Starting phenix.real_space_refine on Sat Jul 4 06:08:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7f8j_31489/07_2026/7f8j_31489.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f8j_31489/07_2026/7f8j_31489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7f8j_31489/07_2026/7f8j_31489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f8j_31489/07_2026/7f8j_31489.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f8j_31489/07_2026/7f8j_31489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f8j_31489/07_2026/7f8j_31489.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7f8j_31489/07_2026/7f8j_31489.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7f8j_31489/07_2026/7f8j_31489.cif" } resolution = 3.6 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 14 5.49 5 S 77 5.16 5 C 12824 2.51 5 N 2765 2.21 5 O 3304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s 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: 18984 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2566 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2566 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2566 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2566 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2566 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2566 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2566 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 146 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'LBN:plan-1': 3, 'LBN:plan-2': 3, 'LBN:plan-3': 3} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 146 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'LBN:plan-1': 3, 'LBN:plan-2': 3, 'LBN:plan-3': 2} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 146 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'LBN:plan-1': 3, 'LBN:plan-2': 3, 'LBN:plan-3': 2} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 146 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'LBN:plan-1': 3, 'LBN:plan-2': 3, 'LBN:plan-3': 2} Unresolved non-hydrogen planarities: 28 Chain: "E" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 146 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'LBN:plan-1': 3, 'LBN:plan-2': 3, 'LBN:plan-3': 2} Unresolved non-hydrogen planarities: 28 Chain: "F" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 146 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'LBN:plan-1': 3, 'LBN:plan-2': 3, 'LBN:plan-3': 2} Unresolved non-hydrogen planarities: 28 Chain: "G" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 146 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'LBN:plan-1': 3, 'LBN:plan-2': 3, 'LBN:plan-3': 2} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 4.13, per 1000 atoms: 0.22 Number of scatterers: 18984 At special positions: 0 Unit cell: (109.35, 110.16, 115.83, 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 14 15.00 O 3304 8.00 N 2765 7.00 C 12824 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=2.03 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: 1.61 Conformation dependent library (CDL) restraints added in 746.2 milliseconds 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4368 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 7 sheets defined 68.8% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 32 through 55 Proline residue: A 46 - end of helix removed outlier: 3.682A pdb=" N PHE A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'A' and resid 108 through 131 Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 158 removed outlier: 3.626A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 removed outlier: 4.172A pdb=" N ASN A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 237 Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 270 through 296 removed outlier: 3.905A pdb=" N VAL A 278 " --> pdb=" O GLN A 274 " (cutoff:3.500A) Proline residue: A 289 - end of helix removed outlier: 3.747A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.988A pdb=" N ILE A 311 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 338 removed outlier: 3.576A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.938A pdb=" N LYS A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 354 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 32 through 55 Proline residue: B 46 - end of helix removed outlier: 3.682A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 108 through 131 Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 158 removed outlier: 3.626A pdb=" N PHE B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 removed outlier: 4.172A pdb=" N ASN B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 237 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 270 through 296 removed outlier: 3.905A pdb=" N VAL B 278 " --> pdb=" O GLN B 274 " (cutoff:3.500A) Proline residue: B 289 - end of helix removed outlier: 3.746A pdb=" N PHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 306 through 312 removed outlier: 3.987A pdb=" N ILE B 311 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 338 removed outlier: 3.575A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.939A pdb=" N LYS B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 354 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 32 through 55 Proline residue: C 46 - end of helix removed outlier: 3.682A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 87 Processing helix chain 'C' and resid 100 through 108 Processing helix chain 'C' and resid 108 through 131 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 158 removed outlier: 3.627A pdb=" N PHE C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU C 144 " --> pdb=" O LYS C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 removed outlier: 4.172A pdb=" N ASN C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 237 Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 270 through 296 removed outlier: 3.905A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) Proline residue: C 289 - end of helix removed outlier: 3.745A pdb=" N PHE C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 301 Processing helix chain 'C' and resid 306 through 312 removed outlier: 3.987A pdb=" N ILE C 311 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 