Starting phenix.real_space_refine on Thu Mar 5 03:37:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f8j_31489/03_2026/7f8j_31489.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f8j_31489/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7f8j_31489/03_2026/7f8j_31489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f8j_31489/03_2026/7f8j_31489.map" model { file = "/net/cci-nas-00/data/ceres_data/7f8j_31489/03_2026/7f8j_31489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f8j_31489/03_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-5986/lib/python3.9/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: 155 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: 155 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: 155 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: 155 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: 155 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: 155 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: 155 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: 4.42, per 1000 atoms: 0.23 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: 1.72 Conformation dependent library (CDL) restraints added in 792.1 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: 0.50 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: 3.29 Time building geometry restraints manager: 2.22 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 - 35.15: 11497 35.15 - 70.30: 280 70.30 - 105.45: 47 105.45 - 140.60: 14 140.60 - 175.76: 42 Dihedral angle restraints: 11880 sinusoidal: 5174 harmonic: 6706 Sorted by residual: dihedral pdb=" O5 LBN B 502 " pdb=" C2 LBN B 502 " pdb=" C3 LBN B 502 " pdb=" O7 LBN B 502 " ideal model delta sinusoidal sigma weight residual 62.67 -113.09 175.76 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN C 502 " pdb=" C2 LBN C 502 " pdb=" C3 LBN C 502 " pdb=" O7 LBN C 502 " ideal model delta sinusoidal sigma weight residual 62.67 -113.08 175.75 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN G 506 " pdb=" C2 LBN G 506 " pdb=" C3 LBN G 506 " pdb=" O7 LBN G 506 " ideal model delta sinusoidal sigma weight residual 62.67 -113.06 175.73 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 11877 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.430 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 : 20.219 175.755 7470 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 covalent geometry : bond 0.00967 (19362) covalent geometry : angle 1.62308 (26005) SS BOND : bond 0.00204 ( 14) SS BOND : angle 0.29621 ( 28) hydrogen bonds : bond 0.21609 ( 1072) hydrogen bonds : angle 6.01502 ( 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 : 0.590 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: 0.1790 time to fit residues: 61.4217 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 : 0.653 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3604 r_free = 0.3604 target = 0.151577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.116839 restraints weight = 19898.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.121216 restraints weight = 11946.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.124074 restraints weight = 8568.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.125736 restraints weight = 6880.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.126970 restraints weight = 5987.578| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1194 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= 0.130 Angle : 1.422 46.683 26033 Z= 0.520 Chirality : 0.040 0.183 2982 Planarity : 0.004 0.034 3100 Dihedral : 23.081 179.523 3242 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.64 % Allowed : 6.43 % Favored : 92.93 % 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: 0.99 (0.18), residues: 2212 helix: 1.96 (0.14), residues: 1491 sheet: None (None), residues: 0 loop : -2.30 (0.20), residues: 721 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 0.010 0.001 TRP E 104 HIS 0.001 0.000 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00278 (19362) covalent geometry : angle 1.42219 (26005) SS BOND : bond 0.00169 ( 14) SS BOND : angle 0.50502 ( 28) hydrogen bonds : bond 0.04823 ( 1072) hydrogen bonds : angle 4.30787 ( 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 217 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 204 time to evaluate : 0.668 Fit side-chains REVERT: A 29 ARG cc_start: 0.7921 (ptp90) cc_final: 0.7615 (ptt-90) REVERT: A 40 CYS cc_start: 0.8669 (t) cc_final: 