Starting phenix.real_space_refine on Thu Mar 5 02:35:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f8n_31490/03_2026/7f8n_31490.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f8n_31490/03_2026/7f8n_31490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f8n_31490/03_2026/7f8n_31490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f8n_31490/03_2026/7f8n_31490.map" model { file = "/net/cci-nas-00/data/ceres_data/7f8n_31490/03_2026/7f8n_31490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f8n_31490/03_2026/7f8n_31490.cif" } resolution = 3.4 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 28 5.49 5 S 77 5.16 5 C 12474 2.51 5 N 2716 2.21 5 O 3227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18522 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2467 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2467 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2467 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2467 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2467 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2467 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2467 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 139 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'LBN:plan-3': 4, 'LBN:plan-1': 3, 'LBN:plan-2': 3} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 179 Unusual residues: {'LBN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'LBN:plan-3': 4, 'LBN:plan-1': 3, 'LBN:plan-2': 3} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'LBN:plan-3': 3, 'LBN:plan-1': 2, 'LBN:plan-2': 2} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 151 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'LBN:plan-3': 4, 'LBN:plan-1': 2, 'LBN:plan-2': 3} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 218 Unusual residues: {'LBN': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'LBN:plan-1': 5, 'LBN:plan-3': 5, 'LBN:plan-2': 4} Unresolved non-hydrogen planarities: 49 Chain: "F" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 179 Unusual residues: {'LBN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'LBN:plan-3': 4, 'LBN:plan-1': 3, 'LBN:plan-2': 3} Unresolved non-hydrogen planarities: 36 Chain: "G" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 219 Unusual residues: {'LBN': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'LBN:plan-3': 4, 'LBN:plan-1': 3, 'LBN:plan-2': 3} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 4.61, per 1000 atoms: 0.25 Number of scatterers: 18522 At special positions: 0 Unit cell: (101.25, 102.06, 119.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 28 15.00 O 3227 8.00 N 2716 7.00 C 12474 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.02 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " 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 Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 734.7 milliseconds 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4214 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 7 sheets defined 71.8% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 32 through 60 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 100 through 120 removed outlier: 3.678A pdb=" N TRP A 104 " --> pdb=" O ASN A 100 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'A' and resid 131 through 160 removed outlier: 3.669A pdb=" N ALA A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 207 through 237 Processing helix chain 'A' and resid 238 through 243 removed outlier: 3.658A pdb=" N ASP A 242 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU A 243 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 269 through 296 Proline residue: A 289 - end of helix removed outlier: 3.753A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.725A pdb=" N GLU A 310 " --> pdb=" O LYS A 307 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 311 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 312 " --> pdb=" O TYR A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 338 Processing helix chain 'A' and resid 342 through 354 removed outlier: 4.201A pdb=" N LYS A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 60 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 100 through 120 removed outlier: 3.677A pdb=" N TRP B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 121 through 131 Processing helix chain 'B' and resid 131 through 160 removed outlier: 3.671A pdb=" N ALA B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 207 through 237 Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.657A pdb=" N ASP B 242 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU B 243 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 269 through 296 Proline residue: B 289 - end of helix removed outlier: 3.754A pdb=" N PHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 removed outlier: 3.726A pdb=" N GLU B 310 " --> pdb=" O LYS B 307 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE B 311 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 312 " --> pdb=" O TYR B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 342 through 354 removed outlier: 4.200A pdb=" N LYS B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 60 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 100 through 120 removed outlier: 3.677A pdb=" N TRP C 104 " --> pdb=" O ASN C 100 " (cutoff:3.500A) Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 121 through 131 Processing helix