338 removed outlier: 3.576A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.938A pdb=" N LYS C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS C 347 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 354 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 32 through 55 Proline residue: D 46 - end of helix removed outlier: 3.682A pdb=" N PHE D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 87 Processing helix chain 'D' and resid 100 through 108 Processing helix chain 'D' and resid 108 through 131 Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 158 removed outlier: 3.627A pdb=" N PHE D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU D 144 " --> pdb=" O LYS D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 4.172A pdb=" N ASN D 205 " --> pdb=" O LYS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 237 Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 270 through 296 removed outlier: 3.906A pdb=" N VAL D 278 " --> pdb=" O GLN D 274 " (cutoff:3.500A) Proline residue: D 289 - end of helix removed outlier: 3.746A pdb=" N PHE D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 301 Processing helix chain 'D' and resid 306 through 312 removed outlier: 3.988A pdb=" N ILE D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 338 removed outlier: 3.575A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 354 removed outlier: 3.938A pdb=" N LYS D 346 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE D 354 " --> pdb=" O VAL D 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 32 through 55 Proline residue: E 46 - end of helix removed outlier: 3.681A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 87 Processing helix chain 'E' and resid 100 through 108 Processing helix chain 'E' and resid 108 through 131 Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 158 removed outlier: 3.627A pdb=" N PHE E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 removed outlier: 4.172A pdb=" N ASN E 205 " --> pdb=" O LYS E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 237 Processing helix chain 'E' and resid 252 through 256 Processing helix chain 'E' and resid 270 through 296 removed outlier: 3.906A pdb=" N VAL E 278 " --> pdb=" O GLN E 274 " (cutoff:3.500A) Proline residue: E 289 - end of helix removed outlier: 3.747A pdb=" N PHE E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 306 through 312 removed outlier: 3.988A pdb=" N ILE E 311 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 338 removed outlier: 3.575A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 354 removed outlier: 3.939A pdb=" N LYS E 346 " --> pdb=" O VAL E 342 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS E 347 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE E 354 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 32 through 55 Proline residue: F 46 - end of helix removed outlier: 3.682A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 87 Processing helix chain 'F' and resid 100 through 108 Processing helix chain 'F' and resid 108 through 131 Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 158 removed outlier: 3.626A pdb=" N PHE F 141 " --> pdb=" O SER F 137 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 removed outlier: 4.172A pdb=" N ASN F 205 " --> pdb=" O LYS F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 237 Processing helix chain 'F' and resid 252 through 256 Processing helix chain 'F' and resid 270 through 296 removed outlier: 3.906A pdb=" N VAL F 278 " --> pdb=" O GLN F 274 " (cutoff:3.500A) Proline residue: F 289 - end of helix removed outlier: 3.746A pdb=" N PHE F 296 " --> pdb=" O VAL F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 306 through 312 removed outlier: 3.988A pdb=" N ILE F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 338 removed outlier: 3.576A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 354 removed outlier: 3.938A pdb=" N LYS F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE F 354 " --> pdb=" O VAL F 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 11 Processing helix chain 'G' and resid 32 through 55 Proline residue: G 46 - end of helix removed outlier: 3.681A pdb=" N PHE G 54 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 87 Processing helix chain 'G' and resid 100 through 108 Processing helix chain 'G' and resid 108 through 131 Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 158 removed outlier: 3.626A pdb=" N PHE G 141 " --> pdb=" O SER G 137 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU G 144 " --> pdb=" O LYS G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 205 removed outlier: 4.173A pdb=" N ASN G 205 " --> pdb=" O LYS G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 237 Processing helix chain 'G' and resid 252 through 256 Processing helix chain 'G' and resid 270 through 296 removed outlier: 3.905A pdb=" N VAL G 278 " --> pdb=" O GLN G 274 " (cutoff:3.500A) Proline residue: G 289 - end of helix removed outlier: 3.746A pdb=" N PHE G 296 " --> pdb=" O VAL G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 301 Processing helix chain 'G' and resid 306 through 312 removed outlier: 3.988A pdb=" N ILE G 311 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 338 removed outlier: 3.575A pdb=" N LEU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 354 removed outlier: 3.939A pdb=" N LYS G 346 " --> pdb=" O VAL G 342 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS G 347 " --> pdb=" O LYS G 343 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE G 354 " --> pdb=" O VAL G 350 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 67 removed outlier: 4.583A 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: 4.584A 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: 4.583A 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: 4.583A 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: 4.583A 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: 4.583A 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: 4.583A pdb=" N GLN G 264 " --> pdb=" O PHE G 67 " (cutoff:3.500A) 1072 hydrogen bonds defined for protein. 