Starting phenix.real_space_refine on Sat Mar 7 06:05:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wbn_21594/03_2026/6wbn_21594.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wbn_21594/03_2026/6wbn_21594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wbn_21594/03_2026/6wbn_21594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wbn_21594/03_2026/6wbn_21594.map" model { file = "/net/cci-nas-00/data/ceres_data/6wbn_21594/03_2026/6wbn_21594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wbn_21594/03_2026/6wbn_21594.cif" } resolution = 2.83 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= 0.002 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 42 5.49 5 S 154 5.16 5 C 25886 2.51 5 N 5726 2.21 5 O 6594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s 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: 38402 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "B" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "C" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "D" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "E" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "F" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "G" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "H" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "I" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "J" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "K" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "L" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "M" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "N" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2539 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 229 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 2, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 66 Chain: "B" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "C" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "D" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "E" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "F" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "G" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 179 Unusual residues: {'3PE': 1, 'CLR': 2, 'PTY': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "H" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "I" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "J" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "K" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "L" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "M" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "N" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'PTY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Time building chain proxies: 8.61, per 1000 atoms: 0.22 Number of scatterers: 38402 At special positions: 0 Unit cell: (109.62, 107.996, 230.608, 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 154 16.00 P 42 15.00 O 6594 8.00 N 5726 7.00 C 25886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, 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 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 265 " distance=2.03 Simple disulfide: pdb=" SG CYS H 84 " - pdb=" SG CYS H 246 " distance=2.03 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 265 " distance=2.03 Simple disulfide: pdb=" SG CYS I 84 " - pdb=" SG CYS I 246 " distance=2.03 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 265 " distance=2.03 Simple disulfide: pdb=" SG CYS J 84 " - pdb=" SG CYS J 246 " distance=2.03 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 265 " distance=2.03 Simple disulfide: pdb=" SG CYS K 84 " - pdb=" SG CYS K 246 " distance=2.03 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 265 " distance=2.03 Simple disulfide: pdb=" SG CYS L 84 " - pdb=" SG CYS L 246 " distance=2.03 Simple disulfide: pdb=" SG CYS M 66 " - pdb=" SG CYS M 265 " distance=2.03 Simple disulfide: pdb=" SG CYS M 84 " - pdb=" SG CYS M 246 " distance=2.03 Simple disulfide: pdb=" SG CYS N 66 " - pdb=" SG CYS N 265 " distance=2.03 Simple disulfide: pdb=" SG CYS N 84 " - pdb=" SG CYS N 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: 3.04 Conformation dependent library (CDL) restraints added in 1.3 seconds 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9240 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 14 sheets defined 71.3% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix removed outlier: 3.697A pdb=" N PHE A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 88 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 162 removed outlier: 3.594A pdb=" N ILE A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'A' and resid 207 through 236 Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU A 253 " --> pdb=" O SER A 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 255 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 296 Proline residue: A 289 - end of helix removed outlier: 3.788A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.511A pdb=" N GLN A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.823A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 358 removed outlier: 3.518A pdb=" N LYS A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.693A pdb=" N LEU A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix removed outlier: 3.697A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 88 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 162 removed outlier: 3.593A pdb=" N ILE B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 204 Processing helix chain 'B' and resid 207 through 236 Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.551A pdb=" N LEU B 253 " --> pdb=" O SER B 250 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B 255 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 296 Proline residue: B 289 - end of helix removed outlier: 3.788A pdb=" N PHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 301 removed outlier: 3.510A pdb=" N GLN B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 312 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 3.823A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 358 removed outlier: 3.518A pdb=" N LYS B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 370 removed outlier: 3.692A pdb=" N LEU B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix removed outlier: 3.697A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 88 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 162 removed outlier: 3.593A pdb=" N ILE C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 207 through 236 Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU C 253 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 255 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 296 Proline residue: C 289 - end of helix removed outlier: 3.788A pdb=" N PHE C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 301 removed outlier: 3.511A pdb=" N GLN C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 339 removed outlier: 3.824A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 358 removed outlier: 3.518A pdb=" N LYS C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 370 removed outlier: 3.692A pdb=" N LEU C 370 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix removed outlier: 3.697A pdb=" N PHE D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 88 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 162 removed outlier: 3.593A pdb=" N ILE D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 204 Processing helix chain 'D' and resid 207 through 236 Processing helix chain 'D' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU D 253 " --> pdb=" O SER D 250 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 255 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 296 Proline residue: D 289 - end of helix removed