chain 'C' and resid 131 through 160 removed outlier: 3.670A pdb=" N ALA C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 205 Processing helix chain 'C' and resid 207 through 237 Processing helix chain 'C' and resid 238 through 243 removed outlier: 3.658A pdb=" N ASP C 242 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU C 243 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 269 through 296 Proline residue: C 289 - end of helix removed outlier: 3.753A pdb=" N PHE C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 removed outlier: 3.725A pdb=" N GLU C 310 " --> pdb=" O LYS C 307 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE C 311 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 312 " --> pdb=" O TYR C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 338 Processing helix chain 'C' and resid 342 through 354 removed outlier: 4.201A pdb=" N LYS C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS C 347 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL C 350 " --> pdb=" O LYS C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 60 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 88 Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.678A pdb=" N TRP D 104 " --> pdb=" O ASN D 100 " (cutoff:3.500A) Proline residue: D 110 - end of helix Processing helix chain 'D' and resid 121 through 131 Processing helix chain 'D' and resid 131 through 160 removed outlier: 3.670A pdb=" N ALA D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 207 through 237 Processing helix chain 'D' and resid 238 through 243 removed outlier: 3.656A pdb=" N ASP D 242 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU D 243 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 269 through 296 Proline residue: D 289 - end of helix removed outlier: 3.753A pdb=" N PHE D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 312 removed outlier: 3.725A pdb=" N GLU D 310 " --> pdb=" O LYS D 307 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 312 " --> pdb=" O TYR D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 338 Processing helix chain 'D' and resid 342 through 354 removed outlier: 4.201A pdb=" N LYS D 346 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 350 " --> pdb=" O LYS D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 60 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 73 through 88 Processing helix chain 'E' and resid 100 through 120 removed outlier: 3.678A pdb=" N TRP E 104 " --> pdb=" O ASN E 100 " (cutoff:3.500A) Proline residue: E 110 - end of helix Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'E' and resid 131 through 160 removed outlier: 3.670A pdb=" N ALA E 160 " --> pdb=" O ALA E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 205 Processing helix chain 'E' and resid 207 through 237 Processing helix chain 'E' and resid 238 through 243 removed outlier: 3.657A pdb=" N ASP E 242 " --> pdb=" O SER E 239 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU E 243 " --> pdb=" O LEU E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 254 Processing helix chain 'E' and resid 269 through 296 Proline residue: E 289 - end of helix removed outlier: 3.753A pdb=" N PHE E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 312 removed outlier: 3.725A pdb=" N GLU E 310 " --> pdb=" O LYS E 307 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE E 311 " --> pdb=" O VAL E 308 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E 312 " --> pdb=" O TYR E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 338 Processing helix chain 'E' and resid 342 through 354 removed outlier: 4.200A pdb=" N LYS E 346 " --> pdb=" O VAL E 342 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS E 347 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL E 350 " --> pdb=" O LYS E 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 60 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 73 through 88 Processing helix chain 'F' and resid 100 through 120 removed outlier: 3.678A pdb=" N TRP F 104 " --> pdb=" O ASN F 100 " (cutoff:3.500A) Proline residue: F 110 - end of helix Processing helix chain 'F' and resid 121 through 131 Processing helix chain 'F' and resid 131 through 160 removed outlier: 3.670A pdb=" N ALA F 160 " --> pdb=" O ALA F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 205 Processing helix chain 'F' and resid 207 through 237 Processing helix chain 'F' and resid 238 through 243 removed outlier: 3.658A pdb=" N ASP F 242 " --> pdb=" O SER F 239 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU F 243 " --> pdb=" O LEU F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 254 Processing helix chain 'F' and resid 269 through 296 Proline residue: F 289 - end of helix removed outlier: 3.753A pdb=" N PHE F 296 " --> pdb=" O VAL F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 312 removed outlier: 3.726A pdb=" N GLU F 310 " --> pdb=" O LYS F 307 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU F 312 " --> pdb=" O TYR F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 338 Processing helix chain 'F' and resid 342 through 354 removed outlier: 4.201A pdb=" N LYS F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL F 350 " --> pdb=" O LYS F 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 60 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 73 through 88 Processing helix chain 'G' and resid 100 through 120 removed outlier: 3.677A pdb=" N TRP G 104 " --> pdb=" O