3069 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.90 Time building geometry restraints manager: 2.11 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: 5364 1.34 - 1.46: 3039 1.46 - 1.57: 10819 1.57 - 1.69: 21 1.69 - 1.81: 119 Bond restraints: 19362 Sorted by residual: bond pdb=" C42 LBN B 506 " pdb=" C5 LBN B 506 " ideal model delta sigma weight residual 1.333 1.552 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C42 LBN E 506 " pdb=" C5 LBN E 506 " ideal model delta sigma weight residual 1.333 1.552 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C42 LBN D 504 " pdb=" C5 LBN D 504 " ideal model delta sigma weight residual 1.333 1.552 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C42 LBN G 504 " pdb=" C5 LBN G 504 " ideal model delta sigma weight residual 1.333 1.551 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C42 LBN C 506 " pdb=" C5 LBN C 506 " ideal model delta sigma weight residual 1.333 1.551 -0.218 2.00e-02 2.50e+03 1.19e+02 ... (remaining 19357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.97: 25965 9.97 - 19.93: 19 19.93 - 29.90: 0 29.90 - 39.86: 0 39.86 - 49.83: 21 Bond angle restraints: 26005 Sorted by residual: angle pdb=" O7 LBN D 505 " pdb=" C34 LBN D 505 " pdb=" O8 LBN D 505 " ideal model delta sigma weight residual 123.50 73.67 49.83 3.00e+00 1.11e-01 2.76e+02 angle pdb=" O7 LBN E 501 " pdb=" C34 LBN E 501 " pdb=" O8 LBN E 501 " ideal model delta sigma weight residual 123.50 73.69 49.81 3.00e+00 1.11e-01 2.76e+02 angle pdb=" O7 LBN F 501 " pdb=" C34 LBN F 501 " pdb=" O8 LBN F 501 " ideal model delta sigma weight residual 123.50 73.69 49.81 3.00e+00 1.11e-01 2.76e+02 angle pdb=" O7 LBN B 501 " pdb=" C34 LBN B 501 " pdb=" O8 LBN B 501 " ideal model delta sigma weight residual 123.50 73.70 49.80 3.00e+00 1.11e-01 2.76e+02 angle pdb=" O7 LBN C 501 " pdb=" C34 LBN C 501 " pdb=" O8 LBN C 501 " ideal model delta sigma weight residual 123.50 73.70 49.80 3.00e+00 1.11e-01 2.76e+02 ... (remaining 26000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.60: 11322 31.60 - 63.19: 336 63.19 - 94.79: 68 94.79 - 126.39: 7 126.39 - 157.98: 28 Dihedral angle restraints: 11761 sinusoidal: 5055 harmonic: 6706 Sorted by residual: dihedral pdb=" C40 LBN E 501 " pdb=" C41 LBN E 501 " pdb=" C42 LBN E 501 " pdb=" C5 LBN E 501 " ideal model delta sinusoidal sigma weight residual 117.80 -40.18 157.98 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C40 LBN C 501 " pdb=" C41 LBN C 501 " pdb=" C42 LBN C 501 " pdb=" C5 LBN C 501 " ideal model delta sinusoidal sigma weight residual 117.80 -40.16 157.96 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C40 LBN B 501 " pdb=" C41 LBN B 501 " pdb=" C42 LBN B 501 " pdb=" C5 LBN B 501 " ideal model delta sinusoidal sigma weight residual 117.80 -40.14 157.94 1 3.00e+01 1.11e-03 2.06e+01 ... (remaining 11758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2252 0.043 - 0.086: 570 0.086 - 0.128: 139 0.128 - 0.171: 7 0.171 - 0.214: 14 Chirality restraints: 2982 Sorted by residual: chirality pdb=" C2 LBN C 502 " pdb=" C1 LBN C 502 " pdb=" C3 LBN C 502 " pdb=" O7 LBN C 502 " both_signs ideal model delta sigma weight residual False -2.36 -2.58 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C2 LBN B 502 " pdb=" C1 LBN B 502 " pdb=" C3 LBN B 502 " pdb=" O7 LBN B 502 " both_signs ideal model delta sigma weight residual False -2.36 -2.58 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C2 LBN D 506 " pdb=" C1 LBN D 506 " pdb=" C3 LBN D 506 " pdb=" O7 LBN D 506 " both_signs ideal model delta sigma weight residual False -2.36 -2.58 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2979 not shown) Planarity restraints: 3100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN D 504 " -0.078 2.00e-02 2.50e+03 7.75e-02 6.01e+01 pdb=" C42 LBN D 504 " 0.078 2.00e-02 2.50e+03 pdb=" C5 LBN D 504 " 0.077 2.00e-02 2.50e+03 pdb=" C8 LBN D 504 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN G 504 " 0.078 2.00e-02 2.50e+03 7.74e-02 5.99e+01 pdb=" C42 LBN G 504 " -0.078 2.00e-02 2.50e+03 pdb=" C5 LBN G 504 " -0.077 2.00e-02 2.50e+03 pdb=" C8 LBN G 504 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN C 506 " -0.077 2.00e-02 2.50e+03 7.73e-02 5.98e+01 pdb=" C42 LBN C 506 " 0.078 2.00e-02 2.50e+03 pdb=" C5 LBN C 506 " 0.077 2.00e-02 2.50e+03 pdb=" C8 LBN C 506 " -0.077 2.00e-02 2.50e+03 ... (remaining 3097 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2383 2.75 - 3.29: 18929 3.29 - 3.83: 29521 3.83 - 4.36: 36062 4.36 - 4.90: 63156 Nonbonded interactions: 150051 Sorted by model distance: nonbonded pdb=" O LEU C 52 " pdb=" OH TYR D 111 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR G 309 " pdb=" OG SER G 344 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR E 309 " pdb=" OG SER E 344 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR C 309 " pdb=" OG SER C 344 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR A 309 " pdb=" OG SER A 344 " model vdw 2.249 3.040 ... (remaining 150046 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 356 or (resid 501 and (name C11 or name C14 or n \ ame C17 or name C20 or name C22 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name C5 or name C \ 8 )) or (resid 502 and (name C10 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C30 or name C31 or name C32 or name C33 or name C4 or name \ C7 )) or resid 504 or (resid 505 and (name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C3 or name C30 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name O5 or name O6 or name O7 or name O8 )) or \ resid 506)) selection = (chain 'B' and (resid 2 through 356 or (resid 501 and (name C11 or name C14 or n \ ame C17 or name C20 or name C22 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name C5 or name C \ 8 )) or (resid 502 and (name C10 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C30 or name C31 or name C32 or name C33 or name C4 or name \ C7 )) or resid 504 or (resid 505 and (name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C3 or name C30 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name O5 or name O6 or name O7 or name O8 )) or \ resid 506)) selection = (chain 'C' and (resid 2 through 356 or (resid 501 and (name C11 or name C14 or n \ ame C17 or name C20 or name C22 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name