0.7806 (m) REVERT: A 207 ASN cc_start: 0.9003 (p0) cc_final: 0.8676 (p0) REVERT: A 243 GLU cc_start: 0.8368 (pt0) cc_final: 0.8168 (pt0) REVERT: C 243 GLU cc_start: 0.8512 (pt0) cc_final: 0.8264 (pt0) REVERT: D 29 ARG cc_start: 0.7809 (ptp90) cc_final: 0.7574 (ptt-90) REVERT: D 207 ASN cc_start: 0.9073 (p0) cc_final: 0.8787 (p0) REVERT: E 40 CYS cc_start: 0.8676 (t) cc_final: 0.8421 (t) REVERT: E 207 ASN cc_start: 0.8967 (p0) cc_final: 0.8617 (p0) REVERT: F 5 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7217 (tm-30) REVERT: F 207 ASN cc_start: 0.8805 (p0) cc_final: 0.8602 (p0) REVERT: G 207 ASN cc_start: 0.8925 (p0) cc_final: 0.8690 (p0) REVERT: G 243 GLU cc_start: 0.8440 (pt0) cc_final: 0.8187 (pt0) outliers start: 13 outliers final: 10 residues processed: 208 average time/residue: 0.1805 time to fit residues: 53.1399 Evaluate side-chains 196 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain C residue 236 SER 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 E residue 236 SER Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 236 SER Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 236 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 34 optimal weight: 0.1980 chunk 89 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 26 optimal weight: 0.0040 chunk 138 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3585 r_free = 0.3585 target = 0.149937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.115421 restraints weight = 20010.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.119699 restraints weight = 12246.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.122454 restraints weight = 8828.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.124054 restraints weight = 7141.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.125333 restraints weight = 6229.338| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19376 Z= 0.116 Angle : 1.409 45.950 26033 Z= 0.509 Chirality : 0.039 0.166 2982 Planarity : 0.004 0.035 3100 Dihedral : 20.985 179.755 3207 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.33 % Allowed : 8.60 % 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: 1.35 (0.19), residues: 2212 helix: 2.18 (0.14), residues: 1456 sheet: None (None), residues: 0 loop : -1.83 (0.22), residues: 756 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 E 104 HIS 0.001 0.000 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00258 (19362) covalent geometry : angle 1.40937 (26005) SS BOND : bond 0.00095 ( 14) SS BOND : angle 0.49869 ( 28) hydrogen bonds : bond 0.03804 ( 1072) hydrogen bonds : angle 3.97628 ( 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 225 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 0.611 Fit side-chains REVERT: A 207 ASN cc_start: 0.9026 (p0) cc_final: 0.8699 (p0) REVERT: A 243 GLU cc_start: 0.8404 (pt0) cc_final: 0.8055 (pt0) REVERT: B 243 GLU cc_start: 0.8372 (pt0) cc_final: 0.8138 (pt0) REVERT: B 268 ILE cc_start: 0.8681 (mt) cc_final: 0.8476 (mt) REVERT: C 207 ASN cc_start: 0.8955 (p0) cc_final: 0.8670 (p0) REVERT: D 207 ASN cc_start: 0.9085 (p0) cc_final: 0.8784 (p0) REVERT: D 243 GLU cc_start: 0.8512 (pt0) cc_final: 0.8214 (pt0) REVERT: E 40 CYS cc_start: 0.8676 (t) cc_final: 0.7726 (m) REVERT: E 207 ASN cc_start: 0.8980 (p0) cc_final: 0.8612 (p0) REVERT: F 337 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7140 (tm-30) REVERT: G 207 ASN cc_start: 0.8952 (p0) cc_final: 0.8722 (p0) REVERT: G 243 GLU cc_start: 0.8470 (pt0) cc_final: 0.8255 (pt0) REVERT: G 268 ILE cc_start: 0.8685 (mt) cc_final: 0.8418 (mt) outliers start: 27 outliers final: 16 residues processed: 216 average time/residue: 0.1834 time to fit residues: 56.2602 Evaluate side-chains 201 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 190 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 170 optimal weight: 0.2980 chunk 185 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN B 338 ASN C 90 GLN C 151 ASN F 151 ASN G 151 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.144545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.108637 restraints weight = 20278.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.112891 restraints weight = 12444.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.115640 restraints weight = 9047.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.117239 restraints weight = 7345.