ASN G 100 " (cutoff:3.500A) Proline residue: G 110 - end of helix Processing helix chain 'G' and resid 121 through 131 Processing helix chain 'G' and resid 131 through 160 removed outlier: 3.670A pdb=" N ALA G 160 " --> pdb=" O ALA G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 205 Processing helix chain 'G' and resid 207 through 237 Processing helix chain 'G' and resid 238 through 243 removed outlier: 3.657A pdb=" N ASP G 242 " --> pdb=" O SER G 239 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU G 243 " --> pdb=" O LEU G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 254 Processing helix chain 'G' and resid 269 through 296 Proline residue: G 289 - end of helix removed outlier: 3.754A pdb=" N PHE G 296 " --> pdb=" O VAL G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 312 removed outlier: 3.726A pdb=" N GLU G 310 " --> pdb=" O LYS G 307 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE G 311 " --> pdb=" O VAL G 308 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU G 312 " --> pdb=" O TYR G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 338 Processing helix chain 'G' and resid 342 through 354 removed outlier: 4.201A pdb=" N LYS G 346 " --> pdb=" O VAL G 342 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS G 347 " --> pdb=" O LYS G 343 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL G 350 " --> pdb=" O LYS G 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 67 removed outlier: 4.380A pdb=" N GLN A 264 " --> pdb=" O PHE A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 67 removed outlier: 4.381A pdb=" N GLN B 264 " --> pdb=" O PHE B 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 67 removed outlier: 4.380A pdb=" N GLN C 264 " --> pdb=" O PHE C 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 67 removed outlier: 4.381A pdb=" N GLN D 264 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 67 removed outlier: 4.381A pdb=" N GLN E 264 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 67 removed outlier: 4.380A pdb=" N GLN F 264 " --> pdb=" O PHE F 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 67 removed outlier: 4.380A pdb=" N GLN G 264 " --> pdb=" O PHE G 67 " (cutoff:3.500A) 1106 hydrogen bonds defined for protein. 3213 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: 2.90 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5131 1.34 - 1.46: 2861 1.46 - 1.57: 10698 1.57 - 1.69: 28 1.69 - 1.81: 147 Bond restraints: 18865 Sorted by residual: bond pdb=" C42 LBN E 507 " pdb=" C5 LBN E 507 " ideal model delta sigma weight residual 1.333 1.558 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C42 LBN D 505 " pdb=" C5 LBN D 505 " ideal model delta sigma weight residual 1.333 1.557 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C42 LBN G 506 " pdb=" C5 LBN G 506 " ideal model delta sigma weight residual 1.333 1.557 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C42 LBN F 505 " pdb=" C5 LBN F 505 " ideal model delta sigma weight residual 1.333 1.557 -0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C42 LBN A 503 " pdb=" C5 LBN A 503 " ideal model delta sigma weight residual 1.333 1.557 -0.224 2.00e-02 2.50e+03 1.25e+02 ... (remaining 18860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 24461 2.42 - 4.85: 529 4.85 - 7.27: 232 7.27 - 9.70: 125 9.70 - 12.12: 14 Bond angle restraints: 25361 Sorted by residual: angle pdb=" N PRO C 23 " pdb=" CA PRO C 23 " pdb=" CB PRO C 23 " ideal model delta sigma weight residual 103.25 110.72 -7.47 1.05e+00 9.07e-01 5.06e+01 angle pdb=" N PRO F 23 " pdb=" CA PRO F 23 " pdb=" CB PRO F 23 " ideal model delta sigma weight residual 103.25 110.72 -7.47 1.05e+00 9.07e-01 5.06e+01 angle pdb=" N PRO D 23 " pdb=" CA PRO D 23 " pdb=" CB PRO D 23 " ideal model delta sigma weight residual 103.25 110.71 -7.46 1.05e+00 9.07e-01 5.05e+01 angle pdb=" N PRO E 23 " pdb=" CA PRO E 23 " pdb=" CB PRO E 23 " ideal model delta sigma weight residual 103.25 110.71 -7.46 1.05e+00 9.07e-01 5.04e+01 angle pdb=" N PRO B 23 " pdb=" CA PRO B 23 " pdb=" CB PRO B 23 " ideal model delta sigma weight residual 103.25 110.69 -7.44 1.05e+00 9.07e-01 5.02e+01 ... (remaining 25356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.55: 11067 32.55 - 65.10: 455 65.10 - 97.65: 63 97.65 - 130.20: 21 130.20 - 162.74: 21 Dihedral angle restraints: 11627 sinusoidal: 5166 harmonic: 6461 Sorted by residual: dihedral pdb=" C1 LBN G 502 " pdb=" O1 LBN G 502 " pdb=" P1 LBN G 502 " pdb=" O3 LBN G 502 " ideal model delta sinusoidal sigma weight residual -84.60 78.14 -162.74 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C1 LBN E 503 " pdb=" O1 LBN E 503 " pdb=" P1 LBN E 503 " pdb=" O3 LBN E 503 " ideal model delta sinusoidal sigma weight residual -84.60 78.11 -162.71 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C1 LBN A 506 " pdb=" O1 LBN A 506 " pdb=" P1 LBN A 506 " pdb=" O3 LBN A 506 " ideal model delta sinusoidal sigma weight residual -84.60 78.11 -162.71 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 11624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2200 0.042 - 0.083: 510 0.083 - 0.125: 119 0.125 - 0.166: 6 0.166 - 0.208: 35 Chirality restraints: 2870 Sorted by residual: chirality pdb=" C2 LBN E 506 " pdb=" C1 LBN E 506 " pdb=" C3 LBN E 506 " pdb=" O7 LBN E 506 " both_signs ideal model delta sigma weight residual False -2.36 -2.57 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C2 LBN C 504 " pdb=" C1 LBN C 504 " pdb=" C3 