT: P 20 ASP cc_start: 0.8526 (m-30) cc_final: 0.8288 (m-30) REVERT: P 52 THR cc_start: 0.8598 (p) cc_final: 0.8378 (p) REVERT: P 56 LEU cc_start: 0.8999 (mt) cc_final: 0.8758 (mm) REVERT: P 76 MET cc_start: 0.7506 (mtt) cc_final: 0.7203 (mtp) REVERT: P 120 TYR cc_start: 0.8933 (p90) cc_final: 0.8662 (p90) REVERT: P 205 VAL cc_start: 0.8777 (t) cc_final: 0.8568 (t) REVERT: P 250 PHE cc_start: 0.6940 (t80) cc_final: 0.6687 (t80) REVERT: P 388 PHE cc_start: 0.8477 (m-10) cc_final: 0.8170 (m-80) REVERT: S 59 LEU cc_start: 0.8154 (mt) cc_final: 0.7952 (mt) REVERT: S 105 ASP cc_start: 0.8651 (p0) cc_final: 0.7638 (t0) REVERT: T 53 ILE cc_start: 0.8517 (mm) cc_final: 0.8270 (mm) outliers start: 3 outliers final: 3 residues processed: 351 average time/residue: 0.3001 time to fit residues: 158.5245 Evaluate side-chains 292 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 289 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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: 5.9990 chunk 42 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 216 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.108209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.089811 restraints weight = 138910.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.093839 restraints weight = 60711.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.096434 restraints weight = 33656.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.098014 restraints weight = 22064.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.098927 restraints weight = 16503.725| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18128 Z= 0.159 Angle : 0.584 6.496 24684 Z= 0.310 Chirality : 0.048 0.375 2709 Planarity : 0.005 0.061 3136 Dihedral : 6.775 58.790 2774 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.21 % Allowed : 1.66 % Favored : 98.13 % 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: -1.87 (0.17), residues: 2235 helix: -2.95 (0.49), residues: 66 sheet: -0.49 (0.17), residues: 893 loop : -1.73 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 28 TYR 0.029 0.002 TYR A 170 PHE 0.012 0.002 PHE S 70 TRP 0.010 0.001 TRP G 96 HIS 0.004 0.001 HIS P 61 Details of bonding type rmsd covalent geometry : bond 0.00357 (18081) covalent geometry : angle 0.57249 (24574) SS BOND : bond 0.00542 ( 31) SS BOND : angle 1.23888 ( 62) hydrogen bonds : bond 0.04236 ( 569) hydrogen bonds : angle 5.85324 ( 1611) link_BETA1-4 : bond 0.00405 ( 8) link_BETA1-4 : angle 2.03670 ( 24) link_NAG-ASN : bond 0.00432 ( 8) link_NAG-ASN : angle 2.75238 ( 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 355 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 351 time to evaluate : 0.954 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: A 116 ASP cc_start: 0.8754 (m-30) cc_final: 0.8405 (m-30) REVERT: A 151 MET cc_start: 0.9039 (mtp) cc_final: 0.8754 (mtp) REVERT: A 250 PHE cc_start: 0.8480 (t80) cc_final: 0.7874 (t80) REVERT: A 263 THR cc_start: 0.7765 (p) cc_final: 0.7497 (p) REVERT: A 347 GLU cc_start: 0.7232 (pt0) cc_final: 0.6826 (pt0) REVERT: D 80 LEU cc_start: 0.7198 (tp) cc_final: 0.6528 (pt) REVERT: D 182 ASN cc_start: 0.7892 (m-40) cc_final: 0.7512 (m-40) REVERT: G 82 SER cc_start: 0.9268 (m) cc_final: 0.8938 (p) REVERT: G 216 MET cc_start: 0.8059 (ttt) cc_final: 0.7503 (tmm) REVERT: G 320 ASN cc_start: 0.8297 (t0) cc_final: 0.8032 (p0) REVERT: H 43 ILE cc_start: 0.8067 (pt) cc_final: 0.7866 (pt) REVERT: I 2 VAL cc_start: 0.8069 (m) cc_final: 0.7768 (m) REVERT: I 84 VAL cc_start: 0.8417 (t) cc_final: 0.8116 (p) REVERT: I 95 GLU cc_start: 0.7797 (mp0) cc_final: 0.7351 (mt-10) REVERT: L 42 LEU cc_start: 0.8253 (tp) cc_final: 