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.118511 restraints weight = 6430.816| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19376 Z= 0.143 Angle : 1.419 46.029 26033 Z= 0.516 Chirality : 0.040 0.187 2982 Planarity : 0.004 0.034 3100 Dihedral : 19.264 179.873 3207 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.88 % Allowed : 10.48 % Favored : 87.64 % 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: 1.48 (0.19), residues: 2212 helix: 2.17 (0.14), residues: 1463 sheet: -0.23 (0.63), residues: 42 loop : -1.61 (0.25), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 128 TYR 0.008 0.001 TYR A 10 PHE 0.025 0.001 PHE F 116 TRP 0.010 0.002 TRP D 74 HIS 0.001 0.000 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00342 (19362) covalent geometry : angle 1.41918 (26005) SS BOND : bond 0.00097 ( 14) SS BOND : angle 0.57465 ( 28) hydrogen bonds : bond 0.03747 ( 1072) hydrogen bonds : angle 3.94594 ( 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 234 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 0.652 Fit side-chains REVERT: A 207 ASN cc_start: 0.9029 (p0) cc_final: 0.8682 (p0) REVERT: A 349 LYS cc_start: 0.8700 (tptt) cc_final: 0.8459 (tptt) REVERT: B 243 GLU cc_start: 0.8507 (pt0) cc_final: 0.8217 (pt0) REVERT: B 338 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.8337 (p0) REVERT: C 207 ASN cc_start: 0.8991 (p0) cc_final: 0.8637 (p0) REVERT: C 243 GLU cc_start: 0.8544 (pt0) cc_final: 0.8194 (pt0) REVERT: D 207 ASN cc_start: 0.9105 (p0) cc_final: 0.8814 (p0) REVERT: D 243 GLU cc_start: 0.8573 (pt0) cc_final: 0.8261 (pt0) REVERT: E 207 ASN cc_start: 0.9025 (p0) cc_final: 0.8666 (p0) REVERT: F 207 ASN cc_start: 0.9005 (p0) cc_final: 0.8684 (p0) REVERT: G 207 ASN cc_start: 0.8953 (p0) cc_final: 0.8714 (p0) outliers start: 38 outliers final: 28 residues processed: 224 average time/residue: 0.1850 time to fit residues: 58.4557 Evaluate side-chains 216 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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 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 236 SER Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 352 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 71 optimal weight: 3.9990 chunk 214 optimal weight: 0.4980 chunk 148 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 216 optimal weight: 0.6980 chunk 178 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 338 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.145463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.110286 restraints weight = 20023.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.114385 restraints weight = 12394.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.117096 restraints weight = 9082.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.118657 restraints weight = 7387.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.119932 restraints weight = 6481.071| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19376 Z= 0.119 Angle : 1.409 45.964 26033 Z= 0.510 Chirality : 0.040 0.178 2982 Planarity : 0.004 0.034 3100 Dihedral : 18.545 178.992 3207 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.68 % Allowed : 12.26 % Favored : 86.06 % 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: 1.56 (0.19), residues: 2212 helix: 2.23 (0.14), residues: 1456 sheet: -0.08 (0.66), residues: 42 loop : -1.56 (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 A 10 PHE 0.023 0.001 PHE C 116 TRP 0.010 0.001 TRP A 104 HIS 0.001 0.000 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00274 (19362) covalent geometry : angle 1.40927 (26005) SS BOND : bond 0.00101 ( 14) SS BOND : angle 0.43309 ( 28) hydrogen bonds : bond 0.03480 ( 1072) hydrogen bonds : angle 3.89323 ( 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 221 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 0.609 Fit side-chains REVERT: A 207 ASN cc_start: 0.9005 (p0) cc_final: 0.8677 (p0) REVERT: A 349 LYS cc_start: 0.8554 (tptt) cc_final: 0.8296 (tptt) REVERT: B 243 GLU cc_start: 0.8548 (pt0) cc_final: 0.8217 (pt0) REVERT: C 207 ASN cc_start: 0.8974 (p0) cc_final: 0.8666 (p0) REVERT: C 243 GLU cc_start: 0.8520 (pt0) cc_final: 0.8019 (mt-10) REVERT: D 207 ASN cc_start: 0.9046 (p0) cc_final: 0.8751 (p0) REVERT: D 243 GLU cc_start: 0.8579 (pt0) cc_final: 0.8260 (pt0) REVERT: E 63 GLN cc_start: 0.8259 (mp10) cc_final: 0.8038 (mp10) REVERT: E 207 ASN cc_start: 0.8998 (p0) cc_final: 0.8654 (p0) REVERT: G 9 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6884 (tt0) REVERT: G 207 ASN cc_start: 0.8932 (p0) cc_final: 0.8724 (p0) outliers start: 34 outliers final: 30 