C5 or name C \ 8 )) or (resid 502 and (name C10 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C30 or name C31 or name C32 or name C33 or name C4 or name \ C7 )) or resid 504 or (resid 505 and (name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C3 or name C30 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name O5 or name O6 or name O7 or name O8 )) or \ resid 506)) selection = (chain 'D' and (resid 2 through 502 or resid 504 or (resid 505 and (name C25 or \ name C26 or name C27 or name C28 or name C29 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name O5 or name O \ 6 or name O7 or name O8 )) or (resid 506 and (name C10 or name C25 or name C26 o \ r name C27 or name C28 or name C29 or name C30 or name C31 or name C32 or name C \ 33 or name C4 or name C7 )))) selection = (chain 'E' and (resid 2 through 356 or (resid 501 and (name C11 or name C14 or n \ ame C17 or name C20 or name C22 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name C5 or name C \ 8 )) or (resid 502 and (name C10 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C30 or name C31 or name C32 or name C33 or name C4 or name \ C7 )) or resid 504 or (resid 505 and (name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C3 or name C30 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name O5 or name O6 or name O7 or name O8 )) or \ resid 506)) selection = (chain 'F' and (resid 2 through 356 or (resid 501 and (name C11 or name C14 or n \ ame C17 or name C20 or name C22 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name C5 or name C \ 8 )) or (resid 502 and (name C10 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C30 or name C31 or name C32 or name C33 or name C4 or name \ C7 )) or resid 504 or (resid 505 and (name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C3 or name C30 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name O5 or name O6 or name O7 or name O8 )) or \ resid 506)) selection = (chain 'G' and (resid 2 through 502 or resid 504 or (resid 505 and (name C25 or \ name C26 or name C27 or name C28 or name C29 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name O5 or name O \ 6 or name O7 or name O8 )) or (resid 506 and (name C10 or name C25 or name C26 o \ r name C27 or name C28 or name C29 or name C30 or name C31 or name C32 or name C \ 33 or name C4 or name C7 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.010 Find NCS groups from input model: 0.540 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: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 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 : 0.010 0.219 19376 Z= 0.480 Angle : 1.622 49.829 26033 Z= 0.581 Chirality : 0.040 0.214 2982 Planarity : 0.005 0.077 3100 Dihedral : 18.325 157.983 7351 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.04 % Allowed : 1.09 % Favored : 97.87 % 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: 0.64 (0.19), residues: 2212 helix: 1.67 (0.14), residues: 1498 sheet: None (None), residues: 0 loop : -2.44 (0.20), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 254 TYR 0.005 0.001 TYR C 83 PHE 0.010 0.001 PHE A 116 TRP 0.006 0.001 TRP E 104 HIS 0.001 0.000 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00967 / 0.48 (19362) covalent geometry : angle 1.62308 / 0.58 (26005) SS BOND : bond 0.00204 / 0.12 ( 14) SS BOND : angle 0.29621 / 0.21 ( 28) hydrogen bonds : bond 0.21609 / 13.89 ( 1072) hydrogen bonds : angle 6.01502 / 4.31 ( 3069) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 222 time to evaluate : 0.716 Fit side-chains REVERT: A 29 ARG cc_start: 0.7862 (ptp90) cc_final: 0.7661 (ptt-90) REVERT: B 243 GLU cc_start: 0.8434 (pt0) cc_final: 0.7986 (pt0) REVERT: C 207 ASN cc_start: 0.8596 (p0) cc_final: 0.8388 (p0) REVERT: C 243 GLU cc_start: 0.8510 (pt0) cc_final: 0.8217 (pt0) REVERT: D 29 ARG cc_start: 0.7755 (ptp90) cc_final: 0.7516 (ptt-90) REVERT: E 29 ARG cc_start: 0.7749 (ptp90) cc_final: 0.7426 (ptt-90) REVERT: F 207 ASN cc_start: 0.8767 (p0) cc_final: 0.8563 (p0) REVERT: G 207 ASN cc_start: 0.8905 (p0) cc_final: 0.8668 (p0) REVERT: G 243 GLU cc_start: 0.8447 (pt0) cc_final: 0.8154 (pt0) outliers start: 21 outliers final: 16 residues processed: 241 average time/residue: 0.1885 time to fit residues: 65.0842 Evaluate side-chains 208 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 344 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 212 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN C 90 GLN D 90 GLN E 90 GLN E 151 ASN F 90 GLN G 90 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.151488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.116635 restraints weight = 19926.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.121039 restraints weight = 12005.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.123903 restraints weight = 8615.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.125645 restraints weight = 6918.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.126897 restraints weight = 5990.051| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19376 Z= 0.129 Angle : 1.422 46.412 26033 Z= 0.519 Chirality : 0.040 0.182 2982 Planarity : 0.004 0.034 3100 Dihedral : 19.691 166.593 3123 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.35 % Allowed : 6.92 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.18), residues: 2212 helix: 2.17 (0.14), residues: 1442 sheet: None (None), residues: 0 loop : -1.85 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 29 TYR 0.006 0.001 TYR A 83 PHE 0.024 0.001 PHE F 116 TRP 0.011 0.001 TRP E 104 HIS 0.001 0.000 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (19362) covalent geometry : angle 1.42253 / 0.52 (26005) SS BOND : bond 0.00163 / 0.10 ( 14) SS BOND : angle 0.51307 / 0.37 ( 28) hydrogen bonds : bond 0.04670 / 3.00 ( 1072) hydrogen bonds : angle 4.27561 / 3.07 ( 3069) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 206 time to evaluate : 0.692 Fit side-chains REVERT: A 29 ARG cc_start: 0.7923 (ptp90) cc_final: 0.7608 (ptt-90) REVERT: A 40 CYS cc_start: 0.8654 (t) cc_final: 0.7803 (m) REVERT: A 207 ASN cc_start: 0.9014 (p0) cc_final: 0.8664 (p0) REVERT: A 243 GLU cc_start: 0.8362 (pt0) cc_final: 0.8159 (pt0) REVERT: C 207 ASN