LBN C 504 " pdb=" O7 LBN C 504 " both_signs ideal model delta sigma weight residual False -2.36 -2.57 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C2 LBN G 502 " pdb=" C1 LBN G 502 " pdb=" C3 LBN G 502 " pdb=" O7 LBN G 502 " both_signs ideal model delta sigma weight residual False -2.36 -2.57 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 2867 not shown) Planarity restraints: 2968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN F 505 " -0.111 2.00e-02 2.50e+03 1.12e-01 1.25e+02 pdb=" C42 LBN F 505 " 0.110 2.00e-02 2.50e+03 pdb=" C5 LBN F 505 " 0.114 2.00e-02 2.50e+03 pdb=" C8 LBN F 505 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN A 503 " 0.112 2.00e-02 2.50e+03 1.12e-01 1.25e+02 pdb=" C42 LBN A 503 " -0.110 2.00e-02 2.50e+03 pdb=" C5 LBN A 503 " -0.114 2.00e-02 2.50e+03 pdb=" C8 LBN A 503 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN C 505 " 0.111 2.00e-02 2.50e+03 1.12e-01 1.25e+02 pdb=" C42 LBN C 505 " -0.110 2.00e-02 2.50e+03 pdb=" C5 LBN C 505 " -0.114 2.00e-02 2.50e+03 pdb=" C8 LBN C 505 " 0.112 2.00e-02 2.50e+03 ... (remaining 2965 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2648 2.75 - 3.29: 18338 3.29 - 3.83: 31185 3.83 - 4.36: 39659 4.36 - 4.90: 65638 Nonbonded interactions: 157468 Sorted by model distance: nonbonded pdb=" OD2 ASP E 138 " pdb=" OH TYR E 331 " model vdw 2.219 3.040 nonbonded pdb=" OD2 ASP A 138 " pdb=" OH TYR A 331 " model vdw 2.219 3.040 nonbonded pdb=" OD2 ASP F 138 " pdb=" OH TYR F 331 " model vdw 2.219 3.040 nonbonded pdb=" OD2 ASP C 138 " pdb=" OH TYR C 331 " model vdw 2.219 3.040 nonbonded pdb=" OD2 ASP D 138 " pdb=" OH TYR D 331 " model vdw 2.219 3.040 ... (remaining 157463 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 13 through 356 or (resid 501 and (name C1 or name C12 or n \ ame C15 or name C18 or name C2 or name C6 or name C9 or name N1 or name O1 or na \ me O2 or name O3 or name O4 or name O5 or name O7 or name O8 or name P1 )) or (r \ esid 502 and (name C1 or name C12 or name C15 or name C18 or name C2 or name C3 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name \ C6 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O5 \ or name O7 or name O8 or name P1 )))) selection = (chain 'B' and (resid 13 through 356 or (resid 501 and (name C1 or name C12 or n \ ame C15 or name C18 or name C2 or name C6 or name C9 or name N1 or name O1 or na \ me O2 or name O3 or name O4 or name O5 or name O7 or name O8 or name P1 )) or (r \ esid 502 and (name C1 or name C12 or name C15 or name C18 or name C2 or name C3 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name \ C6 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O5 \ or name O7 or name O8 or name P1 )))) selection = (chain 'C' and (resid 13 through 356 or (resid 501 and (name C1 or name C12 or n \ ame C15 or name C18 or name C2 or name C6 or name C9 or name N1 or name O1 or na \ me O2 or name O3 or name O4 or name O5 or name O7 or name O8 or name P1 )) or (r \ esid 502 and (name C1 or name C12 or name C15 or name C18 or name C2 or name C3 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name \ C6 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O5 \ or name O7 or name O8 or name P1 )))) selection = (chain 'D' and (resid 13 through 356 or (resid 501 and (name C1 or name C12 or n \ ame C15 or name C18 or name C2 or name C6 or name C9 or name N1 or name O1 or na \ me O2 or name O3 or name O4 or name O5 or name O7 or name O8 or name P1 )) or (r \ esid 502 and (name C1 or name C12 or name C15 or name C18 or name C2 or name C3 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name \ C6 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O5 \ or name O7 or name O8 or name P1 )))) selection = (chain 'E' and (resid 13 through 356 or (resid 501 and (name C1 or name C12 or n \ ame C15 or name C18 or name C2 or name C6 or name C9 or name N1 or name O1 or na \ me O2 or name O3 or name O4 or name O5 or name O7 or name O8 or name P1 )) or (r \ esid 502 and (name C1 or name C12 or name C15 or name C18 or name C2 or name C3 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name \ C6 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O5 \ or name O7 or name O8 or name P1 )))) selection = (chain 'F' and (resid 13 through 356 or (resid 501 and (name C1 or name C12 or n \ ame C15 or name C18 or name C2 or name C6 or name C9 or name N1 or name O1 or na \ me O2 or name O3 or name O4 or name O5 or name O7 or name O8 or name P1 )) or (r \ esid 502 and (name C1 or name C12 or name C15 or name C18 or name C2 or name C3 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name \ C6 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O5 \ or name O7 or name O8 or name P1 )))) selection = (chain 'G' and (resid 13 through 356 or (resid 501 and (name C1 or name C12 or n \ ame C15 or name C18 or name C2 or name C6 or name C9 or name N1 or name O1 or na \ me O2 or name O3 or name O4 or name O5 or name O7 or name O8 or name P1 )) or (r \ esid 502 and (name C1 or name C12 or name C15 or name C18 or name C2 or name C3 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name \ C6 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O5 \ or name O7 or name O8 or name P1 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.620 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 : 0.012 0.225 18879 Z= 0.589 Angle : 1.084 12.119 25389 Z= 0.433 Chirality : 0.043 0.208 2870 Planarity : 0.006 0.112 2968 Dihedral : 