residues processed: 208 average time/residue: 0.1831 time to fit residues: 54.1417 Evaluate side-chains 215 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 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 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 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 352 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 149 optimal weight: 0.7980 chunk 98 optimal weight: 0.0370 chunk 141 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 34 optimal weight: 0.4980 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 ASN C 338 ASN D 338 ASN E 90 GLN G 338 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.145441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.110396 restraints weight = 19935.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.114577 restraints weight = 12331.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.117221 restraints weight = 9012.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.118885 restraints weight = 7335.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.120066 restraints weight = 6407.753| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2233 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= 0.118 Angle : 1.407 45.986 26033 Z= 0.508 Chirality : 0.040 0.168 2982 Planarity : 0.004 0.034 3100 Dihedral : 17.936 175.034 3207 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.98 % Allowed : 12.51 % 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: 1.62 (0.19), residues: 2212 helix: 2.28 (0.14), residues: 1456 sheet: -0.04 (0.65), residues: 42 loop : -1.53 (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 A 10 PHE 0.023 0.001 PHE D 116 TRP 0.009 0.001 TRP A 104 HIS 0.001 0.000 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00272 (19362) covalent geometry : angle 1.40721 (26005) SS BOND : bond 0.00122 ( 14) SS BOND : angle 0.42205 ( 28) hydrogen bonds : bond 0.03366 ( 1072) hydrogen bonds : angle 3.85226 ( 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 227 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.726 Fit side-chains REVERT: A 207 ASN cc_start: 0.8987 (p0) cc_final: 0.8673 (p0) REVERT: A 349 LYS cc_start: 0.8543 (tptt) cc_final: 0.8272 (tptt) REVERT: B 243 GLU cc_start: 0.8552 (pt0) cc_final: 0.8227 (pt0) REVERT: B 299 PHE cc_start: 0.8756 (t80) cc_final: 0.8552 (t80) REVERT: B 337 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7177 (tm-30) REVERT: C 207 ASN cc_start: 0.8985 (p0) cc_final: 0.8675 (p0) REVERT: C 243 GLU cc_start: 0.8543 (pt0) cc_final: 0.7946 (mt-10) REVERT: D 243 GLU cc_start: 0.8585 (pt0) cc_final: 0.8271 (pt0) REVERT: E 143 MET cc_start: 0.7998 (mtp) cc_final: 0.7649 (mmm) REVERT: E 207 ASN cc_start: 0.8995 (p0) cc_final: 0.8663 (p0) REVERT: F 207 ASN cc_start: 0.9009 (p0) cc_final: 0.8724 (p0) REVERT: F 243 GLU cc_start: 0.8604 (pt0) cc_final: 0.8321 (pt0) REVERT: G 9 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6898 (tt0) REVERT: G 207 ASN cc_start: 0.8916 (p0) cc_final: 0.8698 (p0) REVERT: G 346 LYS cc_start: 0.8420 (tppt) cc_final: 0.8201 (tptt) outliers start: 40 outliers final: 35 residues processed: 213 average time/residue: 0.1869 time to fit residues: 56.5504 Evaluate side-chains 218 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 Chi-restraints excluded: chain G residue 352 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 162 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 182 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 90 optimal weight: 0.2980 chunk 30 optimal weight: 7.9990 chunk 32 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 195 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 338 ASN G 90 GLN G 338 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.146554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.111523 restraints weight = 20037.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.115758 restraints weight = 12303.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.118471 restraints weight = 8945.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.120271 restraints weight = 7206.