cc_start: 0.8713 (p0) cc_final: 0.8507 (p0) REVERT: C 243 GLU cc_start: 0.8497 (pt0) cc_final: 0.8252 (pt0) REVERT: D 207 ASN cc_start: 0.9081 (p0) cc_final: 0.8795 (p0) REVERT: E 40 CYS cc_start: 0.8672 (t) cc_final: 0.8424 (t) REVERT: E 207 ASN cc_start: 0.8988 (p0) cc_final: 0.8642 (p0) REVERT: F 5 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: F 207 ASN cc_start: 0.8818 (p0) cc_final: 0.8610 (p0) REVERT: G 207 ASN cc_start: 0.8927 (p0) cc_final: 0.8692 (p0) REVERT: G 243 GLU cc_start: 0.8426 (pt0) cc_final: 0.8174 (pt0) outliers start: 7 outliers final: 4 residues processed: 208 average time/residue: 0.1870 time to fit residues: 55.0678 Evaluate side-chains 191 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 186 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 352 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 34 optimal weight: 0.3980 chunk 89 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 138 optimal weight: 0.5980 chunk 154 optimal weight: 0.0010 chunk 19 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 90 GLN G 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.151491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.117147 restraints weight = 20004.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.121396 restraints weight = 12228.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.124168 restraints weight = 8859.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.125915 restraints weight = 7143.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.126977 restraints weight = 6197.050| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19376 Z= 0.109 Angle : 1.405 46.064 26033 Z= 0.506 Chirality : 0.039 0.157 2982 Planarity : 0.004 0.035 3100 Dihedral : 17.062 152.973 3088 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.38 % Allowed : 8.55 % Favored : 90.06 % 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: 1.36 (0.19), residues: 2212 helix: 2.18 (0.14), residues: 1463 sheet: None (None), residues: 0 loop : -1.84 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 128 TYR 0.006 0.001 TYR D 83 PHE 0.023 0.001 PHE D 116 TRP 0.010 0.001 TRP A 104 HIS 0.000 0.000 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (19362) covalent geometry : angle 1.40575 / 0.51 (26005) SS BOND : bond 0.00077 / 0.05 ( 14) SS BOND : angle 0.45439 / 0.33 ( 28) hydrogen bonds : bond 0.03722 / 2.38 ( 1072) hydrogen bonds : angle 3.94236 / 2.84 ( 3069) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.792 Fit side-chains REVERT: A 29 ARG cc_start: 0.7933 (ptp90) cc_final: 0.7594 (ptt-90) REVERT: A 207 ASN cc_start: 0.9024 (p0) cc_final: 0.8659 (p0) REVERT: A 243 GLU cc_start: 0.8365 (pt0) cc_final: 0.8019 (pt0) REVERT: B 243 GLU cc_start: 0.8327 (pt0) cc_final: 0.8090 (pt0) REVERT: B 268 ILE cc_start: 0.8684 (mt) cc_final: 0.8470 (mt) REVERT: C 207 ASN cc_start: 0.8761 (p0) cc_final: 0.8547 (p0) REVERT: D 207 ASN cc_start: 0.9090 (p0) cc_final: 0.8765 (p0) REVERT: D 243 GLU cc_start: 0.8498 (pt0) cc_final: 0.8118 (pt0) REVERT: D 349 LYS cc_start: 0.8354 (tptt) cc_final: 0.8142 (tptt) REVERT: E 40 CYS cc_start: 0.8663 (t) cc_final: 0.7709 (m) REVERT: E 207 ASN cc_start: 0.8976 (p0) cc_final: 0.8602 (p0) REVERT: F 337 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7117 (tm-30) REVERT: G 207 ASN cc_start: 0.8947 (p0) cc_final: 0.8706 (p0) REVERT: G 243 GLU cc_start: 0.8448 (pt0) cc_final: 0.8238 (pt0) REVERT: G 268 ILE cc_start: 0.8562 (mt) cc_final: 0.8276 (mt) outliers start: 28 outliers final: 18 residues processed: 212 average time/residue: 0.1853 time to fit residues: 56.2115 Evaluate side-chains 204 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 236 SER Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 303 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 171 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 170 optimal weight: 0.6980 chunk 185 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 ASN B 151 ASN B 338 ASN C 90 GLN C 151 ASN D 151 ASN F 151 ASN G 151 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.140491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.105036 restraints weight = 20447.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.109070 restraints weight = 12810.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.111607 restraints weight = 9448.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.113401 restraints weight = 7731.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.114413 restraints weight = 6779.375| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19376 Z= 0.189 Angle : 1.436 45.976 26033 Z= 0.529 Chirality : 0.042 0.212 2982 Planarity : 0.004 0.034 3100 Dihedral : 15.621 155.085 3088 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.88 % Allowed : 10.58 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.19), residues: 2212 helix: 2.06 (0.14), residues: 1456 sheet: 0.20 (0.62), residues: 42 loop : -1.64 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 128 TYR 0.010 0.001 TYR A 284 PHE 0.029 0.002 PHE A 116 TRP 0.012 0.002 TRP C 74 HIS 0.002 0.001 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 (19362) covalent geometry : angle 1.43666 / 0.53 (26005) SS BOND : bond 0.00213 / 0.14 ( 14) SS BOND : angle 0.74484 / 0.54 ( 28) hydrogen bonds : bond 0.04151 / 2.65 ( 1072) hydrogen bonds : angle 4.08777 / 2.95 ( 3069) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 0.640 Fit side-chains REVERT: A 207 ASN cc_start: 0.9035 (p0) cc_final: 0.8708 (p0) REVERT: B 338 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8278 (p0) REVERT: C 207 ASN cc_start: 0.8933 (p0) cc_final: 0.8676 (p0) REVERT: C 243 GLU cc_start: 0.8610 (pt0) cc_final: 0.8341 (pt0) REVERT: C 349 LYS cc_start: 0.8402 (tppt) cc_final: 0.8192 (tptt) REVERT: D 207 ASN cc_start: 0.9098 (p0) cc_final: 0.8794 (p0) REVERT: D 243 GLU cc_start: 0.8634 (pt0) cc_final: 0.8307 (pt0) REVERT: D 349 LYS cc_start: 0.8380 (tptt) cc_final: 0.8107 (tptt) REVERT: E 207 ASN cc_start: 0.9041 (p0) cc_final: 0.8684 (p0) REVERT: F 207 ASN cc_start: 0.9027 (p0) cc_final: 0.8772 (p0) REVERT: F 337 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7439 (tm-30) REVERT: G 9 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6849 (tt0) REVERT: G 207 ASN cc_start: 0.8995 (p0) cc_final: 0.8763 (p0) outliers start: 38 outliers final: 25 residues processed: 228 average time/residue: 0.1768 time to fit residues: 57.6771 Evaluate side-chains 216 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 236 SER Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 303 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 71 optimal weight: 2.9990 chunk 214 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 177 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 180 optimal weight: 0.0470 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 338 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.144539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.109242 restraints weight = 20079.