0.7775 (tp) REVERT: L 76 PHE cc_start: 0.8998 (m-80) cc_final: 0.8379 (m-80) REVERT: M 53 ILE cc_start: 0.6360 (mt) cc_final: 0.5991 (mm) REVERT: P 36 GLU cc_start: 0.9005 (pm20) cc_final: 0.8657 (pm20) REVERT: P 120 TYR cc_start: 0.8894 (p90) cc_final: 0.8622 (p90) REVERT: P 159 MET cc_start: 0.8605 (mtp) cc_final: 0.8232 (mtp) REVERT: P 205 VAL cc_start: 0.8976 (t) cc_final: 0.8764 (t) REVERT: P 388 PHE cc_start: 0.8465 (m-10) cc_final: 0.8144 (m-80) REVERT: S 59 LEU cc_start: 0.8201 (mt) cc_final: 0.7994 (mt) REVERT: T 53 ILE cc_start: 0.8402 (mm) cc_final: 0.8111 (mm) REVERT: T 95 GLN cc_start: 0.8109 (pp30) cc_final: 0.7761 (pm20) outliers start: 4 outliers final: 3 residues processed: 355 average time/residue: 0.3186 time to fit residues: 169.7365 Evaluate side-chains 294 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 291 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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: 9.9990 chunk 134 optimal weight: 8.9990 chunk 160 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.106988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.089280 restraints weight = 131680.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.093311 restraints weight = 55712.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.095865 restraints weight = 29901.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.097456 restraints weight = 19055.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.098319 restraints weight = 13871.192| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 18128 Z= 0.225 Angle : 0.625 6.616 24684 Z= 0.332 Chirality : 0.048 0.398 2709 Planarity : 0.005 0.066 3136 Dihedral : 6.708 59.817 2774 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.16 % Allowed : 1.35 % Favored : 98.49 % 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: -1.94 (0.17), residues: 2235 helix: -2.95 (0.50), residues: 66 sheet: -0.51 (0.17), residues: 908 loop : -1.83 (0.16), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 28 TYR 0.030 0.002 TYR M 91 PHE 0.029 0.002 PHE P 250 TRP 0.011 0.001 TRP P 345 HIS 0.005 0.002 HIS P 61 Details of bonding type rmsd covalent geometry : bond 0.00500 (18081) covalent geometry : angle 0.61262 (24574) SS BOND : bond 0.00452 ( 31) SS BOND : angle 1.48456 ( 62) hydrogen bonds : bond 0.04516 ( 569) hydrogen bonds : angle 5.86625 ( 1611) link_BETA1-4 : bond 0.00580 ( 8) link_BETA1-4 : angle 2.03148 ( 24) link_NAG-ASN : bond 0.00542 ( 8) link_NAG-ASN : angle 2.76186 ( 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 329 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 326 time to evaluate : 0.958 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: A 116 ASP cc_start: 0.8880 (m-30) cc_final: 0.8559 (m-30) REVERT: A 151 MET cc_start: 0.9016 (mtp) cc_final: 0.8726 (mtp) REVERT: A 263 THR cc_start: 0.7866 (p) cc_final: 0.7621 (p) REVERT: A 347 GLU cc_start: 0.7261 (pt0) cc_final: 0.6843 (pt0) REVERT: A 363 SER cc_start: 0.8560 (t) cc_final: 0.8172 (t) REVERT: D 35 ARG cc_start: 0.8239 (tpt90) cc_final: 0.7584 (mmm160) REVERT: D 80 LEU cc_start: 0.7483 (tp) cc_final: 0.6677 (pt) REVERT: D 182 ASN cc_start: 0.7819 (m-40) cc_final: 0.7547 (m-40) REVERT: D 271 PHE cc_start: 0.8077 (p90) cc_final: 0.7642 (p90) REVERT: D 347 GLU cc_start: 0.6413 (pt0) cc_final: 0.6155 (tt0) REVERT: G 82 SER cc_start: 0.9317 (m) cc_final: 0.9038 (p) REVERT: G 320 ASN cc_start: 0.8269 (t0) cc_final: 0.7923 (p0) REVERT: H 43 ILE cc_start: 0.8258 (pt) cc_final: 0.8056 (pt) REVERT: I 2 VAL cc_start: 0.8188 (m) cc_final: 0.7964 (m) REVERT: I 84 VAL cc_start: 0.8325 (t) cc_final: 0.7992 (p) REVERT: I 89 ARG cc_start: 0.7324 (ptt180) cc_final: 0.7028 (ptt180) REVERT: I 95 GLU cc_start: 0.7823 (mp0) cc_final: 0.7374 (mt-10) REVERT: P 36 GLU cc_start: 0.9038 (pm20) cc_final: 0.8778 (pm20) REVERT: P 52 THR cc_start: 0.8748 (p) cc_final: 0.8401 (p) REVERT: P 68 ASP cc_start: 0.8216 (p0) cc_final: 0.7908 (p0) REVERT: P 120 TYR cc_start: 0.8981 (p90) cc_final: 0.8652 (p90) REVERT: P 159 MET cc_start: 0.8628 (mtp) cc_final: 0.8310 (mtp) REVERT: P 205 VAL cc_start: 0.8806 (t) cc_final: 0.8583 (t) REVERT: P 388 PHE cc_start: 0.8474 (m-10) cc_final: 0.8159 (m-80) outliers start: 3 outliers final: 3 residues processed: 329 average time/residue: 0.3089 time to fit residues: 152.4039 Evaluate side-chains 277 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 274 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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: 2.9990 chunk 136 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 144 GLN A 308 ASN ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.106830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.088633 restraints weight = 139352.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.092639 restraints weight = 61420.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.095196 restraints weight = 33897.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.096790 restraints weight = 22234.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.097692 restraints weight = 16597.088| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18128 Z= 0.168 Angle : 0.585 6.058 24684 Z= 0.310 Chirality : 0.048 0.369 2709 Planarity : 0.005 0.071 3136 Dihedral : 6.518 57.771 2774 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.21 % Allowed : 0.88 % Favored : 98.91 % 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: -1.92 (0.17), residues: 2235 helix: -3.01 (0.49), residues: 66 sheet: -0.48 (0.18), residues: 867 loop : -1.79 (0.15), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 73 TYR 0.034 0.001 TYR A 170 PHE 0.013 0.002 PHE I 70 TRP 0.013 0.001 TRP P 157 HIS 0.004 0.001 HIS G 124 Details of bonding type rmsd covalent geometry : bond 0.00373 (18081) covalent geometry : angle 0.57298 (24574) SS BOND : bond 0.00417 ( 31) SS BOND : angle 1.46010 ( 62) hydrogen bonds : bond 0.04069 ( 569) hydrogen bonds : angle 5.71253 ( 1611) link_BETA1-4 : bond 0.00458 ( 8) link_BETA1-4 : angle 1.89109 ( 24) link_NAG-ASN : bond 0.00393 ( 8) link_NAG-ASN : angle 2.58597 ( 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 334 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 330 time to evaluate : 0.825 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: A 116 ASP cc_start: 0.8825 (m-30) cc_final: 0.8556 (m-30) REVERT: A 151 MET cc_start: 0.8998 (mtp) cc_final: 0.8727 (mtp) REVERT: A 250 PHE cc_start: 0.8616 (t80) cc_final: 0.7942 (t80) REVERT: A 334 MET cc_start: 0.8406 (tpp) cc_final: 0.8086 (ttm) REVERT: A 347 GLU cc_start: 0.7270 (pt0) cc_final: 0.6871 (pt0) REVERT: A 363 SER cc_start: 0.8578 (t) cc_final: 0.8175 (t) REVERT: D 35 ARG cc_start: 0.8337 (tpt90) cc_final: 0.7724 (mmm160) REVERT: D 73 ARG cc_start: 0.8055 (mmm-85) cc_final: 0.7654 (mtt90) REVERT: D 80 LEU cc_start: 0.7400 (tp) cc_final: 0.6594 (pt) REVERT: D 182 ASN cc_start: 0.7791 (m-40) cc_final: 0.7519 (m-40) REVERT: D 245 VAL cc_start: 0.8204 (m) cc_final: 0.7981 (p) REVERT: D 271 PHE cc_start: 0.7957 (p90) cc_final: 0.7660 (p90) REVERT: D 347 GLU cc_start: 0.6433 (pt0) cc_final: 0.6062 (tt0) REVERT: G 82 SER cc_start: 0.9280 (m) cc_final: 0.9021 (p) REVERT: G 128 MET cc_start: 0.7391 (ptp) cc_final: 0.7067 (ptp) REVERT: G 216 MET cc_start: 0.8084 (ttt) cc_final: 0.7460 (tmm) REVERT: H 59 LEU