18.972 162.744 7371 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.55 % Allowed : 3.69 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.91 (0.19), residues: 2107 helix: 0.43 (0.14), residues: 1463 sheet: None (None), residues: 0 loop : -3.06 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 300 TYR 0.006 0.001 TYR E 331 PHE 0.012 0.001 PHE A 116 TRP 0.010 0.002 TRP B 104 HIS 0.001 0.000 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.01184 (18865) covalent geometry : angle 1.08423 (25361) SS BOND : bond 0.00386 ( 14) SS BOND : angle 0.95967 ( 28) hydrogen bonds : bond 0.25730 ( 1106) hydrogen bonds : angle 8.45318 ( 3213) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 134 time to evaluate : 0.550 Fit side-chains REVERT: C 209 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8504 (tp) outliers start: 49 outliers final: 18 residues processed: 176 average time/residue: 0.1324 time to fit residues: 36.1584 Evaluate side-chains 128 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.1980 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 0.4980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 92 ASN A 100 ASN B 56 GLN B 92 ASN B 100 ASN C 56 GLN C 92 ASN C 100 ASN D 92 ASN D 100 ASN E 56 GLN E 92 ASN E 100 ASN F 56 GLN F 92 ASN F 100 ASN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN G 100 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.169283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.143062 restraints weight = 17810.743| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.30 r_work: 0.3318 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18879 Z= 0.138 Angle : 0.602 9.023 25389 Z= 0.304 Chirality : 0.041 0.155 2870 Planarity : 0.005 0.042 2968 Dihedral : 22.208 176.873 3330 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.81 % Allowed : 7.06 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.67 (0.18), residues: 2107 helix: 0.54 (0.14), residues: 1470 sheet: None (None), residues: 0 loop : -2.79 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 254 TYR 0.008 0.001 TYR C 325 PHE 0.021 0.001 PHE A 116 TRP 0.020 0.002 TRP F 74 HIS 0.000 0.000 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00295 (18865) covalent geometry : angle 0.60200 (25361) SS BOND : bond 0.00147 ( 14) SS BOND : angle 0.93033 ( 28) hydrogen bonds : bond 0.05482 ( 1106) hydrogen bonds : angle 5.17413 ( 3213) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 102 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 299 PHE cc_start: 0.7840 (m-10) cc_final: 0.7314 (t80) REVERT: G 299 PHE cc_start: 0.8049 (t80) cc_final: 0.7410 (m-10) outliers start: 54 outliers final: 26 residues processed: 155 average time/residue: 0.1132 time to fit residues: 28.7196 Evaluate side-chains 123 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 83 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN E 100 ASN F 100 ASN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.165918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.139702 restraints weight = 17955.149| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.29 r_work: 0.3279 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18879 Z= 0.162 Angle : 0.606 9.695 25389 Z= 0.300 Chirality : 0.042 0.162 2870 Planarity : 0.004 0.042 2968 Dihedral : 20.594 179.921 3326 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.75 % Allowed : 8.26 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.18), residues: 2107 helix: 0.59 (0.14), residues: 1470 sheet: None (None), residues: 0 loop : -2.78 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 254 TYR 0.009 0.001 TYR D 331 PHE 0.021 0.001 PHE C 116 TRP 0.016 0.002 TRP F 74 HIS 0.001 0.000 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00379 (18865) covalent geometry : angle 0.60511 (25361) SS BOND : bond 0.00473 ( 14) SS BOND : angle 1.27780 ( 28) hydrogen bonds : bond 0.04822 ( 1106) hydrogen bonds : angle 4.81470 ( 3213) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 112 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 PHE cc_start: 0.7965 (m-10) cc_final: 0.7494 (t80) REVERT: C 311 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7873 (mp) REVERT: D 311 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.8007 (mp) REVERT: D 351 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7887 (mp) REVERT: E 299 PHE cc_start: 0.7962 (m-10) cc_final: 0.7413 (t80) REVERT: E 311 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.7970 (mp) REVERT: F 299 PHE cc_start: 0.8006 (m-10) cc_final: 0.7683 (t80) REVERT: F 311 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7901 (mp) outliers start: 53 outliers final: 26 residues processed: 164 average time/residue: 0.1192 time to fit residues: 32.0249 Evaluate side-chains 133 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 25 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 139 optimal weight: 0.2980 chunk 40 optimal weight: 0.6980 chunk 200 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 100 ASN C 100 ASN D 100 ASN ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.169118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.142116 restraints weight = 17756.604| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.31 r_work: 0.3303 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18879 Z= 0.118 Angle : 0.553 7.744 25389 Z= 0.274 Chirality : 0.040 0.202 2870 Planarity : 0.004 0.041 2968 Dihedral : 19.537 179.868 3326 