Starting phenix.real_space_refine on Sat Jul 4 04:49:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7f8n_31490/07_2026/7f8n_31490.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f8n_31490/07_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_31490/07_2026/7f8n_31490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f8n_31490/07_2026/7f8n_31490.map" model { file = "/net/cci-nas-00/data/ceres_data/7f8n_31490/07_2026/7f8n_31490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f8n_31490/07_2026/7f8n_31490.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7f8n_31490/07_2026/7f8n_31490.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7f8n_31490/07_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-6108/lib/python3.11/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: 136 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: 148 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: 119 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: 126 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: 199 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: 148 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: 160 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: 4.14, per 1000 atoms: 0.22 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: 1.68 Conformation dependent library (CDL) restraints added in 650.5 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: 0.51 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: 2.63 Time building geometry restraints manager: 2.20 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: 10976 32.55 - 65.10: 322 65.10 - 97.65: 49 97.65 - 130.20: 21 130.20 - 162.74: 7 Dihedral angle restraints: 11375 sinusoidal: 4914 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 11372 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: 1.210 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.190 Find NCS groups from input model: 0.510 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 : 16.484 162.744 7119 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/Z covalent geometry : bond 0.01184 / 0.59 (18865) covalent geometry : angle 1.08423 / 0.43 (25361) SS BOND : bond 0.00386 / 0.23 ( 14) SS BOND : angle 0.95967 / 0.61 ( 28) hydrogen bonds : bond 0.25730 / 16.84 ( 1106) hydrogen bonds : angle 8.45318 / 5.93 ( 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 : 0.666 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: 0.1412 time to fit residues: 38.9058 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 : 0.664 ------------------------------------------------------------------------------- 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... 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 G 92 ASN G 100 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.169834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.143664 restraints weight = 17818.397| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.30 r_work: 0.3326 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18879 Z= 0.135 Angle : 0.602 9.233 25389 Z= 0.304 Chirality : 0.041 0.155 2870 Planarity : 0.005 0.038 2968 Dihedral : 18.319 174.297 3078 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.81 % Allowed : 7.27 % Favored : 89.92 % 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: -0.69 (0.18), residues: 2107 helix: 0.51 (0.14), residues: 1470 sheet: None (None), residues: 0 loop : -2.77 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 254 TYR 0.010 0.001 TYR C 325 PHE 0.023 0.001 PHE A 116 TRP 0.019 0.002 TRP F 74 HIS 0.001 0.000 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (18865) covalent geometry : angle 0.60119 / 0.30 (25361) SS BOND : bond 0.00136 / 0.08 ( 14) SS BOND : angle 0.93451 / 0.61 ( 28) hydrogen bonds : bond 0.04901 / 3.26 ( 1106) hydrogen bonds : angle 5.07562 / 3.57 ( 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 163 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 109 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 HIS cc_start: 0.8585 (m-70) cc_final: 0.8374 (m90) REVERT: B 25 PHE cc_start: 0.8470 (m-10) cc_final: 0.8241 (m-10) REVERT: E 299 PHE cc_start: 0.7835 (m-10) cc_final: 0.7328 (t80) REVERT: G 299 PHE cc_start: 0.8061 (t80) cc_final: 0.7383 (m-10) outliers start: 54 outliers final: 26 residues processed: 162 average time/residue: 0.1195 time to fit residues: 31.5012 Evaluate side-chains 125 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 305 VAL 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 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: 0.8980 chunk 195 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** 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 = 0.3770 r_free = 0.3770 target = 0.169117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.142524 restraints weight = 17883.960| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.33 r_work: 0.3335 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18879 Z= 0.133 Angle : 0.577 10.090 25389 Z= 0.285 Chirality : 0.041 0.159 2870 Planarity : 0.004 0.042 2968 Dihedral : 17.021 172.636 3073 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.65 % Allowed : 8.42 % Favored : 88.94 % 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: -0.46 (0.18), residues: 2107 helix: 0.70 (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 0.004 0.000 ARG G 254 TYR 0.008 0.001 TYR A 331 PHE 0.022 0.001 PHE C 116 