cc_start: 0.8775 (mt) cc_final: 0.8511 (mt) REVERT: I 2 VAL cc_start: 0.8083 (m) cc_final: 0.7872 (m) REVERT: I 67 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8412 (mmmm) REVERT: I 84 VAL cc_start: 0.8323 (t) cc_final: 0.7992 (p) REVERT: I 89 ARG cc_start: 0.7385 (ptt180) cc_final: 0.7119 (ptt180) REVERT: I 95 GLU cc_start: 0.7833 (mp0) cc_final: 0.7394 (mt-10) REVERT: M 42 LEU cc_start: 0.8220 (mt) cc_final: 0.7777 (mt) REVERT: P 35 ARG cc_start: 0.8322 (tpt90) cc_final: 0.7717 (tpt90) REVERT: P 68 ASP cc_start: 0.8197 (p0) cc_final: 0.7856 (p0) REVERT: P 76 MET cc_start: 0.7567 (mtt) cc_final: 0.7254 (mtp) REVERT: P 120 TYR cc_start: 0.8916 (p90) cc_final: 0.8628 (p90) REVERT: P 165 ASN cc_start: 0.8712 (m-40) cc_final: 0.8362 (m-40) REVERT: P 348 MET cc_start: 0.7134 (mpp) cc_final: 0.6682 (mpp) REVERT: P 388 PHE cc_start: 0.8466 (m-10) cc_final: 0.8147 (m-80) REVERT: T 95 GLN cc_start: 0.8107 (pp30) cc_final: 0.7888 (pp30) outliers start: 4 outliers final: 3 residues processed: 334 average time/residue: 0.2819 time to fit residues: 142.1330 Evaluate side-chains 280 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 277 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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: 0.9980 chunk 197 optimal weight: 5.9990 chunk 221 optimal weight: 3.9990 chunk 26 optimal weight: 0.0170 chunk 150 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 198 optimal weight: 0.4980 chunk 151 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.3020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** 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 = 0.3689 r_free = 0.3689 target = 0.106618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.088803 restraints weight = 131222.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.092873 restraints weight = 55862.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.095474 restraints weight = 29912.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.096976 restraints weight = 19024.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.098001 restraints weight = 14049.641| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.6051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18128 Z= 0.138 Angle : 0.565 8.119 24684 Z= 0.297 Chirality : 0.047 0.364 2709 Planarity : 0.005 0.072 3136 Dihedral : 6.314 56.071 2774 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.21 % Allowed : 0.52 % Favored : 99.27 % 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: -1.83 (0.17), residues: 2235 helix: -2.95 (0.49), residues: 66 sheet: -0.45 (0.17), residues: 867 loop : -1.70 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 106 TYR 0.029 0.001 TYR A 170 PHE 0.015 0.002 PHE M 76 TRP 0.011 0.001 TRP D 345 HIS 0.004 0.001 HIS G 124 Details of bonding type rmsd covalent geometry : bond 0.00316 (18081) covalent geometry : angle 0.55390 (24574) SS BOND : bond 0.00228 ( 31) SS BOND : angle 1.19960 ( 62) hydrogen bonds : bond 0.03771 ( 569) hydrogen bonds : angle 5.61704 ( 1611) link_BETA1-4 : bond 0.00381 ( 8) link_BETA1-4 : angle 1.86289 ( 24) link_NAG-ASN : bond 0.00372 ( 8) link_NAG-ASN : angle 2.55028 ( 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 324 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 320 time to evaluate : 0.821 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: A 116 ASP cc_start: 0.8754 (m-30) cc_final: 0.8492 (m-30) REVERT: A 151 MET cc_start: 0.8987 (mtp) cc_final: 0.8724 (mtp) REVERT: A 263 THR cc_start: 0.7687 (p) cc_final: 0.7358 (t) REVERT: A 334 MET cc_start: 0.8420 (tpp) cc_final: 0.8101 (ttm) REVERT: A 347 GLU cc_start: 0.7220 (pt0) cc_final: 0.6822 (pt0) REVERT: A 363 SER cc_start: 0.8539 (t) cc_final: 0.8049 (t) REVERT: D 73 ARG cc_start: 0.8017 (mmm-85) cc_final: 0.7777 (mmt90) REVERT: D 80 LEU cc_start: 0.7274 (tp) cc_final: 0.6417 (pt) REVERT: D 182 ASN cc_start: 0.7831 (m-40) cc_final: 0.7522 (m-40) REVERT: D 245 VAL cc_start: 0.8242 (m) cc_final: 0.8006 (p) REVERT: D 271 PHE cc_start: 0.7938 (p90) cc_final: 0.7718 (p90) REVERT: D 347 GLU cc_start: 0.6373 (pt0) cc_final: 0.6144 (pt0) REVERT: G 82 SER cc_start: 0.9309 (m) cc_final: 0.9048 (p) REVERT: G 216 MET cc_start: 0.8064 (ttt) cc_final: 0.7429 (tmm) REVERT: G 320 ASN cc_start: 0.8178 (t0) cc_final: 0.7886 (p0) REVERT: I 2 VAL cc_start: 0.8141 (m) cc_final: 0.7882 (m) REVERT: I 67 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8397 (mmmm) REVERT: I 84 VAL cc_start: 0.8321 (t) cc_final: 0.7982 (p) REVERT: P 35 ARG cc_start: 0.8142 (tpt90) cc_final: 0.7543 (tpt90) REVERT: P 68 ASP cc_start: 0.8183 (p0) cc_final: 0.7787 (p0) REVERT: P 159 MET cc_start: 0.8463 (mtt) cc_final: 0.8242 (mmt) REVERT: P 165 ASN cc_start: 0.8724 (m-40) cc_final: 0.8350 (m-40) REVERT: P 205 VAL cc_start: 0.8680 (t) cc_final: 0.8473 (t) REVERT: P 348 MET cc_start: 0.7118 (mpp) cc_final: 0.6617 (mpp) REVERT: P 388 PHE cc_start: 0.8433 (m-10) cc_final: 0.8113 (m-80) REVERT: S 68 ASN cc_start: 0.7153 (m-40) cc_final: 0.6935 (m-40) REVERT: T 83 VAL cc_start: 0.8026 (m) cc_final: 0.7744 (p) outliers start: 4 outliers final: 3 residues processed: 324 average time/residue: 0.2871 time to fit residues: 140.9226 Evaluate side-chains 276 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 273 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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: 3.9990 chunk 29 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 181 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 83 optimal weight: 0.0870 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN D 124 HIS ** D 176 HIS ** 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 = 0.3716 r_free = 0.3716 target = 0.108050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.089858 restraints weight = 137976.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.093864 restraints weight = 60023.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.096466 restraints weight = 33210.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.098074 restraints weight = 21683.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.099123 restraints weight = 16122.304| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.6134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18128 Z= 0.113 Angle : 0.540 5.285 24684 Z= 0.283 Chirality : 0.047 0.341 2709 Planarity : 0.005 0.070 3136 Dihedral : 6.061 54.777 2774 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.26 % Allowed : 0.47 % Favored : 99.27 % 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: -1.74 (0.17), residues: 2235 helix: -2.85 (0.50), residues: 66 sheet: -0.48 (0.17), residues: 859 loop : -1.56 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 73 TYR 0.030 0.001 TYR A 170 PHE 0.012 0.001 PHE S 70 TRP 0.015 0.001 TRP P 345 HIS 0.003 0.001 HIS D 61 Details of bonding type rmsd covalent geometry : bond 0.00260 (18081) covalent geometry : angle 0.52951 (24574) SS BOND : bond 0.00250 ( 31) SS BOND : angle 1.23044 ( 62) hydrogen bonds : bond 0.03457 ( 569) hydrogen bonds : angle 5.44651 ( 1611) link_BETA1-4 : bond 0.00481 ( 8) link_BETA1-4 : angle 1.86949 ( 24) link_NAG-ASN : bond 0.00335 ( 8) link_NAG-ASN : angle 2.41665 ( 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 328 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 323 time to evaluate : 0.901 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: A 116 ASP cc_start: 0.8690 (m-30) cc_final: 0.8441 (m-30) REVERT: A 151 MET cc_start: 0.8916 (mtp) cc_final: 0.8644 (mtp) REVERT: A 263 THR cc_start: 0.7550 (p) cc_final: 0.7344 (t) REVERT: A 334 MET cc_start: 0.8407 (tpp) cc_final: 0.8113 (ttm) REVERT: A 347 GLU cc_start: 0.7222 (pt0) cc_final: 0.6828 (pt0) REVERT: A 363 SER cc_start: 0.8601 (t) cc_final: 0.8187 (t) REVERT: D 73 ARG cc_start: 0.7988 (mmm-85) cc_final: 0.7759 (mmt90) REVERT: D 80 LEU cc_start: 0.7258 (tp) cc_final: 0.6359 (pt) REVERT: D 124 HIS cc_start: 0.7908 (OUTLIER) cc_final: 0.7196 (m-70) REVERT: D 182 ASN cc_start: 0.7901 (m-40) cc_final: 0.7575 (m-40) REVERT: D 245 VAL cc_start: 0.8239 (m) cc_final: 0.8004 (p) REVERT: D 271 PHE cc_start: 0.7884 (p90) cc_final: 0.7654 (p90) REVERT: G 82 SER cc_start: 0.9284 (m) cc_final: 0.9040 (p) REVERT: G 216 MET cc_start: 0.8035 (ttt) cc_final: 0.7379 (tmm) REVERT: G 320 ASN cc_start: 0.8160 (t0) cc_final: 0.7868 (p0) REVERT: I 2 VAL cc_start: 0.8175 (m) cc_final: 0.7880 (m) REVERT: I 67 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8383 (mmmm) REVERT: I 84 VAL cc_start: 0.8319 (t) cc_final: 0.7982 (p) REVERT: M 42 LEU cc_start: 0.8313 (mt) cc_final: 0.7874 (mt) REVERT: P 20 ASP cc_start: 0.8431 (m-30) cc_final: 0.7828 (p0) REVERT: P 35 ARG cc_start: 0.8026 (tpt90) cc_final: 0.7407 (tpt90) REVERT: P 165 ASN cc_start: 0.8711 (m-40) cc_final: 0.8317 (m-40) REVERT: P 205 VAL cc_start: 0.8872 (t) cc_final: 0.8663 (t) REVERT: P 348 MET cc_start: 0.7255 (mpp) cc_final: 0.6768 (mpp) REVERT: P 388 PHE cc_start: 0.8390 (m-10) cc_final: 0.8057 (m-80) REVERT: S 68 ASN cc_start: 0.7121 (m-40) cc_final: 0.6900 (m-40) REVERT: T 83 VAL cc_start: 0.8012 (m) cc_final: 0.7728 (p) outliers start: 5 outliers final: 3 residues processed: 328 average time/residue: 0.2881 time to fit residues: 143.3799 Evaluate side-chains 281 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 277 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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: 3.9990 chunk 168 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 chunk 8 optimal weight: 0.0970 chunk 183 optimal weight: 0.0970 chunk 146 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.109577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.091767 restraints weight = 130510.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.095943 restraints weight = 54722.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.098600 restraints weight = 29016.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.100158 restraints weight = 18287.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.101257 restraints weight = 13329.165| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.6259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 18128 Z= 0.097 Angle : 0.542 11.097 24684 Z= 0.283 Chirality : 0.047 0.327 2709 Planarity : 0.004 0.072 3136 Dihedral : 5.905 54.058 2774 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.74 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: -1.63 (0.17), residues: 2235 helix: -2.78 (0.51), residues: 66 sheet: -0.43 (0.17), residues: 882 loop : -1.48 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 73 TYR 0.020 0.001 TYR P 72 PHE 0.014 0.001 PHE M 76 TRP 0.018 0.001 TRP P 345 HIS 0.007 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00228 (18081) covalent geometry : angle 0.52424 (24574) SS BOND : bond 0.00246 ( 31) SS BOND : angle 2.12316 ( 62) hydrogen bonds : bond 0.03282 ( 569) hydrogen bonds : angle 5.38884 ( 1611) link_BETA1-4 : bond 0.00364 ( 8) link_BETA1-4 : angle 1.83941 ( 