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.44 % Allowed : 9.40 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.18), residues: 2107 helix: 0.77 (0.14), residues: 1470 sheet: None (None), residues: 0 loop : -2.73 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 254 TYR 0.009 0.001 TYR B 325 PHE 0.022 0.001 PHE G 116 TRP 0.015 0.002 TRP G 104 HIS 0.000 0.000 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00264 (18865) covalent geometry : angle 0.55217 (25361) SS BOND : bond 0.00178 ( 14) SS BOND : angle 0.83766 ( 28) hydrogen bonds : bond 0.04180 ( 1106) hydrogen bonds : angle 4.53454 ( 3213) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 PHE cc_start: 0.7936 (m-10) cc_final: 0.7374 (t80) REVERT: A 311 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7721 (mp) REVERT: A 343 LYS cc_start: 0.8417 (mtmt) cc_final: 0.8135 (mtpt) REVERT: B 311 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7789 (mp) REVERT: D 351 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7934 (mp) REVERT: E 299 PHE cc_start: 0.7996 (m-10) cc_final: 0.7382 (t80) REVERT: F 299 PHE cc_start: 0.8124 (m-10) cc_final: 0.7643 (t80) outliers start: 47 outliers final: 30 residues processed: 162 average time/residue: 0.1153 time to fit residues: 30.6506 Evaluate side-chains 139 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 1 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 205 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN B 100 ASN C 100 ASN D 100 ASN E 100 ASN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.164432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.136854 restraints weight = 17711.552| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.33 r_work: 0.3251 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18879 Z= 0.166 Angle : 0.593 8.238 25389 Z= 0.294 Chirality : 0.042 0.169 2870 Planarity : 0.004 0.043 2968 Dihedral : 18.980 179.983 3324 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.81 % Allowed : 10.23 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.19), residues: 2107 helix: 0.74 (0.14), residues: 1477 sheet: None (None), residues: 0 loop : -2.66 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 254 TYR 0.009 0.001 TYR B 325 PHE 0.022 0.001 PHE B 116 TRP 0.014 0.002 TRP B 74 HIS 0.007 0.001 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00389 (18865) covalent geometry : angle 0.59126 (25361) SS BOND : bond 0.00481 ( 14) SS BOND : angle 1.34485 ( 28) hydrogen bonds : bond 0.04402 ( 1106) hydrogen bonds : angle 4.54888 ( 3213) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 109 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 299 PHE cc_start: 0.7994 (m-10) cc_final: 0.7433 (t80) REVERT: A 311 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7750 (mp) REVERT: B 311 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7835 (mp) REVERT: C 311 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7843 (mp) REVERT: D 311 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7958 (mp) REVERT: D 351 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7940 (mp) REVERT: E 299 PHE cc_start: 0.8014 (m-10) cc_final: 0.7431 (t80) REVERT: E 311 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.7924 (mp) REVERT: F 299 PHE cc_start: 0.8106 (m-10) cc_final: 0.7648 (t80) REVERT: F 311 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7890 (mp) outliers start: 54 outliers final: 30 residues processed: 162 average time/residue: 0.1170 time to fit residues: 31.2284 Evaluate side-chains 138 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 166 optimal weight: 0.8980 chunk 196 optimal weight: 0.9980 chunk 95 optimal weight: 0.0030 chunk 133 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 201 optimal weight: 0.0980 chunk 162 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN C 100 ASN D 100 ASN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.169224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.142207 restraints weight = 17497.347| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.33 r_work: 0.3299 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18879 Z= 0.113 Angle : 0.544 7.287 25389 Z= 0.270 Chirality : 0.040 0.190 2870 Planarity : 0.004 0.042 2968 Dihedral : 18.514 179.404 3324 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.75 % Allowed : 11.27 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.19), residues: 2107 helix: 0.80 (0.14), residues: 1491 sheet: None (None), residues: 0 loop : -2.54 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 254 TYR 0.010 0.001 TYR B 325 PHE 0.023 0.001 PHE E 116 TRP 0.014 0.002 TRP G 104 HIS 0.004 0.000 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00254 (18865) covalent geometry : angle 0.54331 (25361) SS BOND : bond 0.00165 ( 14) SS BOND : angle 0.83565 ( 28) hydrogen bonds : bond 0.03926 ( 1106) hydrogen bonds : angle 4.37372 ( 3213) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 105 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 299 PHE cc_start: 0.7926 (m-10) cc_final: 0.7372 (t80) REVERT: A 311 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7778 (mp) REVERT: A 343 LYS cc_start: 0.8407 (mtmt) cc_final: 0.8185 (mtpt) REVERT: B 311 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7785 (mp) REVERT: B 343 LYS cc_start: 0.8520 (mtmt) cc_final: 0.8273 (mtmt) REVERT: D 351 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7850 (mp) REVERT: E 299 PHE