outlier: 3.788A pdb=" N PHE D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 301 removed outlier: 3.510A pdb=" N GLN D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 312 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 339 removed outlier: 3.824A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 358 removed outlier: 3.518A pdb=" N LYS D 346 " --> pdb=" O VAL D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 370 removed outlier: 3.693A pdb=" N LEU D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix removed outlier: 3.696A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 88 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 162 removed outlier: 3.594A pdb=" N ILE E 135 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 204 Processing helix chain 'E' and resid 207 through 236 Processing helix chain 'E' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU E 253 " --> pdb=" O SER E 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA E 255 " --> pdb=" O ILE E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 296 Proline residue: E 289 - end of helix removed outlier: 3.788A pdb=" N PHE E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 301 removed outlier: 3.511A pdb=" N GLN E 301 " --> pdb=" O VAL E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL E 308 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR E 309 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU E 312 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 339 removed outlier: 3.823A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 358 removed outlier: 3.518A pdb=" N LYS E 346 " --> pdb=" O VAL E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 370 removed outlier: 3.693A pdb=" N LEU E 370 " --> pdb=" O LEU E 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix removed outlier: 3.697A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 88 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 162 removed outlier: 3.595A pdb=" N ILE F 135 " --> pdb=" O ALA F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 204 Processing helix chain 'F' and resid 207 through 236 Processing helix chain 'F' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU F 253 " --> pdb=" O SER F 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA F 255 " --> pdb=" O ILE F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 296 Proline residue: F 289 - end of helix removed outlier: 3.788A pdb=" N PHE F 296 " --> pdb=" O VAL F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 301 removed outlier: 3.510A pdb=" N GLN F 301 " --> pdb=" O VAL F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 312 removed outlier: 4.122A pdb=" N VAL F 308 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR F 309 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU F 312 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 339 removed outlier: 3.824A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 358 removed outlier: 3.517A pdb=" N LYS F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 370 removed outlier: 3.693A pdb=" N LEU F 370 " --> pdb=" O LEU F 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 11 Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix removed outlier: 3.697A pdb=" N PHE G 54 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 88 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 162 removed outlier: 3.594A pdb=" N ILE G 135 " --> pdb=" O ALA G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 204 Processing helix chain 'G' and resid 207 through 236 Processing helix chain 'G' and resid 250 through 255 removed outlier: 3.551A pdb=" N LEU G 253 " --> pdb=" O SER G 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA G 255 " --> pdb=" O ILE G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 296 Proline residue: G 289 - end of helix removed outlier: 3.789A pdb=" N PHE G 296 " --> pdb=" O VAL G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 301 removed outlier: 3.511A pdb=" N GLN G 301 " --> pdb=" O VAL G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL G 308 " --> pdb=" O ASP G 304 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR G 309 " --> pdb=" O VAL G 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU G 312 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 339 removed outlier: 3.824A pdb=" N LEU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 358 removed outlier: 3.517A pdb=" N LYS G 346 " --> pdb=" O VAL G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 370 removed outlier: 3.693A pdb=" N LEU G 370 " --> pdb=" O LEU G 366 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 11 Processing helix chain 'H' and resid 32 through 54 Proline residue: H 46 - end of helix removed outlier: 3.697A pdb=" N PHE H 54 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 88 Processing helix chain 'H' and resid 100 through 108 Processing helix chain 'H' and resid 108 through 131 Proline residue: H 123 - end of helix Processing helix chain 'H' and resid 131 through 162 removed outlier: 3.593A pdb=" N ILE H 135 " --> pdb=" O ALA H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 204 Processing helix chain 'H' and resid 207 through 236 Processing helix chain 'H' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU H 253 " --> pdb=" O SER H 250 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA H 255 " --> pdb=" O ILE H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 296 Proline residue: H 289 - end of helix removed outlier: 3.788A pdb=" N PHE H 296 " --> pdb=" O VAL H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 301 removed outlier: 3.510A pdb=" N GLN H 301 " --> pdb=" O VAL H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL H 308 " --> pdb=" O ASP H 304 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR H 309 " --> pdb=" O VAL H 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU H 312 " --> pdb=" O VAL H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 339 removed outlier: 3.823A pdb=" N LEU H 330 " --> pdb=" O ASN H 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 358 removed outlier: 3.517A pdb=" N LYS H 346 " --> pdb=" O VAL H 342 " (cutoff:3.500A) Processing helix chain 'H' and resid 361 through 370 removed outlier: 3.693A pdb=" N LEU H 370 " --> pdb=" O LEU H 366 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 11 Processing helix chain 'I' and resid 32 through 54 Proline residue: I 46 - end of helix removed outlier: 3.696A pdb=" N PHE I 54 " --> pdb=" O ILE I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 88 Processing helix chain 'I' and resid 100 through 108 Processing helix chain 'I' and resid 108 through 131 Proline residue: I 123 - end of helix Processing helix chain 'I' and resid 131 through 162 removed outlier: 3.594A pdb=" N ILE I 135 " --> pdb=" O ALA I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 204 Processing helix chain 'I' and resid 207 through 236 Processing helix chain 'I' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU I 253 " --> pdb=" O SER I 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA I 255 " --> pdb=" O ILE I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 296 Proline residue: I 289 - end of helix removed outlier: 3.787A pdb=" N PHE I 296 " --> pdb=" O VAL I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 296 through 301 removed outlier: 3.511A pdb=" N GLN I 301 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 312 removed outlier: 4.122A pdb=" N VAL I 308 " --> pdb=" O ASP I 304 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR I 309 " --> pdb=" O VAL I 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU I 312 " --> pdb=" O VAL I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 339 removed outlier: 3.823A pdb=" N LEU I 330 " --> pdb=" O ASN I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 