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.121320 restraints weight = 6304.364| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19376 Z= 0.109 Angle : 1.403 46.029 26033 Z= 0.506 Chirality : 0.039 0.164 2982 Planarity : 0.004 0.033 3100 Dihedral : 17.530 171.481 3207 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.78 % Allowed : 13.10 % 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: 1.69 (0.19), residues: 2212 helix: 2.34 (0.14), residues: 1456 sheet: 0.04 (0.69), residues: 42 loop : -1.50 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 128 TYR 0.009 0.001 TYR B 345 PHE 0.023 0.001 PHE G 116 TRP 0.009 0.001 TRP B 104 HIS 0.001 0.000 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00243 (19362) covalent geometry : angle 1.40329 (26005) SS BOND : bond 0.00101 ( 14) SS BOND : angle 0.41385 ( 28) hydrogen bonds : bond 0.03240 ( 1072) hydrogen bonds : angle 3.79426 ( 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 221 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.683 Fit side-chains REVERT: A 207 ASN cc_start: 0.8978 (p0) cc_final: 0.8691 (p0) REVERT: A 349 LYS cc_start: 0.8605 (tptt) cc_final: 0.8362 (tptt) REVERT: B 243 GLU cc_start: 0.8537 (pt0) cc_final: 0.8148 (pt0) REVERT: B 299 PHE cc_start: 0.8733 (t80) cc_final: 0.8532 (t80) REVERT: C 207 ASN cc_start: 0.8988 (p0) cc_final: 0.8685 (p0) REVERT: C 243 GLU cc_start: 0.8504 (pt0) cc_final: 0.7922 (mt-10) REVERT: D 243 GLU cc_start: 0.8551 (pt0) cc_final: 0.8243 (pt0) REVERT: E 63 GLN cc_start: 0.8239 (mp10) cc_final: 0.8020 (mp10) REVERT: E 143 MET cc_start: 0.7996 (mtp) cc_final: 0.7658 (mmm) REVERT: E 207 ASN cc_start: 0.8990 (p0) cc_final: 0.8689 (p0) REVERT: F 207 ASN cc_start: 0.9009 (p0) cc_final: 0.8698 (p0) REVERT: F 243 GLU cc_start: 0.8563 (pt0) cc_final: 0.8230 (pt0) REVERT: G 9 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6881 (tt0) REVERT: G 207 ASN cc_start: 0.8886 (p0) cc_final: 0.8686 (p0) outliers start: 36 outliers final: 31 residues processed: 205 average time/residue: 0.1831 time to fit residues: 53.4734 Evaluate side-chains 213 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 236 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 40 CYS 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 58 ILE 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 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 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 303 THR Chi-restraints excluded: chain G residue 338 ASN Chi-restraints excluded: chain G residue 352 GLU 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: 6.9990 chunk 102 optimal weight: 0.0980 chunk 112 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 119 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 213 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 338 ASN B 90 GLN E 338 ASN F 338 ASN G 338 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.146790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.111590 restraints weight = 19935.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.115788 restraints weight = 12291.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.118627 restraints weight = 8923.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.120233 restraints weight = 7206.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.121443 restraints weight = 6311.251| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19376 Z= 0.112 Angle : 1.404 46.040 26033 Z= 0.507 Chirality : 0.040 0.232 2982 Planarity : 0.004 0.034 3100 Dihedral : 16.655 164.867 3207 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.22 % Allowed : 12.95 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.19), residues: 2212 helix: 2.37 (0.14), residues: 1456 sheet: 0.11 (0.70), residues: 42 loop : -1.56 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 128 TYR 0.009 0.001 TYR A 10 PHE 0.023 0.001 PHE G 116 TRP 0.009 0.001 TRP B 104 HIS 0.001 0.000 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00255 (19362) covalent geometry : angle 1.40518 (26005) SS BOND : bond 0.00109 ( 14) SS BOND : angle 0.44681 ( 28) hydrogen bonds : bond 0.03215 ( 1072) hydrogen bonds : angle 3.73173 ( 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 231 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 0.693 Fit side-chains REVERT: A 207 ASN cc_start: 0.8965 (p0) cc_final: 0.8682 (p0) REVERT: B 63 GLN cc_start: 0.8196 (mp10) cc_final: 0.7983 (mp10) REVERT: B 243 GLU cc_start: 0.8525 (pt0) cc_final: 0.8142 (pt0) REVERT: C 207 ASN cc_start: 0.8984 (p0) cc_final: 0.8704 (p0) REVERT: C 243 GLU cc_start: 0.8512 (pt0) cc_final: 0.7923 (mt-10) REVERT: D 243 GLU cc_start: 0.8566 (pt0) cc_final: 0.8253 (pt0) REVERT: E 143 MET cc_start: 0.7970 (mtp) cc_final: 0.7663 (mmm) REVERT: E 207 ASN cc_start: 0.8964 (p0) cc_final: 0.8642 (p0) REVERT: F 207 ASN cc_start: 0.9005 (p0) cc_final: 0.8680 (p0) REVERT: F 243 GLU cc_start: 0.8586 (pt0) cc_final: 0.8259 (pt0) REVERT: G 9 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6884 (tt0) outliers start: 45 outliers final: 39 residues processed: 215 average time/residue: 0.1798 time to fit residues: 55.1364 Evaluate side-chains 221 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 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 C residue 11 VAL Chi-restraints excluded: chain C residue 40 CYS 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 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 268 ILE 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 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 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 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: 5.9990 chunk 91 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN 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 = 0.3527 r_free = 0.3527 target = 0.145010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.109425 restraints weight = 19972.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.113590 restraints weight = 12425.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.116179 restraints weight = 9101.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.118046 restraints weight = 7428.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.119062 restraints weight = 6514.801| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2443 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= 0.135 Angle : 1.413 46.029 26033 Z= 0.513 Chirality : 0.040 0.182 2982 Planarity : 0.004 0.034 3100 Dihedral : 16.204 159.454 3207 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.32 % Allowed : 13.10 % Favored : 84.58 % 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: 1.66 (0.19), residues: 2212 helix: 2.34 (0.14), residues: 1456 sheet: 0.27 (0.71), residues: 42 loop : -1.61 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 128 TYR 0.009 0.001 TYR A 10 PHE 0.024 0.001 PHE G 116 TRP 0.009 0.002 TRP B 104 HIS 0.001 0.000 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00325 (19362) covalent geometry : angle 1.41413 (26005) SS BOND : bond 0.00166 ( 14) SS BOND : angle 0.54654 ( 28) hydrogen bonds : bond 0.03373 ( 1072) hydrogen bonds : angle 3.75909 ( 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 233 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 186 time to evaluate : 0.587 Fit side-chains REVERT: A 207 ASN cc_start: 0.8984 (p0) cc_final: 0.8706 (p0) REVERT: B 63 GLN cc_start: 0.8198 (mp10) cc_final: 0.7967 (mp10) REVERT: B 243 GLU cc_start: 0.8553 (pt0) cc_final: 0.8183 (pt0) REVERT: B 299 PHE cc_start: 0.8757 (t80) cc_final: 0.8505 (t80) REVERT: C 207 ASN cc_start: 0.8993 (p0) cc_final: 0.8694 (p0) REVERT: C 243 GLU cc_start: 0.8534 (pt0) cc_final: 0.7946 (mt-10) REVERT: D 243 GLU cc_start: 0.8595 (pt0) cc_final: 0.8292 (pt0) REVERT: E 63 GLN cc_start: 0.8256 (mp10) cc_final: 0.8040 (mp10) REVERT: E 143 MET cc_start: 0.8026 (mtp) cc_final: 0.7708 (mmm) REVERT: E 207 ASN cc_start: 0.8983 (p0) cc_final: 0.8686 (p0) REVERT: F 207 ASN cc_start: 0.9016 (p0) cc_final: 0.8715 (p0) REVERT: F 243 GLU cc_start: 0.8605 (pt0) cc_final: 0.8294 (pt0) REVERT: G 9 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6917 (tt0) outliers start: 47 outliers final: 42 residues processed: 217 average time/residue: 0.1710 time to fit residues: 52.7777 Evaluate side-chains 225 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 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 40 CYS 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 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 268 ILE 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 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 338 ASN 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 278 VAL 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: 0.5980 chunk 62 optimal weight: 0.1980 chunk 9 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 105 optimal weight: 0.5980 chunk 211 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 338 ASN B 90 GLN E 338 ASN F 338 ASN G 338 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.146437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.110939 restraints weight = 19910.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.115136 restraints weight = 12308.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.117911 restraints weight = 8998.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.119654 restraints weight = 7305.