cc_start: 0.8005 (m-10) cc_final: 0.7399 (t80) REVERT: E 311 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7857 (mp) REVERT: F 311 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7821 (mp) outliers start: 53 outliers final: 37 residues processed: 154 average time/residue: 0.1231 time to fit residues: 30.9114 Evaluate side-chains 141 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 99 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 208 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 182 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN C 100 ASN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN G 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.167594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.140256 restraints weight = 17610.144| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.33 r_work: 0.3265 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18879 Z= 0.133 Angle : 0.552 7.269 25389 Z= 0.276 Chirality : 0.041 0.199 2870 Planarity : 0.004 0.042 2968 Dihedral : 18.196 179.819 3324 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.65 % Allowed : 11.53 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.17 (0.19), residues: 2107 helix: 0.83 (0.14), residues: 1491 sheet: None (None), residues: 0 loop : -2.48 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 254 TYR 0.009 0.001 TYR C 331 PHE 0.022 0.001 PHE B 116 TRP 0.013 0.002 TRP F 74 HIS 0.002 0.000 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00308 (18865) covalent geometry : angle 0.55127 (25361) SS BOND : bond 0.00300 ( 14) SS BOND : angle 1.06654 ( 28) hydrogen bonds : bond 0.04022 ( 1106) hydrogen bonds : angle 4.35016 ( 3213) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 99 time to evaluate : 0.664 Fit side-chains REVERT: A 299 PHE cc_start: 0.7986 (m-10) cc_final: 0.7400 (t80) REVERT: A 311 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7786 (mp) REVERT: A 343 LYS cc_start: 0.8413 (mtmt) cc_final: 0.8183 (mtpt) REVERT: B 311 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7758 (mp) REVERT: D 311 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7890 (mp) REVERT: D 351 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7893 (mp) REVERT: E 299 PHE cc_start: 0.8028 (m-10) cc_final: 0.7414 (t80) REVERT: E 311 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7890 (mp) REVERT: F 299 PHE cc_start: 0.8115 (m-10) cc_final: 0.7626 (t80) REVERT: F 311 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7850 (mp) outliers start: 51 outliers final: 34 residues processed: 145 average time/residue: 0.1236 time to fit residues: 29.0444 Evaluate side-chains 137 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 28 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 165 optimal weight: 3.9990 chunk 183 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN C 100 ASN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.168600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.141433 restraints weight = 17578.410| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.33 r_work: 0.3287 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18879 Z= 0.118 Angle : 0.539 6.893 25389 Z= 0.270 Chirality : 0.041 0.206 2870 Planarity : 0.004 0.042 2968 Dihedral : 17.746 179.260 3324 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.44 % Allowed : 11.90 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.19), residues: 2107 helix: 0.89 (0.14), residues: 1491 sheet: None (None), residues: 0 loop : -2.44 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 254 TYR 0.009 0.001 TYR B 325 PHE 0.023 0.001 PHE E 116 TRP 0.025 0.002 TRP D 74 HIS 0.002 0.000 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00271 (18865) covalent geometry : angle 0.53858 (25361) SS BOND : bond 0.00199 ( 14) SS BOND : angle 0.91377 ( 28) hydrogen bonds : bond 0.03865 ( 1106) hydrogen bonds : angle 4.27998 ( 3213) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 102 time to evaluate : 0.659 Fit side-chains REVERT: A 299 PHE cc_start: 0.7977 (m-10) cc_final: 0.7382 (t80) REVERT: A 311 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7783 (mp) REVERT: A 343 LYS cc_start: 0.8394 (mtmt) cc_final: 0.8177 (mtpt) REVERT: B 311 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7827 (mp) REVERT: D 311 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7868 (mp) REVERT: D 351 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7893 (mp) REVERT: E 299 PHE cc_start: 0.8038 (m-10) cc_final: 0.7413 (t80) REVERT: E 311 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7845 (mp) REVERT: F 299 PHE cc_start: 0.8076 (m-10) cc_final: 0.7628 (t80) REVERT: F 311 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7838 (mp) outliers start: 47 outliers final: 36 residues processed: 144 average time/residue: 0.1292 time to fit residues: 30.2228 Evaluate side-chains 143 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 101 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 204 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 195 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN D 100 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS ** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.165350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.137595 restraints weight = 17637.806| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.34 r_work: 0.3239 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18879 Z= 