TRP 0.016 0.002 TRP F 74 HIS 0.001 0.000 HIS G 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (18865) covalent geometry : angle 0.57625 / 0.28 (25361) SS BOND : bond 0.00310 / 0.19 ( 14) SS BOND : angle 1.03168 / 0.66 ( 28) hydrogen bonds : bond 0.04637 / 3.09 ( 1106) hydrogen bonds : angle 4.69037 / 3.29 ( 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 164 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 113 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 LYS cc_start: 0.8419 (mtmt) cc_final: 0.8112 (mtpt) REVERT: C 311 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7830 (mp) REVERT: D 211 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7532 (mm) REVERT: D 351 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7956 (mp) REVERT: E 299 PHE cc_start: 0.7952 (m-10) cc_final: 0.7374 (t80) REVERT: E 311 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8007 (mp) REVERT: F 311 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7884 (mp) outliers start: 51 outliers final: 27 residues processed: 161 average time/residue: 0.1213 time to fit residues: 31.6260 Evaluate side-chains 132 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 236 SER 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 211 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 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 214 ILE 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: 0.2980 chunk 136 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN B 100 ASN C 100 ASN D 100 ASN E 100 ASN F 100 ASN ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.173149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.147904 restraints weight = 17687.927| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.29 r_work: 0.3329 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18879 Z= 0.124 Angle : 0.547 7.949 25389 Z= 0.273 Chirality : 0.040 0.158 2870 Planarity : 0.004 0.042 2968 Dihedral : 16.028 164.524 3072 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.81 % Allowed : 9.25 % Favored : 87.95 % 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: -0.29 (0.19), residues: 2107 helix: 0.82 (0.14), residues: 1470 sheet: None (None), residues: 0 loop : -2.64 (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 0.022 0.001 PHE D 116 TRP 0.014 0.002 TRP G 104 HIS 0.000 0.000 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (18865) covalent geometry : angle 0.54659 / 0.27 (25361) SS BOND : bond 0.00240 / 0.15 ( 14) SS BOND : angle 0.94998 / 0.62 ( 28) hydrogen bonds : bond 0.04144 / 2.76 ( 1106) hydrogen bonds : angle 4.50739 / 3.17 ( 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 171 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 117 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7730 (mp) REVERT: A 343 LYS cc_start: 0.8445 (mtmt) cc_final: 0.8130 (mtpt) REVERT: B 311 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7771 (mp) REVERT: D 311 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7925 (mp) REVERT: D 351 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8011 (mp) REVERT: E 299 PHE cc_start: 0.7973 (m-10) cc_final: 0.7434 (t80) REVERT: F 250 SER cc_start: 0.8716 (p) cc_final: 0.8507 (m) outliers start: 54 outliers final: 31 residues processed: 169 average time/residue: 0.1180 time to fit residues: 32.7251 Evaluate side-chains 145 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 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 211 ILE Chi-restraints excluded: chain E residue 305 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 1 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 131 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN B 89 GLN B 100 ASN C 100 ASN D 100 ASN ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN G 100 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.166527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.139371 restraints weight = 17668.459| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.32 r_work: 0.3273 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18879 Z= 0.139 Angle : 0.559 8.585 25389 Z= 0.278 Chirality : 0.041 0.164 2870 Planarity : 0.004 0.042 2968 Dihedral : 15.426 160.887 3072 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.96 % Allowed : 9.82 % Favored : 87.22 % 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: -0.27 (0.19), residues: 2107 helix: 0.77 (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 0.008 0.001 TYR G 331 PHE 0.021 0.001 PHE E 116 TRP 0.013 0.002 TRP B 74 HIS 0.007 0.000 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (18865) covalent geometry : angle 0.55842 / 0.28 (25361) SS BOND : bond 0.00352 / 0.21 ( 14) SS BOND : angle 1.13162 / 0.73 ( 28) hydrogen bonds : bond 0.04194 / 2.80 ( 1106) hydrogen bonds : angle 4.46000 / 3.14 ( 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 166 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 109 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 299 PHE cc_start: 0.7929 (m-10) cc_final: 0.7372 (t80) REVERT: A 311 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7739 (mp) REVERT: B 311 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7770 (mp) REVERT: C 311 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7814 (mp) REVERT: D 311 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7937 (mp) REVERT: D 351 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7919 (mp) REVERT: E 299 PHE cc_start: 0.8033 (m-10) cc_final: 0.7422 (t80) REVERT: E 311 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7920 (mp) REVERT: F 299 PHE cc_start: 0.8078 (m-10) cc_final: 0.7632 (t80) REVERT: F 311 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7860 (mp) outliers start: 57 outliers final: 34 residues processed: 164 average time/residue: 0.1152 time to fit residues: 30.9901 Evaluate side-chains 142 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 101 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 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 211 ILE 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 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 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 257 SER 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: 1.9990 chunk 196 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.3980 chunk 201 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 100 ASN D 100 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 GLN ** 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 = 0.3711 r_free = 0.3711 target = 0.164910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.137522 restraints weight = 17649.700| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.33 r_work: 0.3248 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18879 Z= 0.152 Angle : 0.569 8.167 25389 Z= 0.285 Chirality : 0.041 0.198 2870 Planarity : 0.004 0.043 2968 Dihedral : 15.069 158.190 3072 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.06 % Allowed : 10.60 % Favored : 86.34 % 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: -0.28 (0.19), residues: 2107 helix: 0.76 (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 0.008 0.001 TYR G 331 PHE 0.021 0.001 PHE D 116 TRP 0.013 0.002 TRP G 74 HIS 0.005 0.000 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (18865) covalent geometry : angle 0.56821 / 0.28 (25361) SS BOND : bond 0.00405 / 0.24 ( 14) SS BOND : angle 1.18829 / 0.77 ( 28) hydrogen bonds : bond 0.04203 / 2.81 ( 1106) hydrogen bonds : angle 4.45750 / 3.13 ( 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 159 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 100 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 299 PHE cc_start: 0.7993 (m-10) cc_final: 0.7423 (t80) REVERT: A 311 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7816 (mp) REVERT: B 311 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7814 (mp) REVERT: C 311 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7809 (mp) REVERT: D 311 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7943 (mp) REVERT: D 351 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7948 (mp) REVERT: E 299 PHE cc_start: 0.8025 (m-10) cc_final: 0.7434 (t80) REVERT: E 311 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7918 (mp) REVERT: F 299 PHE cc_start: 0.8117 (m-10) cc_final: 0.7629 (t80) REVERT: F 311 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7872 (mp) outliers start: 59 outliers final: 36 residues processed: 153 average time/residue: 0.1204 time to fit residues: 30.1977 Evaluate side-chains 143 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 100 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 311 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 211 ILE 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 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 G residue 16 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 214 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: 0.9990 chunk 41 optimal weight: 0.8980 chunk 208 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 199 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G 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 = 0.3725 r_free = 0.3725 target = 0.166139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.138716 restraints weight = 17669.788| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.34 r_work: 0.3264 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18879 Z= 0.132 Angle : 0.549 7.734 25389 Z= 0.274 Chirality : 0.041 0.193 2870 Planarity : 0.004 0.042 2968 Dihedral : 14.629 156.882 3072 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.75 % Allowed : 11.32 % Favored : 85.92 % 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: -0.20 (0.19), residues: 2107 helix: 0.82 (0.14), residues: 1491 sheet: None (None), residues: 0 loop : -2.52 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 254 TYR 0.009 0.001 TYR B 325 PHE 0.022 0.001 PHE E 116 TRP 0.012 0.002 TRP G 104 HIS 0.002 0.000 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (18865) covalent geometry : angle 0.54827 / 0.27 (25361) SS BOND : bond 0.00300 / 0.18 ( 14) SS BOND : angle 1.04610 / 0.68 ( 28) hydrogen bonds : bond 0.04024 / 2.69 ( 1106) hydrogen bonds : angle 4.37605 / 3.08 ( 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 152 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 99 time to evaluate : 0.521 Fit side-chains REVERT: A 299 PHE cc_start: 0.7985 (m-10) cc_final: 0.7398 (t80) REVERT: A 311 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7827 (mp) REVERT: A 343 LYS cc_start: 0.8449 (mtmt) cc_final: 0.8217 (mtpt) REVERT: B 311 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7795 (mp) REVERT: C 311 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7803 (mp) REVERT: D 311 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7906 (mp) REVERT: D 351 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7909 (mp) REVERT: E 299 PHE cc_start: 0.8063 (m-10) cc_final: 0.7454 (t80) REVERT: E 311 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7912 (mp) REVERT: F 299 PHE cc_start: 0.8099 (m-10) cc_final: 0.7626 (t80) REVERT: F 311 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7856 (mp) outliers start: 53 outliers final: 38 residues processed: 148 average time/residue: 0.1236 time to fit residues: 30.0060 Evaluate side-chains 140 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 95 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 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 311 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 211 ILE 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 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 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 214 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: 5.9990 chunk 91 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN ** 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** ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 GLN ** 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 = 0.3731 r_free = 0.3731 target = 0.166936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.139664 restraints weight = 17610.565| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.33 r_work: 0.3272 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2783 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= 0.124 Angle : 0.540 7.389 25389 Z= 0.271 Chirality : 0.040 0.172 2870 Planarity : 0.004 0.042 2968 Dihedral : 14.180 154.737 3072 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.86 % Allowed : 11.58 % 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: -0.10 (0.19), residues: 2107 helix: 0.88 (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 0.007 0.000 ARG G 254 TYR 0.010 0.001 TYR B 325 PHE 0.022 0.001 PHE E 116 TRP 0.027 0.002 TRP D 74 HIS 0.001 0.000 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (18865) covalent geometry : angle 0.53970 / 0.27 (25361) SS BOND : bond 0.00242 / 0.15 ( 14) SS BOND : angle 0.96994 / 0.63 ( 28) hydrogen bonds : bond 0.03915 / 2.62 ( 1106) hydrogen bonds : angle 4.30065 / 3.03 ( 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 161 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 106 time to evaluate : 0.656 Fit side-chains REVERT: A 299 PHE cc_start: 0.7978 (m-10) cc_final: 0.7381 (t80) REVERT: A 311 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7834 (mp) REVERT: A 343 LYS cc_start: 0.8448 (mtmt) cc_final: 0.8239 (mtpt) REVERT: B 70 SER cc_start: 0.8697 (m) cc_final: 0.8465 (t) REVERT: B 311 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7778 (mp) REVERT: C 311 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7806 (mp) REVERT: D 311 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7905 (mp) REVERT: E 299 PHE cc_start: 0.8057 (m-10) cc_final: 0.7451 (t80) REVERT: E 311 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7894 (mp) REVERT: F 299 PHE cc_start: 0.8052 (m-10) cc_final: 0.7580 (t80) REVERT: F 311 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7850 (mp) outliers start: 55 outliers final: 37 residues processed: 154 average time/residue: 0.1215 time to fit residues: 30.3992 Evaluate side-chains 145 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 102 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 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 311 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 211 ILE 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 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 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 214 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: 0.8980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 186 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** B 100 ASN C 100 ASN D 100 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.166244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.138899 restraints weight = 17670.231| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.33 r_work: 0.3257 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18879 Z= 0.133 Angle : 0.548 7.474 25389 Z= 0.275 Chirality : 0.041 0.201 2870 Planarity : 0.004 0.042 2968 Dihedral : 14.004 153.150 3072 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.65 % Allowed : 11.58 % Favored : 85.77 % 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: -0.10 (0.19), residues: 2107 helix: 0.88 (0.14), residues: 1491 sheet: None (None), residues: 0 loop : -2.45 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 254 TYR 0.009 0.001 TYR B 325 PHE 0.021 0.001 PHE E 116 TRP 0.024 0.002 TRP D 74 HIS 0.002 0.000 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (18865) covalent geometry : angle 0.54678 / 0.27 (25361) SS BOND : bond 0.00293 / 0.18 ( 14) SS BOND : angle 1.05568 / 0.68 ( 28) hydrogen bonds : bond 0.03964 / 2.65 ( 1106) hydrogen bonds : angle 4.31255 / 3.04 ( 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 150 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 99 time to evaluate : 0.660 Fit side-chains REVERT: A 299 PHE cc_start: 0.7996 (m-10) cc_final: 0.7402 (t80) REVERT: A 311 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7846 (mp) REVERT: A 343 LYS cc_start: 0.8470 (mtmt) cc_final: 0.8251 (mtpt) REVERT: B 311 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7766 (mp) REVERT: C 120 LEU cc_start: 0.9014 (mt) cc_final: 0.8789 (mt) REVERT: C 311 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7826 (mp) REVERT: D 311 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7898 (mp) REVERT: E 299 PHE cc_start: 0.8074 (m-10) cc_final: 0.7458 (t80) REVERT: E 311 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7895 (mp) REVERT: F 299 PHE cc_start: 0.8016 (m-10) cc_final: 0.7525 (t80) REVERT: F 311 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7854 (mp) outliers start: 51 outliers final: 39 residues processed: 144 average time/residue: 0.1259 time to fit residues: 29.3501 Evaluate side-chains 142 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 97 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 336 GLU 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 311 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 211 ILE 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 E residue 16 LEU 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 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 214 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: 5.9990 chunk 13 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 111 optimal weight: 0.9980 chunk 157 optimal weight: 0.5980 chunk 123 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 158 optimal weight: 0.0980 chunk 153 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** B 100 ASN ** C 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 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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 = 0.3754 r_free = 0.3754 target = 0.169599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.142042 restraints weight = 17486.308| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.36 r_work: 0.3312 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18879 Z= 0.111 Angle : 0.528 6.827 25389 Z= 0.265 Chirality : 0.040 0.178 2870 Planarity : 0.004 0.041 2968 Dihedral : 13.587 150.690 3072 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.60 % Allowed : 11.69 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.03 (0.19), residues: 2107 helix: 0.99 (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 G 254 TYR 0.010 0.001 TYR B 325 PHE 0.023 0.001 PHE E 116 TRP 0.020 0.002 TRP D 74 HIS 0.010 0.001 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (18865) covalent geometry : angle 0.52775 / 0.26 (25361) SS BOND : bond 0.00154 / 0.10 ( 14) SS BOND : angle 0.78963 / 0.51 ( 28) hydrogen bonds : bond 0.03738 / 2.49 ( 1106) hydrogen bonds : angle 4.20576 / 2.97 ( 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 155 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 105 time to evaluate : 0.681 Fit side-chains REVERT: A 19 GLU cc_start: 0.6750 (pt0) cc_final: 0.5839 (mm-30) REVERT: A 299 PHE cc_start: 0.7930 (m-10) cc_final: 0.7357 (t80) REVERT: A 343 LYS cc_start: 0.8451 (mtmt) cc_final: 0.7945 (mtpp) REVERT: B 311 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7782 (mp) REVERT: D 311 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7870 (mp) REVERT: E 299 PHE cc_start: 0.8048 (m-10) cc_final: 0.7422 (t80) REVERT: E 311 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7836 (mp) REVERT: F 299 PHE cc_start: 0.8026 (m-10) cc_final: 0.7470 (t80) REVERT: F 311 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7837 (mp) outliers start: 50 outliers final: 38 residues processed: 149 average time/residue: 0.1353 time to fit residues: 32.2252 Evaluate side-chains 142 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 100 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 224 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 336 GLU 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 211 ILE 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 E residue 16 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 47 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 115 optimal weight: 0.3980 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 5 optimal weight: 0.0050 chunk 118 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN ** C 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 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.169648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.142534 restraints weight = 17576.994| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.33 r_work: 0.3296 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18879 Z= 0.112 Angle : 0.529 6.674 25389 Z= 0.266 Chirality : 0.040 0.174 2870 Planarity : 0.004 0.042 2968 Dihedral : 13.381 148.572 3072 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.60 % Allowed : 11.84 % 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: 0.12 (0.19), residues: 2107 helix: 1.04 (0.14), residues: 1491 sheet: None (None), residues: 0 loop : -2.37 (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 F 325 PHE 0.023 0.001 PHE E 116 TRP 0.020 0.002 TRP D 74 HIS 0.010 0.001 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (18865) covalent geometry : angle 0.52885 / 0.27 (25361) SS BOND : bond 0.00175 / 0.11 ( 14) SS BOND : angle 0.88098 / 0.57 ( 28) hydrogen bonds : bond 0.03770 / 2.52 ( 1106) hydrogen bonds : angle 4.17750 / 2.95 ( 3213) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3569.40 seconds wall clock time: 62 minutes 31.93 seconds (3751.93 seconds total)