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.113410 restraints weight = 12459.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.116158 restraints weight = 9076.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.117735 restraints weight = 7400.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.118892 restraints weight = 6504.823| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19376 Z= 0.119 Angle : 1.410 45.968 26033 Z= 0.512 Chirality : 0.040 0.175 2982 Planarity : 0.004 0.034 3100 Dihedral : 14.558 150.347 3088 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.48 % Allowed : 12.31 % Favored : 86.21 % 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: 1.39 (0.19), residues: 2212 helix: 2.12 (0.14), residues: 1463 sheet: None (None), residues: 0 loop : -1.60 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 128 TYR 0.008 0.001 TYR A 10 PHE 0.022 0.001 PHE E 116 TRP 0.009 0.001 TRP A 104 HIS 0.001 0.000 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (19362) covalent geometry : angle 1.41103 / 0.51 (26005) SS BOND : bond 0.00113 / 0.07 ( 14) SS BOND : angle 0.41271 / 0.30 ( 28) hydrogen bonds : bond 0.03567 / 2.28 ( 1072) hydrogen bonds : angle 3.93100 / 2.83 ( 3069) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.705 Fit side-chains REVERT: A 207 ASN cc_start: 0.9010 (p0) cc_final: 0.8694 (p0) REVERT: B 243 GLU cc_start: 0.8419 (pt0) cc_final: 0.8112 (pt0) REVERT: C 207 ASN cc_start: 0.8877 (p0) cc_final: 0.8633 (p0) REVERT: C 243 GLU cc_start: 0.8535 (pt0) cc_final: 0.7903 (mt-10) REVERT: D 207 ASN cc_start: 0.9047 (p0) cc_final: 0.8757 (p0) REVERT: D 243 GLU cc_start: 0.8502 (pt0) cc_final: 0.8147 (pt0) REVERT: D 349 LYS cc_start: 0.8294 (tptt) cc_final: 0.7957 (tptt) REVERT: E 207 ASN cc_start: 0.9010 (p0) cc_final: 0.8670 (p0) REVERT: E 243 GLU cc_start: 0.8568 (pt0) cc_final: 0.8311 (pt0) REVERT: G 207 ASN cc_start: 0.8949 (p0) cc_final: 0.8728 (p0) REVERT: G 243 GLU cc_start: 0.8384 (pt0) cc_final: 0.8089 (pt0) outliers start: 30 outliers final: 28 residues processed: 205 average time/residue: 0.1784 time to fit residues: 52.0105 Evaluate side-chains 207 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 236 SER Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 303 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 149 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 123 optimal weight: 0.3980 chunk 197 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 34 optimal weight: 0.0270 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 338 ASN C 338 ASN D 338 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.146010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.110770 restraints weight = 19955.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.114960 restraints weight = 12358.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.117650 restraints weight = 9009.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.119267 restraints weight = 7363.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.120537 restraints weight = 6448.555| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19376 Z= 0.113 Angle : 1.405 46.013 26033 Z= 0.507 Chirality : 0.039 0.193 2982 Planarity : 0.004 0.034 3100 Dihedral : 13.762 145.140 3088 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.78 % Allowed : 12.70 % Favored : 85.52 % 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: 1.60 (0.19), residues: 2212 helix: 2.25 (0.14), residues: 1456 sheet: 0.28 (0.64), residues: 42 loop : -1.52 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 128 TYR 0.008 0.001 TYR F 10 PHE 0.022 0.001 PHE C 116 TRP 0.010 0.001 TRP B 104 HIS 0.001 0.000 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (19362) covalent geometry : angle 1.40554 / 0.51 (26005) SS BOND : bond 0.00110 / 0.07 ( 14) SS BOND : angle 0.42667 / 0.31 ( 28) hydrogen bonds : bond 0.03328 / 2.13 ( 1072) hydrogen bonds : angle 3.84941 / 2.77 ( 3069) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.663 Fit side-chains REVERT: A 207 ASN cc_start: 0.9009 (p0) cc_final: 0.8692 (p0) REVERT: B 243 GLU cc_start: 0.8402 (pt0) cc_final: 0.8118 (pt0) REVERT: B 337 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7190 (tm-30) REVERT: C 207 ASN cc_start: 0.8858 (p0) cc_final: 0.8621 (p0) REVERT: C 243 GLU cc_start: 0.8515 (pt0) cc_final: 0.7892 (mt-10) REVERT: D 243 GLU cc_start: 0.8473 (pt0) cc_final: 0.8154 (pt0) REVERT: D 349 LYS cc_start: 0.8357 (tptt) cc_final: 0.8021 (tptt) REVERT: E 207 ASN cc_start: 0.9008 (p0) cc_final: 0.8680 (p0) REVERT: E 243 GLU cc_start: 0.8556 (pt0) cc_final: 0.8282 (pt0) REVERT: F 207 ASN cc_start: 0.9012 (p0) cc_final: 0.8766 (p0) REVERT: G 207 ASN cc_start: 0.8921 (p0) cc_final: 0.8711 (p0) REVERT: G 243 GLU cc_start: 0.8359 (pt0) cc_final: 0.8053 (pt0) outliers start: 36 outliers final: 32 residues processed: 210 average time/residue: 0.1706 time to fit residues: 51.2002 Evaluate side-chains 215 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 236 SER Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 303 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 162 optimal weight: 0.2980 chunk 150 optimal weight: 0.5980 chunk 182 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 158 optimal weight: 0.1980 chunk 90 optimal weight: 0.6980 chunk 30 optimal weight: 0.0000 chunk 32 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 195 optimal weight: 6.9990 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 338 ASN E 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.148396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.113445 restraints weight = 19982.