0.152 Angle : 0.564 7.441 25389 Z= 0.283 Chirality : 0.042 0.187 2870 Planarity : 0.004 0.042 2968 Dihedral : 17.679 179.902 3324 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.49 % Allowed : 11.84 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.19), residues: 2107 helix: 0.84 (0.14), residues: 1491 sheet: None (None), residues: 0 loop : -2.46 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 254 TYR 0.009 0.001 TYR C 331 PHE 0.022 0.001 PHE A 116 TRP 0.027 0.002 TRP D 74 HIS 0.003 0.000 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00362 (18865) covalent geometry : angle 0.56297 (25361) SS BOND : bond 0.00381 ( 14) SS BOND : angle 1.21277 ( 28) hydrogen bonds : bond 0.04085 ( 1106) hydrogen bonds : angle 4.34620 ( 3213) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 100 time to evaluate : 0.643 Fit side-chains REVERT: A 299 PHE cc_start: 0.8008 (m-10) cc_final: 0.7391 (t80) REVERT: A 311 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7794 (mp) REVERT: B 70 SER cc_start: 0.8705 (m) cc_final: 0.8489 (t) REVERT: B 311 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7798 (mp) REVERT: C 120 LEU cc_start: 0.9007 (mt) cc_final: 0.8771 (mt) REVERT: D 311 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7929 (mp) REVERT: D 351 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7847 (mp) REVERT: E 299 PHE cc_start: 0.8090 (m-10) cc_final: 0.7428 (t80) REVERT: E 311 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7876 (mp) REVERT: F 299 PHE cc_start: 0.8026 (m-10) cc_final: 0.7546 (t80) REVERT: F 311 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7855 (mp) outliers start: 48 outliers final: 35 residues processed: 143 average time/residue: 0.1279 time to fit residues: 29.5689 Evaluate side-chains 139 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 chunk 157 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 158 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN D 100 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 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 = 0.3743 r_free = 0.3743 target = 0.168119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.140594 restraints weight = 17526.503| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.34 r_work: 0.3275 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18879 Z= 0.120 Angle : 0.541 6.930 25389 Z= 0.271 Chirality : 0.041 0.188 2870 Planarity : 0.004 0.041 2968 Dihedral : 17.379 179.144 3324 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.29 % Allowed : 12.05 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.19), residues: 2107 helix: 0.90 (0.14), residues: 1491 sheet: None (None), residues: 0 loop : -2.44 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 254 TYR 0.010 0.001 TYR B 325 PHE 0.022 0.001 PHE E 116 TRP 0.022 0.002 TRP D 74 HIS 0.003 0.000 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00275 (18865) covalent geometry : angle 0.54000 (25361) SS BOND : bond 0.00179 ( 14) SS BOND : angle 0.90809 ( 28) hydrogen bonds : bond 0.03875 ( 1106) hydrogen bonds : angle 4.26879 ( 3213) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 98 time to evaluate : 0.529 Fit side-chains REVERT: A 299 PHE cc_start: 0.7996 (m-10) cc_final: 0.7374 (t80) REVERT: A 311 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7822 (mp) REVERT: B 70 SER cc_start: 0.8672 (m) cc_final: 0.8462 (t) REVERT: B 311 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7812 (mp) REVERT: D 311 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7888 (mp) REVERT: D 351 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7861 (mp) REVERT: E 299 PHE cc_start: 0.8073 (m-10) cc_final: 0.7430 (t80) REVERT: E 311 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7836 (mp) REVERT: F 311 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7842 (mp) outliers start: 44 outliers final: 33 residues processed: 137 average time/residue: 0.1222 time to fit residues: 27.0715 Evaluate side-chains 135 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 96 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 47 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 19 optimal weight: 0.0370 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 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 = 0.3745 r_free = 0.3745 target = 0.168368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.140785 restraints weight = 17620.959| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.35 r_work: 0.3269 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18879 Z= 0.123 Angle : 0.540 6.741 25389 Z= 0.271 Chirality : 0.041 0.177 2870 Planarity : 0.004 0.042 2968 Dihedral : 17.012 178.694 3324 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.23 % Allowed : 12.21 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.01 (0.19), residues: 2107 helix: 0.95 (0.14), residues: 1491 sheet: None (None), residues: 0 loop : -2.41 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 254 TYR 0.009 0.001 TYR B 325 PHE 0.023 0.001 PHE E 116 TRP 0.022 0.002 TRP D 74 HIS 0.004 0.000 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00283 (18865) covalent geometry : angle 0.53950 (25361) SS BOND : bond 0.00223 ( 14) SS BOND : angle 0.98618 ( 28) hydrogen bonds : bond 0.03860 ( 1106) hydrogen bonds : angle 4.22998 ( 3213) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3506.18 seconds wall clock time: 61 minutes 52.72 seconds (3712.72 seconds total)