24) link_NAG-ASN : bond 0.00334 ( 8) link_NAG-ASN : angle 2.34283 ( 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 334 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 330 time to evaluate : 0.856 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: A 116 ASP cc_start: 0.8684 (m-30) cc_final: 0.8330 (m-30) REVERT: A 263 THR cc_start: 0.7475 (p) cc_final: 0.7251 (t) REVERT: A 334 MET cc_start: 0.8461 (tpp) cc_final: 0.8135 (ttm) REVERT: A 347 GLU cc_start: 0.7108 (pt0) cc_final: 0.6734 (pt0) REVERT: A 363 SER cc_start: 0.8621 (t) cc_final: 0.8263 (t) REVERT: D 73 ARG cc_start: 0.7951 (mmm-85) cc_final: 0.7735 (mmt90) REVERT: D 80 LEU cc_start: 0.7275 (tp) cc_final: 0.6443 (pt) REVERT: D 182 ASN cc_start: 0.7942 (m-40) cc_final: 0.7628 (m-40) REVERT: D 271 PHE cc_start: 0.7794 (p90) cc_final: 0.7590 (p90) REVERT: G 65 THR cc_start: 0.7982 (p) cc_final: 0.7736 (p) REVERT: G 82 SER cc_start: 0.9275 (m) cc_final: 0.9069 (p) REVERT: G 320 ASN cc_start: 0.8166 (t0) cc_final: 0.7904 (p0) REVERT: G 329 THR cc_start: 0.8927 (p) cc_final: 0.8524 (t) REVERT: I 2 VAL cc_start: 0.8141 (m) cc_final: 0.7886 (m) REVERT: I 67 LYS cc_start: 0.8571 (mmtt) cc_final: 0.8366 (mmmm) REVERT: I 84 VAL cc_start: 0.8311 (t) cc_final: 0.7964 (p) REVERT: I 95 GLU cc_start: 0.7595 (mp0) cc_final: 0.7316 (mt-10) REVERT: P 20 ASP cc_start: 0.8448 (m-30) cc_final: 0.7849 (p0) REVERT: P 165 ASN cc_start: 0.8715 (m-40) cc_final: 0.8241 (m-40) REVERT: P 205 VAL cc_start: 0.8869 (t) cc_final: 0.8668 (t) REVERT: P 388 PHE cc_start: 0.8321 (m-10) cc_final: 0.7967 (m-80) REVERT: T 83 VAL cc_start: 0.7929 (m) cc_final: 0.7658 (p) outliers start: 4 outliers final: 3 residues processed: 334 average time/residue: 0.2845 time to fit residues: 145.6306 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 : 1.015 ------------------------------------------------------------------------------- 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: 2.9990 chunk 22 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 206 optimal weight: 0.9990 chunk 178 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3727 r_free = 0.3727 target = 0.108497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.090696 restraints weight = 130116.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.094804 restraints weight = 54874.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.097423 restraints weight = 29318.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.098894 restraints weight = 18597.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.099922 restraints weight = 13791.698| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18128 Z= 0.120 Angle : 0.538 5.556 24684 Z= 0.281 Chirality : 0.046 0.331 2709 Planarity : 0.004 0.072 3136 Dihedral : 5.848 52.804 2774 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % 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: -1.61 (0.17), residues: 2235 helix: -2.74 (0.51), residues: 66 sheet: -0.46 (0.17), residues: 900 loop : -1.45 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 73 TYR 0.019 0.001 TYR A 170 PHE 0.013 0.001 PHE M 76 TRP 0.016 0.001 TRP P 345 HIS 0.004 0.001 HIS G 124 Details of bonding type rmsd covalent geometry : bond 0.00276 (18081) covalent geometry : angle 0.52552 (24574) SS BOND : bond 0.00325 ( 31) SS BOND : angle 1.52305 ( 62) hydrogen bonds : bond 0.03387 ( 569) hydrogen bonds : angle 5.35368 ( 1611) link_BETA1-4 : bond 0.00402 ( 8) link_BETA1-4 : angle 1.82577 ( 24) link_NAG-ASN : bond 0.00322 ( 8) link_NAG-ASN : angle 2.30847 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5485.98 seconds wall clock time: 94 minutes 38.06 seconds (5678.06 seconds total)