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.117754 restraints weight = 12282.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.120499 restraints weight = 8932.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.122248 restraints weight = 7231.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.123504 restraints weight = 6276.405| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19376 Z= 0.103 Angle : 1.400 46.039 26033 Z= 0.505 Chirality : 0.039 0.180 2982 Planarity : 0.004 0.034 3100 Dihedral : 13.145 138.494 3088 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.48 % Allowed : 13.30 % Favored : 85.22 % 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: 1.71 (0.19), residues: 2212 helix: 2.38 (0.14), residues: 1449 sheet: 0.09 (0.70), residues: 42 loop : -1.53 (0.25), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 128 TYR 0.008 0.001 TYR C 10 PHE 0.023 0.001 PHE A 116 TRP 0.010 0.001 TRP B 104 HIS 0.000 0.000 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (19362) covalent geometry : angle 1.40093 / 0.50 (26005) SS BOND : bond 0.00079 / 0.05 ( 14) SS BOND : angle 0.39698 / 0.29 ( 28) hydrogen bonds : bond 0.03103 / 1.98 ( 1072) hydrogen bonds : angle 3.76446 / 2.71 ( 3069) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.656 Fit side-chains REVERT: A 207 ASN cc_start: 0.8974 (p0) cc_final: 0.8699 (p0) REVERT: B 63 GLN cc_start: 0.8194 (mp10) cc_final: 0.7974 (mp10) REVERT: B 243 GLU cc_start: 0.8382 (pt0) cc_final: 0.8045 (pt0) REVERT: D 243 GLU cc_start: 0.8444 (pt0) cc_final: 0.8130 (pt0) REVERT: D 349 LYS cc_start: 0.8341 (tptt) cc_final: 0.8099 (tptt) REVERT: E 143 MET cc_start: 0.7967 (mtp) cc_final: 0.7642 (mmm) REVERT: E 207 ASN cc_start: 0.8990 (p0) cc_final: 0.8680 (p0) REVERT: E 243 GLU cc_start: 0.8533 (pt0) cc_final: 0.8248 (pt0) REVERT: F 207 ASN cc_start: 0.9026 (p0) cc_final: 0.8731 (p0) REVERT: G 243 GLU cc_start: 0.8314 (pt0) cc_final: 0.7999 (pt0) outliers start: 30 outliers final: 26 residues processed: 206 average time/residue: 0.1679 time to fit residues: 49.3597 Evaluate side-chains 208 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 303 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 29 optimal weight: 8.9990 chunk 191 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 192 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 ASN B 338 ASN E 338 ASN F 338 ASN G 338 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.144947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.109444 restraints weight = 20079.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.113587 restraints weight = 12529.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.116331 restraints weight = 9164.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.118084 restraints weight = 7479.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.119104 restraints weight = 6538.355| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19376 Z= 0.137 Angle : 1.413 46.001 26033 Z= 0.513 Chirality : 0.040 0.173 2982 Planarity : 0.004 0.034 3100 Dihedral : 13.098 136.666 3088 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.13 % Allowed : 12.75 % Favored : 85.12 % 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: 1.67 (0.19), residues: 2212 helix: 2.36 (0.14), residues: 1449 sheet: 0.26 (0.70), residues: 42 loop : -1.59 (0.25), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 128 TYR 0.009 0.001 TYR F 10 PHE 0.023 0.001 PHE E 116 TRP 0.009 0.002 TRP B 104 HIS 0.001 0.000 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (19362) covalent geometry : angle 1.41319 / 0.51 (26005) SS BOND : bond 0.00170 / 0.11 ( 14) SS BOND : angle 0.52999 / 0.38 ( 28) hydrogen bonds : bond 0.03393 / 2.16 ( 1072) hydrogen bonds : angle 3.80984 / 2.75 ( 3069) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 0.519 Fit side-chains REVERT: A 207 ASN cc_start: 0.8990 (p0) cc_final: 0.8702 (p0) REVERT: B 243 GLU cc_start: 0.8512 (pt0) cc_final: 0.8127 (pt0) REVERT: C 243 GLU cc_start: 0.8547 (pt0) cc_final: 0.7911 (mt-10) REVERT: C 346 LYS cc_start: 0.8385 (tppt) cc_final: 0.8153 (tptt) REVERT: D 243 GLU cc_start: 0.8540 (pt0) cc_final: 0.8216 (pt0) REVERT: E 63 GLN cc_start: 0.8257 (mp10) cc_final: 0.8035 (mp10) REVERT: E 143 MET cc_start: 0.8003 (mtp) cc_final: 0.7645 (mmm) REVERT: E 207 ASN cc_start: 0.8997 (p0) cc_final: 0.8689 (p0) REVERT: E 243 GLU cc_start: 0.8600 (pt0) cc_final: 0.8318 (pt0) REVERT: F 243 GLU cc_start: 0.8610 (pt0) cc_final: 0.8337 (pt0) REVERT: G 9 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6914 (tt0) REVERT: G 243 GLU cc_start: 0.8449 (pt0) cc_final: 0.8152 (pt0) outliers start: 43 outliers final: 34 residues processed: 214 average time/residue: 0.1580 time to fit residues: 48.6773 Evaluate side-chains 219 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 236 SER Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 338 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 188 optimal weight: 0.4980 chunk 91 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 134 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN B 338 ASN E 338 ASN F 338 ASN G 338 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.146398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.110878 restraints weight = 19906.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.115108 restraints weight = 12360.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.117855 restraints weight = 9042.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.119575 restraints weight = 7367.