358 removed outlier: 3.517A pdb=" N LYS I 346 " --> pdb=" O VAL I 342 " (cutoff:3.500A) Processing helix chain 'I' and resid 361 through 370 removed outlier: 3.692A pdb=" N LEU I 370 " --> pdb=" O LEU I 366 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 11 Processing helix chain 'J' and resid 32 through 54 Proline residue: J 46 - end of helix removed outlier: 3.696A pdb=" N PHE J 54 " --> pdb=" O ILE J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 88 Processing helix chain 'J' and resid 100 through 108 Processing helix chain 'J' and resid 108 through 131 Proline residue: J 123 - end of helix Processing helix chain 'J' and resid 131 through 162 removed outlier: 3.594A pdb=" N ILE J 135 " --> pdb=" O ALA J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 204 Processing helix chain 'J' and resid 207 through 236 Processing helix chain 'J' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU J 253 " --> pdb=" O SER J 250 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA J 255 " --> pdb=" O ILE J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 296 Proline residue: J 289 - end of helix removed outlier: 3.788A pdb=" N PHE J 296 " --> pdb=" O VAL J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 296 through 301 removed outlier: 3.510A pdb=" N GLN J 301 " --> pdb=" O VAL J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL J 308 " --> pdb=" O ASP J 304 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR J 309 " --> pdb=" O VAL J 305 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU J 312 " --> pdb=" O VAL J 308 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 339 removed outlier: 3.823A pdb=" N LEU J 330 " --> pdb=" O ASN J 326 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 358 removed outlier: 3.518A pdb=" N LYS J 346 " --> pdb=" O VAL J 342 " (cutoff:3.500A) Processing helix chain 'J' and resid 361 through 370 removed outlier: 3.693A pdb=" N LEU J 370 " --> pdb=" O LEU J 366 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 11 Processing helix chain 'K' and resid 32 through 54 Proline residue: K 46 - end of helix removed outlier: 3.697A pdb=" N PHE K 54 " --> pdb=" O ILE K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 88 Processing helix chain 'K' and resid 100 through 108 Processing helix chain 'K' and resid 108 through 131 Proline residue: K 123 - end of helix Processing helix chain 'K' and resid 131 through 162 removed outlier: 3.594A pdb=" N ILE K 135 " --> pdb=" O ALA K 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 204 Processing helix chain 'K' and resid 207 through 236 Processing helix chain 'K' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU K 253 " --> pdb=" O SER K 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA K 255 " --> pdb=" O ILE K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 269 through 296 Proline residue: K 289 - end of helix removed outlier: 3.787A pdb=" N PHE K 296 " --> pdb=" O VAL K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 296 through 301 removed outlier: 3.510A pdb=" N GLN K 301 " --> pdb=" O VAL K 297 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL K 308 " --> pdb=" O ASP K 304 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR K 309 " --> pdb=" O VAL K 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU K 312 " --> pdb=" O VAL K 308 " (cutoff:3.500A) Processing helix chain 'K' and resid 326 through 339 removed outlier: 3.822A pdb=" N LEU K 330 " --> pdb=" O ASN K 326 " (cutoff:3.500A) Processing helix chain 'K' and resid 342 through 358 removed outlier: 3.517A pdb=" N LYS K 346 " --> pdb=" O VAL K 342 " (cutoff:3.500A) Processing helix chain 'K' and resid 361 through 370 removed outlier: 3.693A pdb=" N LEU K 370 " --> pdb=" O LEU K 366 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 11 Processing helix chain 'L' and resid 32 through 54 Proline residue: L 46 - end of helix removed outlier: 3.697A pdb=" N PHE L 54 " --> pdb=" O ILE L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 88 Processing helix chain 'L' and resid 100 through 108 Processing helix chain 'L' and resid 108 through 131 Proline residue: L 123 - end of helix Processing helix chain 'L' and resid 131 through 162 removed outlier: 3.594A pdb=" N ILE L 135 " --> pdb=" O ALA L 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 204 Processing helix chain 'L' and resid 207 through 236 Processing helix chain 'L' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU L 253 " --> pdb=" O SER L 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA L 255 " --> pdb=" O ILE L 252 " (cutoff:3.500A) Processing helix chain 'L' and resid 269 through 296 Proline residue: L 289 - end of helix removed outlier: 3.788A pdb=" N PHE L 296 " --> pdb=" O VAL L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 301 removed outlier: 3.511A pdb=" N GLN L 301 " --> pdb=" O VAL L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL L 308 " --> pdb=" O ASP L 304 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR L 309 " --> pdb=" O VAL L 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU L 312 " --> pdb=" O VAL L 308 " (cutoff:3.500A) Processing helix chain 'L' and resid 326 through 339 removed outlier: 3.824A pdb=" N LEU L 330 " --> pdb=" O ASN L 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 342 through 358 removed outlier: 3.518A pdb=" N LYS L 346 " --> pdb=" O VAL L 342 " (cutoff:3.500A) Processing helix chain 'L' and resid 361 through 370 removed outlier: 3.693A pdb=" N LEU L 370 " --> pdb=" O LEU L 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 11 Processing helix chain 'M' and resid 32 through 54 Proline residue: M 46 - end of helix removed outlier: 3.697A pdb=" N PHE M 54 " --> pdb=" O ILE M 50 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 88 Processing helix chain 'M' and resid 100 through 108 Processing helix chain 'M' and resid 108 through 131 Proline residue: M 123 - end of helix Processing helix chain 'M' and resid 131 through 162 removed outlier: 3.594A pdb=" N ILE M 135 " --> pdb=" O ALA M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 204 Processing helix chain 'M' and resid 207 through 236 Processing helix chain 'M' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU M 253 " --> pdb=" O SER M 250 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA M 255 " --> pdb=" O ILE M 252 " (cutoff:3.500A) Processing helix chain 'M' and resid 269 through 296 Proline residue: M 289 - end of helix removed outlier: 3.788A pdb=" N PHE M 296 " --> pdb=" O VAL M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 296 through 301 removed outlier: 3.511A pdb=" N GLN M 301 " --> pdb=" O VAL M 297 " (cutoff:3.500A) Processing helix chain 'M' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL M 308 " --> pdb=" O ASP M 304 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR M 309 " --> pdb=" O VAL M 305 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU M 312 " --> pdb=" O VAL M 308 " (cutoff:3.500A) Processing helix chain 'M' and resid 326 through 339 removed outlier: 3.823A pdb=" N LEU M 330 " --> pdb=" O ASN M 326 " (cutoff:3.500A) Processing helix chain 'M' and resid 342 through 358 removed outlier: 3.518A pdb=" N LYS M 346 " --> pdb=" O VAL M 342 " (cutoff:3.500A) Processing helix chain 'M' and resid 361 through 370 removed outlier: 3.693A pdb=" N LEU M 370 " --> pdb=" O LEU M 366 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 11 Processing helix chain 'N' and resid 32 through 54 Proline residue: N 46 - end of helix removed outlier: 3.696A pdb=" N PHE N 54 " --> pdb=" O ILE N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 88 Processing helix chain 'N' and resid 100 through 108 Processing helix chain 'N' and resid 108 through 131 Proline residue: N 123 - end of helix Processing helix chain 'N' and resid 131 through 162 removed