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.120653 restraints weight = 6382.904| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19376 Z= 0.117 Angle : 1.411 46.051 26033 Z= 0.512 Chirality : 0.040 0.162 2982 Planarity : 0.004 0.034 3100 Dihedral : 15.816 157.175 3207 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.17 % Allowed : 13.64 % Favored : 84.18 % 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: 1.69 (0.19), residues: 2212 helix: 2.41 (0.14), residues: 1449 sheet: 0.25 (0.72), residues: 42 loop : -1.68 (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 G 116 TRP 0.009 0.001 TRP B 104 HIS 0.001 0.000 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00264 (19362) covalent geometry : angle 1.41202 (26005) SS BOND : bond 0.00114 ( 14) SS BOND : angle 0.48564 ( 28) hydrogen bonds : bond 0.03276 ( 1072) hydrogen bonds : angle 3.70539 ( 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 225 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 181 time to evaluate : 0.544 Fit side-chains REVERT: A 207 ASN cc_start: 0.8954 (p0) cc_final: 0.8704 (p0) REVERT: B 63 GLN cc_start: 0.8205 (mp10) cc_final: 0.7967 (mp10) REVERT: B 243 GLU cc_start: 0.8571 (pt0) cc_final: 0.8199 (pt0) REVERT: B 299 PHE cc_start: 0.8748 (t80) cc_final: 0.8500 (t80) REVERT: C 207 ASN cc_start: 0.9002 (p0) cc_final: 0.8718 (p0) REVERT: C 243 GLU cc_start: 0.8520 (pt0) cc_final: 0.7912 (mt-10) REVERT: D 29 ARG cc_start: 0.7702 (ptt-90) cc_final: 0.7452 (ptt-90) REVERT: D 243 GLU cc_start: 0.8555 (pt0) cc_final: 0.8168 (pt0) REVERT: D 338 ASN cc_start: 0.8270 (p0) cc_final: 0.8060 (p0) REVERT: E 63 GLN cc_start: 0.8250 (mp10) cc_final: 0.8036 (mp10) REVERT: E 143 MET cc_start: 0.7984 (mtp) cc_final: 0.7682 (mmm) REVERT: E 207 ASN cc_start: 0.8958 (p0) cc_final: 0.8636 (p0) REVERT: F 207 ASN cc_start: 0.9011 (p0) cc_final: 0.8672 (p0) REVERT: F 243 GLU cc_start: 0.8590 (pt0) cc_final: 0.8293 (pt0) REVERT: G 9 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6898 (tt0) outliers start: 44 outliers final: 41 residues processed: 211 average time/residue: 0.1723 time to fit residues: 51.9225 Evaluate side-chains 222 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 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 236 SER 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 236 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 40 CYS 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 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 268 ILE 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 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 338 ASN 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 278 VAL 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 8 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 chunk 176 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 90 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 338 ASN F 90 GLN G 338 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.146621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.110938 restraints weight = 20037.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.115174 restraints weight = 12380.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.117873 restraints weight = 9031.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.119596 restraints weight = 7366.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.120574 restraints weight = 6433.670| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.212 19376 Z= 0.207 Angle : 1.568 59.199 26033 Z= 0.667 Chirality : 0.054 1.769 2982 Planarity : 0.006 0.167 3100 Dihedral : 15.814 157.160 3207 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.03 % Allowed : 13.79 % Favored : 84.18 % Cbeta Deviations : 0.18 % 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: 1.69 (0.19), residues: 2212 helix: 2.41 (0.14), residues: 1449 sheet: 0.26 (0.73), residues: 42 loop : -1.68 (0.25), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 128 TYR 0.008 0.001 TYR C 10 PHE 0.024 0.001 PHE G 116 TRP 0.009 0.001 TRP B 104 HIS 0.001 0.000 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00417 (19362) covalent geometry : angle 1.56910 (26005) SS BOND : bond 0.00117 ( 14) SS BOND : angle 0.48377 ( 28) hydrogen bonds : bond 0.03379 ( 1072) hydrogen bonds : angle 3.71158 ( 3069) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2630.82 seconds wall clock time: 46 minutes 56.43 seconds (2816.43 seconds total)