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.120659 restraints weight = 6422.484| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19376 Z= 0.116 Angle : 1.409 46.003 26033 Z= 0.511 Chirality : 0.040 0.163 2982 Planarity : 0.004 0.034 3100 Dihedral : 12.877 133.859 3088 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.98 % Allowed : 13.10 % Favored : 84.92 % 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: 1.71 (0.19), residues: 2212 helix: 2.40 (0.14), residues: 1449 sheet: 0.36 (0.73), residues: 42 loop : -1.59 (0.25), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 128 TYR 0.009 0.001 TYR F 10 PHE 0.023 0.001 PHE D 116 TRP 0.009 0.001 TRP B 104 HIS 0.001 0.000 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (19362) covalent geometry : angle 1.41015 / 0.51 (26005) SS BOND : bond 0.00113 / 0.07 ( 14) SS BOND : angle 0.43358 / 0.31 ( 28) hydrogen bonds : bond 0.03282 / 2.09 ( 1072) hydrogen bonds : angle 3.76229 / 2.71 ( 3069) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.827 Fit side-chains REVERT: A 207 ASN cc_start: 0.8971 (p0) cc_final: 0.8710 (p0) REVERT: B 63 GLN cc_start: 0.8206 (mp10) cc_final: 0.8002 (mp10) REVERT: B 243 GLU cc_start: 0.8484 (pt0) cc_final: 0.8097 (pt0) REVERT: C 243 GLU cc_start: 0.8530 (pt0) cc_final: 0.7880 (mt-10) REVERT: D 243 GLU cc_start: 0.8524 (pt0) cc_final: 0.8188 (pt0) REVERT: D 349 LYS cc_start: 0.8487 (tptt) cc_final: 0.8125 (tptt) REVERT: E 63 GLN cc_start: 0.8250 (mp10) cc_final: 0.8013 (mp10) REVERT: E 143 MET cc_start: 0.7966 (mtp) cc_final: 0.7626 (mmm) REVERT: E 207 ASN cc_start: 0.8970 (p0) cc_final: 0.8661 (p0) REVERT: E 243 GLU cc_start: 0.8578 (pt0) cc_final: 0.8301 (pt0) REVERT: F 243 GLU cc_start: 0.8598 (pt0) cc_final: 0.8286 (pt0) REVERT: G 243 GLU cc_start: 0.8411 (pt0) cc_final: 0.8118 (pt0) outliers start: 40 outliers final: 36 residues processed: 214 average time/residue: 0.1763 time to fit residues: 53.7277 Evaluate side-chains 217 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 236 SER Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 338 ASN Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 338 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 55 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 9 optimal weight: 0.0970 chunk 201 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 211 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 overall best weight: 1.1180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 ASN B 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.146219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.110724 restraints weight = 19957.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.114925 restraints weight = 12377.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.117661 restraints weight = 9056.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.119385 restraints weight = 7369.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.120459 restraints weight = 6436.505| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 19376 Z= 0.171 Angle : 1.538 59.200 26033 Z= 0.644 Chirality : 0.043 0.551 2982 Planarity : 0.005 0.119 3100 Dihedral : 12.887 133.859 3088 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.83 % Allowed : 13.64 % Favored : 84.53 % Cbeta Deviations : 0.09 % 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: 1.68 (0.19), residues: 2212 helix: 2.37 (0.14), residues: 1449 sheet: 0.37 (0.73), residues: 42 loop : -1.60 (0.25), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 128 TYR 0.009 0.001 TYR F 10 PHE 0.024 0.001 PHE D 116 TRP 0.010 0.001 TRP B 104 HIS 0.001 0.000 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (19362) covalent geometry : angle 1.53875 / 0.64 (26005) SS BOND : bond 0.00124 / 0.08 ( 14) SS BOND : angle 0.41255 / 0.30 ( 28) hydrogen bonds : bond 0.03334 / 2.12 ( 1072) hydrogen bonds : angle 3.76502 / 2.71 ( 3069) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 0.729 Fit side-chains REVERT: A 207 ASN cc_start: 0.8968 (p0) cc_final: 0.8708 (p0) REVERT: B 63 GLN cc_start: 0.8211 (mp10) cc_final: 0.8006 (mp10) REVERT: B 243 GLU cc_start: 0.8482 (pt0) cc_final: 0.8099 (pt0) REVERT: C 243 GLU cc_start: 0.8537 (pt0) cc_final: 0.7885 (mt-10) REVERT: D 243 GLU cc_start: 0.8527 (pt0) cc_final: 0.8195 (pt0) REVERT: D 349 LYS cc_start: 0.8482 (tptt) cc_final: 0.8113 (tptt) REVERT: E 143 MET cc_start: 0.7975 (mtp) cc_final: 0.7635 (mmm) REVERT: E 207 ASN cc_start: 0.8967 (p0) cc_final: 0.8660 (p0) REVERT: E 243 GLU cc_start: 0.8584 (pt0) cc_final: 0.8307 (pt0) REVERT: F 243 GLU cc_start: 0.8598 (pt0) cc_final: 0.8290 (pt0) REVERT: G 9 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6947 (tt0) REVERT: G 243 GLU cc_start: 0.8417 (pt0) cc_final: 0.8127 (pt0) outliers start: 37 outliers final: 35 residues processed: 205 average time/residue: 0.1851 time to fit residues: 54.3887 Evaluate side-chains 216 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 236 SER Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 303 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 0.0040 chunk 176 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN F 338 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.146193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.110638 restraints weight = 20096.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.114824 restraints weight = 12451.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.117542 restraints weight = 9092.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.119340 restraints weight = 7358.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.120503 restraints weight = 6438.061| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.190 19376 Z= 0.172 Angle : 1.570 59.010 26033 Z= 0.674 Chirality : 0.047 1.132 2982 Planarity : 0.005 0.111 3100 Dihedral : 12.880 133.846 3088 Min Nonbonded Distance : 1.506 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.98 % Allowed : 13.30 % Favored : 84.73 % Cbeta Deviations : 0.14 % 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: 1.68 (0.19), residues: 2212 helix: 2.37 (0.14), residues: 1449 sheet: 0.37 (0.73), residues: 42 loop : -1.60 (0.25), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 128 TYR 0.009 0.001 TYR F 10 PHE 0.024 0.001 PHE D 116 TRP 0.010 0.001 TRP B 104 HIS 0.001 0.000 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (19362) covalent geometry : angle 1.57054 / 0.67 (26005) SS BOND : bond 0.00120 / 0.08 ( 14) SS BOND : angle 0.43214 / 0.31 ( 28) hydrogen bonds : bond 0.03292 / 2.10 ( 1072) hydrogen bonds : angle 3.75762 / 2.71 ( 3069) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2675.78 seconds wall clock time: 47 minutes 32.43 seconds (2852.43 seconds total)