outlier: 3.593A pdb=" N ILE N 135 " --> pdb=" O ALA N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 204 Processing helix chain 'N' and resid 207 through 236 Processing helix chain 'N' and resid 250 through 255 removed outlier: 3.552A pdb=" N LEU N 253 " --> pdb=" O SER N 250 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA N 255 " --> pdb=" O ILE N 252 " (cutoff:3.500A) Processing helix chain 'N' and resid 269 through 296 Proline residue: N 289 - end of helix removed outlier: 3.788A pdb=" N PHE N 296 " --> pdb=" O VAL N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 296 through 301 removed outlier: 3.510A pdb=" N GLN N 301 " --> pdb=" O VAL N 297 " (cutoff:3.500A) Processing helix chain 'N' and resid 304 through 312 removed outlier: 4.123A pdb=" N VAL N 308 " --> pdb=" O ASP N 304 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR N 309 " --> pdb=" O VAL N 305 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU N 312 " --> pdb=" O VAL N 308 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 339 removed outlier: 3.823A pdb=" N LEU N 330 " --> pdb=" O ASN N 326 " (cutoff:3.500A) Processing helix chain 'N' and resid 342 through 358 removed outlier: 3.517A pdb=" N LYS N 346 " --> pdb=" O VAL N 342 " (cutoff:3.500A) Processing helix chain 'N' and resid 361 through 370 removed outlier: 3.693A pdb=" N LEU N 370 " --> pdb=" O LEU N 366 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 65 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 65 Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 65 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 65 Processing sheet with id=AA8, first strand: chain 'H' and resid 64 through 65 Processing sheet with id=AA9, first strand: chain 'I' and resid 64 through 65 Processing sheet with id=AB1, first strand: chain 'J' and resid 64 through 65 Processing sheet with id=AB2, first strand: chain 'K' and resid 64 through 65 Processing sheet with id=AB3, first strand: chain 'L' and resid 64 through 65 Processing sheet with id=AB4, first strand: chain 'M' and resid 64 through 65 Processing sheet with id=AB5, first strand: chain 'N' and resid 64 through 65 2367 hydrogen bonds defined for protein. 7017 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: 6.39 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5807 1.32 - 1.44: 9642 1.44 - 1.56: 23527 1.56 - 1.69: 84 1.69 - 1.81: 182 Bond restraints: 39242 Sorted by residual: bond pdb=" N ASP B 256 " pdb=" CA ASP B 256 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.25e-02 6.40e+03 8.23e+00 bond pdb=" N ASP H 256 " pdb=" CA ASP H 256 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.25e-02 6.40e+03 8.20e+00 bond pdb=" N ASP D 256 " pdb=" CA ASP D 256 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.25e-02 6.40e+03 8.20e+00 bond pdb=" N ASP M 256 " pdb=" CA ASP M 256 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.25e-02 6.40e+03 8.12e+00 bond pdb=" N ASP I 256 " pdb=" CA ASP I 256 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.25e-02 6.40e+03 8.11e+00 ... (remaining 39237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 51411 2.04 - 4.08: 1532 4.08 - 6.12: 257 6.12 - 8.16: 14 8.16 - 10.20: 42 Bond angle restraints: 53256 Sorted by residual: angle pdb=" C THR G 258 " pdb=" N VAL G 259 " pdb=" CA VAL G 259 " ideal model delta sigma weight residual 122.59 125.27 -2.68 7.20e-01 1.93e+00 1.39e+01 angle pdb=" C THR I 258 " pdb=" N VAL I 259 " pdb=" CA VAL I 259 " ideal model delta sigma weight residual 122.59 125.26 -2.67 7.20e-01 1.93e+00 1.37e+01 angle pdb=" C THR D 258 " pdb=" N VAL D 259 " pdb=" CA VAL D 259 " ideal model delta sigma weight residual 122.59 125.25 -2.66 7.20e-01 1.93e+00 1.37e+01 angle pdb=" C THR H 258 " pdb=" N VAL H 259 " pdb=" CA VAL H 259 " ideal model delta sigma weight residual 122.59 125.25 -2.66 7.20e-01 1.93e+00 1.37e+01 angle pdb=" C THR E 258 " pdb=" N VAL E 259 " pdb=" CA VAL E 259 " ideal model delta sigma weight residual 122.59 125.24 -2.65 7.20e-01 1.93e+00 1.36e+01 ... (remaining 53251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.84: 24164 33.84 - 67.67: 1050 67.67 - 101.51: 28 101.51 - 135.35: 28 135.35 - 169.19: 14 Dihedral angle restraints: 25284 sinusoidal: 11074 harmonic: 14210 Sorted by residual: dihedral pdb=" N1 PTY M 401 " pdb=" C2 PTY M 401 " pdb=" C3 PTY M 401 " pdb=" O11 PTY M 401 " ideal model delta sinusoidal sigma weight residual 65.33 -103.86 169.19 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" N1 PTY N 402 " pdb=" C2 PTY N 402 " pdb=" C3 PTY N 402 " pdb=" O11 PTY N 402 " ideal model delta sinusoidal sigma weight residual 65.33 -103.84 169.17 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" N1 PTY K 401 " pdb=" C2 PTY K 401 " pdb=" C3 PTY K 401 " pdb=" O11 PTY K 401 " ideal model delta sinusoidal sigma weight residual 65.33 -103.84 169.17 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 25281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3797 0.038 - 0.076: 1784 0.076 - 0.114: 584 0.114 - 0.152: 135 0.152 - 0.190: 14 Chirality restraints: 6314 Sorted by residual: chirality pdb=" CA LEU I 146 " pdb=" N LEU I 146 " pdb=" C LEU I 146 " pdb=" CB LEU I 146 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" CA LEU D 146 " pdb=" N LEU D 146 " pdb=" C LEU D 146 " pdb=" CB LEU D 146 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" CA LEU E 146 " pdb=" N LEU E 146 " pdb=" C LEU E 146 " pdb=" CB LEU E 146 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.99e-01 ... (remaining 6311 not shown) Planarity restraints: 6230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU I 122 " 0.024 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO I 123 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO I 123 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 123 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 122 " 0.024 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO B 123 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 122 " -0.024 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO D 123 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 123 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 123 " -0.020 5.00e-02 4.00e+02 ... (remaining 6227 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 300 2.64 - 3.20: 36403 3.20 - 3.77: 59687 3.77 - 4.33: 79174 4.33 - 4.90: 132891 Nonbonded interactions: 308455 Sorted by model distance: nonbonded pdb=" NZ LYS I 148 " pdb=" O ASN J 369 " model vdw 2.069 3.120 nonbonded pdb=" NZ LYS M 148 " pdb=" O ASN N 369 " model vdw 2.073 3.120 nonbonded pdb=" O ASN H 369 " pdb=" NZ LYS N 148 " model vdw 2.076 3.120 nonbonded pdb=" NZ LYS L 148 " pdb=" O ASN M 369 " model vdw 2.078 3.120 nonbonded pdb=" NZ LYS K 148 " pdb=" O ASN L 369 " model vdw 2.084 3.120 ... (remaining 308450 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'B' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'C' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'D' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'E' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'F' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'G' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'H' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'I' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'J' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'K' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'L' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'M' and (resid 2 through 373 or resid 402 or resid 405)) selection = (chain 'N' and (resid 2 through 373 or (resid 402 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 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 C37 or name \ C38 or name C39 or name C40 or name C41 or name C5 or name C6 or name C8 or nam \ e N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or \ name O4 or name O7 or name P1 )) or resid 405)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 30.530 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 0.049 39270 Z= 0.451 Angle : 0.876 10.199 53312 Z= 0.455 Chirality : 0.048 0.190 6314 Planarity : 0.004 0.035 6230 Dihedral : 16.955 169.187 15960 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.80 % Allowed : 11.41 % Favored : 87.79 % 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: -0.59 (0.12), residues: 4718 helix: 0.55 (0.09), residues: 3150 sheet: None (None), residues: 0 loop : -2.35 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG M 29 TYR 0.021 0.002 TYR N 345 PHE 0.021 0.002 PHE M 67 TRP 0.008 0.002 TRP F 104 HIS 0.004 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00986 (39242) covalent geometry : angle 0.87641 (53256) SS BOND : bond 0.00162 ( 28) SS BOND : angle 0.72476 ( 56) hydrogen bonds : bond 0.12113 ( 2367) hydrogen bonds : angle 5.35271 ( 7017) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 377 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.8348 (mpt-90) cc_final: 0.8122 (mmm-85) REVERT: I 256 ASP cc_start: 0.8345 (t0) cc_final: 0.8038 (t0) REVERT: K 200 LEU cc_start: 0.7787 (tt) cc_final: 0.7572 (mp) REVERT: N 89 GLN cc_start: 0.8555 (mp10) cc_final: 0.7695 (mt0) REVERT: N 200 LEU cc_start: 0.7770 (tt) cc_final: 0.7538 (mp) outliers start: 28 outliers final: 10 residues processed: 405 average time/residue: 0.8661 time to fit residues: 412.4349 Evaluate side-chains 264 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 254 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain M residue 88 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 470 optimal weight: 0.0050 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 76 GLN A 89 GLN A 134 HIS A 208 ASN A 274 GLN B 76 GLN B 89 GLN B 134 HIS B 208 ASN B 264 GLN B 274 GLN B 353 ASN C 76 GLN C 89 GLN C 134 HIS C 208 ASN C 274 GLN C 353 ASN D 76 GLN D 89 GLN D 134 HIS D 208 ASN D 264 GLN D 274 GLN E 76 GLN E 89 GLN E 134 HIS E 208 ASN E 264 GLN E 274 GLN E 353 ASN F 76 GLN F 89 GLN F 134 HIS F 208 ASN F 274 GLN G 76 GLN G 89 GLN G 134 HIS G 208 ASN G 274 GLN G 353 ASN H 76 GLN H 134 HIS H 208 ASN H 264 GLN H 274 GLN H 353 ASN I 76 GLN I 134 HIS I 208 ASN I 264 GLN I 274 GLN J 76 GLN J 134 HIS J 208 ASN J 274 GLN K 76 GLN K 134 HIS K 208 ASN K 274 GLN L 76 GLN L 89 GLN L 134 HIS L 208 ASN L 274 GLN L 353 ASN M 76 GLN M 89 GLN M 134 HIS M 208 ASN M 274 GLN M 353 ASN N 76 GLN N 89 GLN N 134 HIS N 208 ASN N 264 GLN N 274 GLN Total number of N/Q/H flips: 80 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.108919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.071632 restraints weight = 84476.518| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.61 r_work: 0.3037 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 39270 Z= 0.125 Angle : 0.583 7.444 53312 Z= 0.290 Chirality : 0.040 0.126 6314 Planarity : 0.004 0.035 6230 Dihedral : 15.250 135.875 8704 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.27 % Allowed : 15.08 % Favored : 81.64 % 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: 0.81 (0.12), residues: 4718 helix: 1.64 (0.09), residues: 3234 sheet: None (None), residues: 0 loop : -2.05 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 254 TYR 0.017 0.001 TYR E 345 PHE 0.010 0.001 PHE H 54 TRP 0.009 0.001 TRP H 104 HIS 0.003 0.002 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00264 (39242) covalent geometry : angle 0.58280 (53256) SS BOND : bond 0.00172 ( 28) SS BOND : angle 0.26222 ( 56) hydrogen bonds : bond 0.03849 ( 2367) hydrogen bonds : angle 4.08498 ( 7017) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 306 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8042 (tm-30) REVERT: A 140 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8196 (ptpp) REVERT: B 5 GLN cc_start: 0.8967 (tt0) cc_final: 0.8683 (tm-30) REVERT: B 9 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8219 (tm-30) REVERT: C 5 GLN cc_start: 0.8854 (tt0) cc_final: 0.8627 (tp40) REVERT: C 9 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8175 (tm-30) REVERT: D 9 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8166 (tm-30) REVERT: E 5 GLN cc_start: 0.8965 (tt0) cc_final: 0.8719 (tp40) REVERT: E 9 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8194 (tm-30) REVERT: F 5 GLN cc_start: 0.8908 (mt0) cc_final: 0.8674 (tp40) REVERT: F 9 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8241 (tm-30) REVERT: G 9 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8216 (tm-30) REVERT: H 5 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7855 (tm-30) REVERT: H 9 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7906 (tm-30) REVERT: I 5 GLN cc_start: 0.8634 (mt0) cc_final: 0.8232 (tm-30) REVERT: I 9 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7938 (tm-30) REVERT: J 9 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7856 (tm-30) REVERT: K 5 GLN cc_start: 0.8543 (mt0) cc_final: 0.8245 (tm-30) REVERT: K 9 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7964 (tm-30) REVERT: L 9 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7892 (tm-30) REVERT: L 143 MET cc_start: 0.8639 (mtp) cc_final: 0.8329 (mtm) REVERT: M 5 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7846 (tm-30) REVERT: M 9 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7893 (tm-30) REVERT: M 57 GLU cc_start: 0.8472 (pm20) cc_final: 0.8168 (pm20) REVERT: N 5 GLN cc_start: 0.8641 (mt0) cc_final: 0.8218 (tm-30) REVERT: N 9 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7975 (tm-30) outliers start: 115 outliers final: 38 residues processed: 380 average time/residue: 0.7057 time to fit residues: 325.1762 Evaluate side-chains 317 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 278 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 31 GLU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain I residue 31 GLU Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain K residue 31 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain L residue 31 GLU Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain M residue 354 ILE Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 246 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 183 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 399 optimal weight: 7.9990 chunk 445 optimal weight: 8.9990 chunk 209 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 312 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN B 89 GLN B 264 GLN C 89 GLN D 89 GLN D 264 GLN E 264 GLN F 89 GLN H 264 GLN I 89 GLN I 264 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 ASN K 353 ASN L 89 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 264 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.105794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.068180 restraints weight = 85449.066| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.59 r_work: 0.2946 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 39270 Z= 0.192 Angle : 0.600 7.672 53312 Z= 0.298 Chirality : 0.041 0.233 6314 Planarity : 0.004 0.035 6230 Dihedral : 12.833 101.939 8704 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.64 % Allowed : 16.90 % Favored : 79.45 % 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: 1.28 (0.13), residues: 4718 helix: 1.96 (0.09), residues: 3262 sheet: None (None), residues: 0 loop : -1.84 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 254 TYR 0.022 0.002 TYR E 345 PHE 0.014 0.001 PHE H 67 TRP 0.007 0.001 TRP G 104 HIS 0.002 0.001 HIS L 106 Details of bonding type rmsd covalent geometry : bond 0.00458 (39242) covalent geometry : angle 0.60034 (53256) SS BOND : bond 0.00188 ( 28) SS BOND : angle 0.43608 ( 56) hydrogen bonds : bond 0.04208 ( 2367) hydrogen bonds : angle 4.04341 ( 7017) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 284 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8165 (tm-30) REVERT: B 9 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8237 (tm-30) REVERT: B 29 ARG cc_start: 0.8063 (mmm-85) cc_final: 0.7734 (mmt90) REVERT: B 143 MET cc_start: 0.9017 (mtm) cc_final: 0.8804 (mtp) REVERT: C 5 GLN cc_start: 0.8875 (tt0) cc_final: 0.8654 (tm-30) REVERT: C 9 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8168 (tm-30) REVERT: C 143 MET cc_start: 0.8922 (mtm) cc_final: 0.8676 (mtp) REVERT: C 353 ASN cc_start: 0.9114 (OUTLIER) cc_final: 0.8626 (t0) REVERT: D 5 GLN cc_start: 0.8595 (tp40) cc_final: 0.8285 (tm-30) REVERT: D 9 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8208 (tm-30) REVERT: D 29 ARG cc_start: 0.8027 (mmm-85) cc_final: 0.7804 (mmt90) REVERT: D 89 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8573 (mt0) REVERT: D 254 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8726 (ttm110) REVERT: E 9 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8207 (tm-30) REVERT: E 29 ARG cc_start: 0.8112 (mmm-85) cc_final: 0.7679 (mmm-85) REVERT: E 353 ASN cc_start: 0.9009 (OUTLIER) cc_final: 0.8526 (t0) REVERT: F 9 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8305 (tm-30) REVERT: F 29 ARG cc_start: 0.8115 (mmm-85) cc_final: 0.7833 (mmm-85) REVERT: G 5 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8198 (tp40) REVERT: G 9 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8214 (tm-30) REVERT: G 353 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8536 (t0) REVERT: H 5 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7717 (tm-30) REVERT: H 9 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7823 (tm-30) REVERT: H 89 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8541 (mt0) REVERT: I 9 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7838 (tm-30) REVERT: I 138 ASP cc_start: 0.7830 (m-30) cc_final: 0.7530 (m-30) REVERT: I 152 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.6180 (mtm110) REVERT: J 9 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7800 (tm-30) REVERT: K 9 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7793 (tm-30) REVERT: K 89 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8473 (mt0) REVERT: K 138 ASP cc_start: 0.7843 (m-30) cc_final: 0.7613 (m-30) REVERT: L 9 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7820 (tm-30) REVERT: L 143 MET cc_start: 0.8639 (mtp) cc_final: 0.8367 (mtm) REVERT: L 152 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6252 (mtm110) REVERT: M 5 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7791 (tm-30) REVERT: M 9 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7822 (tm-30) REVERT: M 57 GLU cc_start: 0.8750 (pm20) cc_final: 0.8307 (pm20) REVERT: N 9 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7846 (tm-30) REVERT: N 89 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8947 (mm-40) outliers start: 128 outliers final: 49 residues processed: 375 average time/residue: 0.7071 time to fit residues: 320.2265 Evaluate side-chains 320 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 260 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 254 ARG Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 152 ARG Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 246 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 336 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 chunk 379 optimal weight: 3.9990 chunk 360 optimal weight: 6.9990 chunk 445 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 454 optimal weight: 0.8980 chunk 254 optimal weight: 3.9990 chunk 206 optimal weight: 30.0000 chunk 255 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 GLN G 264 GLN I 353 ASN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN M 89 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.105298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.067821 restraints weight = 85148.414| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.56 r_work: 0.2938 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 39270 Z= 0.187 Angle : 0.582 8.600 53312 Z= 0.289 Chirality : 0.041 0.136 6314 Planarity : 0.004 0.035 6230 Dihedral : 12.157 95.462 8704 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.56 % Allowed : 17.42 % Favored : 79.03 % 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: 1.53 (0.13), residues: 4718 helix: 2.13 (0.09), residues: 3262 sheet: None (None), residues: 0 loop : -1.72 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 254 TYR 0.019 0.001 TYR F 345 PHE 0.017 0.001 PHE K 244 TRP 0.011 0.002 TRP L 104 HIS 0.002 0.001 HIS J 134 Details of bonding type rmsd covalent geometry : bond 0.00447 (39242) covalent geometry : angle 0.58198 (53256) SS BOND : bond 0.00173 ( 28) SS BOND : angle 0.43146 ( 56) hydrogen bonds : bond 0.03890 ( 2367) hydrogen bonds : angle 3.84852 ( 7017) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 280 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8196 (tm-30) REVERT: B 9 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8282 (tm-30) REVERT: B 29 ARG cc_start: 0.8121 (mmm-85) cc_final: 0.7850 (mmm-85) REVERT: B 143 MET cc_start: 0.9080 (mtm) cc_final: 0.8834 (mtp) REVERT: C 5 GLN cc_start: 0.8877 (tt0) cc_final: 0.8655 (tm-30) REVERT: C 9 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8158 (tm-30) REVERT: C 31 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8473 (mt-10) REVERT: C 143 MET cc_start: 0.8977 (mtm) cc_final: 0.8713 (mtp) REVERT: C 254 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8736 (ttm110) REVERT: D 5 GLN cc_start: 0.8644 (tp40) cc_final: 0.8301 (tm-30) REVERT: D 9 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8209 (tm-30) REVERT: D 29 ARG cc_start: 0.8061 (mmm-85) cc_final: 0.7758 (mmm-85) REVERT: E 9 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8214 (tm-30) REVERT: E 29 ARG cc_start: 0.8110 (mmm-85) cc_final: 0.7645 (mmm-85) REVERT: F 9 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8303 (tm-30) REVERT: G 5 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8222 (tm-30) REVERT: G 9 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8191 (tm-30) REVERT: G 254 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8703 (ttm110) REVERT: H 5 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7833 (tm-30) REVERT: H 9 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7787 (tm-30) REVERT: H 138 ASP cc_start: 0.7887 (m-30) cc_final: 0.7630 (m-30) REVERT: I 9 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7798 (tm-30) REVERT: I 138 ASP cc_start: 0.7870 (m-30) cc_final: 0.7602 (m-30) REVERT: I 152 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6155 (mtm110) REVERT: J 9 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7748 (tm-30) REVERT: J 138 ASP cc_start: 0.7891 (m-30) cc_final: 0.7620 (m-30) REVERT: K 9 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7743 (tm-30) REVERT: K 138 ASP cc_start: 0.7951 (m-30) cc_final: 0.7674 (m-30) REVERT: L 9 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7815 (tm-30) REVERT: L 89 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8226 (mt0) REVERT: L 143 MET cc_start: 0.8693 (mtp) cc_final: 0.8408 (mtm) REVERT: M 5 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7802 (tm-30) REVERT: M 9 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7739 (tm-30) REVERT: N 9 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7859 (tm-30) outliers start: 125 outliers final: 57 residues processed: 371 average time/residue: 0.7121 time to fit residues: 319.2915 Evaluate side-chains 321 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 259 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 254 ARG Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 254 ARG Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 56 GLN Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 152 ARG Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain L residue 37 MET Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain M residue 261 ASP Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 246 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 189 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 471 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 328 optimal weight: 5.9990 chunk 208 optimal weight: 0.9990 chunk 366 optimal weight: 7.9990 chunk 243 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 403 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 89 GLN F 264 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN L 89 GLN N 89 GLN N 353 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.105169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.067814 restraints weight = 85564.526| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.56 r_work: 0.2936 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 39270 Z= 0.178 Angle : 0.578 9.211 53312 Z= 0.287 Chirality : 0.040 0.141 6314 Planarity : 0.004 0.035 6230 Dihedral : 11.690 87.119 8704 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.41 % Allowed : 16.73 % Favored : 78.86 % 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: 1.68 (0.13), residues: 4718 helix: 2.25 (0.09), residues: 3262 sheet: None (None), residues: 0 loop : -1.66 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 128 TYR 0.017 0.001 TYR G 345 PHE 0.011 0.001 PHE E 67 TRP 0.018 0.002 TRP A 74 HIS 0.002 0.001 HIS H 134 Details of bonding type rmsd covalent geometry : bond 0.00426 (39242) covalent geometry : angle 0.57848 (53256) SS BOND : bond 0.00159 ( 28) SS BOND : angle 0.48101 ( 56) hydrogen bonds : bond 0.03783 ( 2367) hydrogen bonds : angle 3.79405 ( 7017) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 279 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8242 (tm-30) REVERT: B 9 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8253 (tm-30) REVERT: B 29 ARG cc_start: 0.8130 (mmm-85) cc_final: 0.7840 (mmm-85) REVERT: B 143 MET cc_start: 0.9089 (mtm) cc_final: 0.8855 (mtp) REVERT: C 9 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8163 (tm-30) REVERT: C 143 MET cc_start: 0.9007 (mtm) cc_final: 0.8718 (mtp) REVERT: D 5 GLN cc_start: 0.8678 (tp40) cc_final: 0.8322 (tm-30) REVERT: D 9 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8222 (tm-30) REVERT: D 31 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8557 (mt-10) REVERT: E 9 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8225 (tm-30) REVERT: E 29 ARG cc_start: 0.8150 (mmm-85) cc_final: 0.7899 (mmm-85) REVERT: F 9 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8348 (tm-30) REVERT: F 29 ARG cc_start: 0.8224 (mmm-85) cc_final: 0.7616 (mmt90) REVERT: F 143 MET cc_start: 0.9167 (mtp) cc_final: 0.8867 (mtp) REVERT: F 147 ASP cc_start: 0.8998 (m-30) cc_final: 0.8776 (p0) REVERT: G 5 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8236 (tm-30) REVERT: G 9 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8240 (tm-30) REVERT: G 31 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8505 (mt-10) REVERT: G 143 MET cc_start: 0.9130 (mtp) cc_final: 0.8746 (mtp) REVERT: G 147 ASP cc_start: 0.8993 (m-30) cc_final: 0.8756 (p0) REVERT: G 268 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8930 (mm) REVERT: H 5 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7811 (tm-30) REVERT: H 9 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7838 (tm-30) REVERT: H 138 ASP cc_start: 0.7984 (m-30) cc_final: 0.7748 (m-30) REVERT: I 9 GLU cc_start: 0.8405 (tm-30) cc_final: 0.7842 (tm-30) REVERT: I 138 ASP cc_start: 0.8030 (m-30) cc_final: 0.7771 (m-30) REVERT: I 152 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.6144 (mtm110) REVERT: J 9 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7811 (tm-30) REVERT: J 138 ASP cc_start: 0.7917 (m-30) cc_final: 0.7684 (m-30) REVERT: J 150 TYR cc_start: 0.6831 (t80) cc_final: 0.6585 (t80) REVERT: K 9 GLU cc_start: 0.8456 (tm-30) cc_final: 0.7845 (tm-30) REVERT: K 138 ASP cc_start: 0.8034 (m-30) cc_final: 0.7740 (m-30) REVERT: L 9 GLU cc_start: 0.8408 (tm-30) cc_final: 0.7848 (tm-30) REVERT: L 143 MET cc_start: 0.8744 (mtp) cc_final: 0.8474 (mtm) REVERT: L 152 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6335 (mtm110) REVERT: M 5 GLN cc_start: 0.8307 (tm-30) cc_final: 0.7912 (tm-30) REVERT: M 9 GLU cc_start: 0.8449 (tm-30) cc_final: 0.7869 (tm-30) REVERT: M 57 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8533 (OUTLIER) REVERT: M 138 ASP cc_start: 0.7927 (m-30) cc_final: 0.7680 (m-30) REVERT: M 354 ILE cc_start: 0.7938 (mm) cc_final: 0.7676 (mt) REVERT: N 9 GLU cc_start: 0.8480 (tm-30) cc_final: 0.7908 (tm-30) REVERT: N 138 ASP cc_start: 0.7945 (m-30) cc_final: 0.7717 (m-30) outliers start: 155 outliers final: 76 residues processed: 394 average time/residue: 0.6743 time to fit residues: 324.3048 Evaluate side-chains 338 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 259 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 56 GLN Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 152 ARG Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain L residue 37 MET Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain L residue 285 VAL Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain M residue 285 VAL Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 146 LEU Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 246 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 105 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 403 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 28 optimal weight: 40.0000 chunk 397 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 130 optimal weight: 0.0050 chunk 424 optimal weight: 0.5980 chunk 182 optimal weight: 2.9990 overall best weight: 1.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 GLN C 264 GLN D 264 GLN E 264 GLN I 89 GLN J 89 GLN L 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.106243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.069352 restraints weight = 85205.705| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.57 r_work: 0.2976 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 39270 Z= 0.121 Angle : 0.544 9.887 53312 Z= 0.269 Chirality : 0.039 0.143 6314 Planarity : 0.004 0.035 6230 Dihedral : 11.185 78.163 8704 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.27 % Allowed : 18.21 % Favored : 78.51 % 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: 1.88 (0.13), residues: 4718 helix: 2.42 (0.09), residues: 3248 sheet: None (None), residues: 0 loop : -1.62 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 128 TYR 0.015 0.001 TYR G 345 PHE 0.013 0.001 PHE J 141 TRP 0.020 0.001 TRP G 74 HIS 0.002 0.001 HIS H 134 Details of bonding type rmsd covalent geometry : bond 0.00275 (39242) covalent geometry : angle 0.54442 (53256) SS BOND : bond 0.00108 ( 28) SS BOND : angle 0.43409 ( 56) hydrogen bonds : bond 0.03358 ( 2367) hydrogen bonds : angle 3.65518 ( 7017) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 291 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8286 (tm-30) REVERT: B 5 GLN cc_start: 0.8923 (tt0) cc_final: 0.8700 (tm-30) REVERT: B 9 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8296 (tm-30) REVERT: B 29 ARG cc_start: 0.7994 (mmm-85) cc_final: 0.7738 (mmm-85) REVERT: B 74 TRP cc_start: 0.8840 (t60) cc_final: 0.8543 (t-100) REVERT: B 143 MET cc_start: 0.9104 (mtm) cc_final: 0.8867 (mtp) REVERT: C 9 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8199 (tm-30) REVERT: C 143 MET cc_start: 0.9034 (mtm) cc_final: 0.8759 (mtp) REVERT: D 5 GLN cc_start: 0.8666 (tp40) cc_final: 0.8308 (tm-30) REVERT: D 9 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8215 (tm-30) REVERT: D 31 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8540 (mt-10) REVERT: E 9 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8279 (tm-30) REVERT: F 9 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8368 (tm-30) REVERT: F 29 ARG cc_start: 0.8210 (mmm-85) cc_final: 0.7710 (mmm-85) REVERT: F 143 MET cc_start: 0.9160 (mtp) cc_final: 0.8864 (mtp) REVERT: F 147 ASP cc_start: 0.8978 (m-30) cc_final: 0.8753 (p0) REVERT: G 5 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8231 (tm-30) REVERT: G 9 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8232 (tm-30) REVERT: G 31 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8481 (mt-10) REVERT: G 37 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8496 (ttt) REVERT: G 143 MET cc_start: 0.9129 (mtp) cc_final: 0.8749 (mtp) REVERT: G 147 ASP cc_start: 0.8961 (m-30) cc_final: 0.8733 (p0) REVERT: H 5 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7851 (tm-30) REVERT: H 9 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7837 (tm-30) REVERT: H 215 SER cc_start: 0.9169 (m) cc_final: 0.8963 (p) REVERT: I 9 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7833 (tm-30) REVERT: I 138 ASP cc_start: 0.8031 (m-30) cc_final: 0.7795 (m-30) REVERT: J 9 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7829 (tm-30) REVERT: J 138 ASP cc_start: 0.7913 (m-30) cc_final: 0.7702 (m-30) REVERT: J 150 TYR cc_start: 0.6788 (t80) cc_final: 0.6566 (t80) REVERT: J 215 SER cc_start: 0.9151 (m) cc_final: 0.8946 (p) REVERT: K 9 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7817 (tm-30) REVERT: K 138 ASP cc_start: 0.8030 (m-30) cc_final: 0.7767 (m-30) REVERT: L 9 GLU cc_start: 0.8412 (tm-30) cc_final: 0.7837 (tm-30) REVERT: M 5 GLN cc_start: 0.8287 (tm-30) cc_final: 0.7885 (tm-30) REVERT: M 9 GLU cc_start: 0.8497 (tm-30) cc_final: 0.7854 (tm-30) REVERT: M 57 GLU cc_start: 0.8715 (pm20) cc_final: 0.8291 (pm20) REVERT: M 138 ASP cc_start: 0.7935 (m-30) cc_final: 0.7652 (m-30) REVERT: M 354 ILE cc_start: 0.7806 (mm) cc_final: 0.7523 (mt) REVERT: N 9 GLU cc_start: 0.8453 (tm-30) cc_final: 0.7894 (tm-30) REVERT: N 138 ASP cc_start: 0.7964 (m-30) cc_final: 0.7745 (m-30) outliers start: 115 outliers final: 53 residues processed: 387 average time/residue: 0.6550 time to fit residues: 310.6730 Evaluate side-chains 310 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 256 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 246 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 267 optimal weight: 9.9990 chunk 370 optimal weight: 0.7980 chunk 352 optimal weight: 4.9990 chunk 206 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 304 optimal weight: 20.0000 chunk 264 optimal weight: 10.0000 chunk 443 optimal weight: 6.9990 chunk 462 optimal weight: 7.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN D 264 GLN F 5 GLN L 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.104227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.066770 restraints weight = 86106.234| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.57 r_work: 0.2916 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 39270 Z= 0.207 Angle : 0.613 10.336 53312 Z= 0.300 Chirality : 0.041 0.148 6314 Planarity : 0.004 0.034 6230 Dihedral : 11.349 71.116 8704 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.73 % Allowed : 18.10 % Favored : 78.17 % 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: 1.83 (0.13), residues: 4718 helix: 2.39 (0.09), residues: 3248 sheet: None (None), residues: 0 loop : -1.63 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 75 TYR 0.016 0.001 TYR A 345 PHE 0.013 0.001 PHE J 67 TRP 0.039 0.003 TRP H 74 HIS 0.002 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00497 (39242) covalent geometry : angle 0.61261 (53256) SS BOND : bond 0.00219 ( 28) SS BOND : angle 0.58122 ( 56) hydrogen bonds : bond 0.03905 ( 2367) hydrogen bonds : angle 3.81733 ( 7017) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 259 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8265 (tm-30) REVERT: B 5 GLN cc_start: 0.8901 (tt0) cc_final: 0.8676 (tm-30) REVERT: B 9 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8280 (tm-30) REVERT: B 29 ARG cc_start: 0.8154 (mmm-85) cc_final: 0.7866 (mmm-85) REVERT: B 143 MET cc_start: 0.9133 (mtm) cc_final: 0.8742 (mtp) REVERT: C 9 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8169 (tm-30) REVERT: C 143 MET cc_start: 0.9061 (mtm) cc_final: 0.8777 (mtp) REVERT: D 5 GLN cc_start: 0.8696 (tp40) cc_final: 0.8360 (tm-30) REVERT: D 9 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8239 (tm-30) REVERT: D 31 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8519 (mt-10) REVERT: E 5 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8459 (tp40) REVERT: E 9 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8254 (tm-30) REVERT: F 5 GLN cc_start: 0.8610 (tp40) cc_final: 0.8398 (tp40) REVERT: F 9 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8347 (tm-30) REVERT: F 29 ARG cc_start: 0.8309 (mmm-85) cc_final: 0.7740 (mmm-85) REVERT: F 147 ASP cc_start: 0.8958 (m-30) cc_final: 0.8740 (p0) REVERT: G 5 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8270 (tm-30) REVERT: G 9 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8243 (tm-30) REVERT: G 31 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8481 (mt-10) REVERT: G 143 MET cc_start: 0.9141 (mtp) cc_final: 0.8795 (mtp) REVERT: G 147 ASP cc_start: 0.8970 (m-30) cc_final: 0.8753 (p0) REVERT: G 268 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8957 (mm) REVERT: H 5 GLN cc_start: 0.8320 (tm-30) cc_final: 0.7854 (tm-30) REVERT: H 9 GLU cc_start: 0.8432 (tm-30) cc_final: 0.7898 (tm-30) REVERT: I 9 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7850 (tm-30) REVERT: I 138 ASP cc_start: 0.8088 (m-30) cc_final: 0.7782 (m-30) REVERT: J 9 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7819 (tm-30) REVERT: J 138 ASP cc_start: 0.7980 (m-30) cc_final: 0.7742 (m-30) REVERT: J 150 TYR cc_start: 0.6830 (t80) cc_final: 0.6598 (t80) REVERT: K 9 GLU cc_start: 0.8455 (tm-30) cc_final: 0.7838 (tm-30) REVERT: K 89 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8465 (mt0) REVERT: K 138 ASP cc_start: 0.8065 (m-30) cc_final: 0.7759 (m-30) REVERT: L 9 GLU cc_start: 0.8421 (tm-30) cc_final: 0.7862 (tm-30) REVERT: L 138 ASP cc_start: 0.8075 (m-30) cc_final: 0.7866 (m-30) REVERT: L 143 MET cc_start: 0.9031 (mtm) cc_final: 0.8757 (mtm) REVERT: M 5 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7879 (tm-30) REVERT: M 9 GLU cc_start: 0.8488 (tm-30) cc_final: 0.7923 (tm-30) REVERT: M 57 GLU cc_start: 0.8751 (pm20) cc_final: 0.8350 (pm20) REVERT: N 9 GLU cc_start: 0.8503 (tm-30) cc_final: 0.7891 (tm-30) outliers start: 131 outliers final: 68 residues processed: 368 average time/residue: 0.6551 time to fit residues: 296.3046 Evaluate side-chains 308 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 238 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain K residue 278 VAL Chi-restraints excluded: chain L residue 37 MET Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 246 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 377 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 444 optimal weight: 0.7980 chunk 329 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 376 optimal weight: 0.0370 chunk 38 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 289 optimal weight: 10.0000 chunk 316 optimal weight: 0.6980 chunk 305 optimal weight: 7.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.106468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.069961 restraints weight = 85199.579| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.62 r_work: 0.3008 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 39270 Z= 0.110 Angle : 0.560 10.805 53312 Z= 0.272 Chirality : 0.039 0.141 6314 Planarity : 0.004 0.035 6230 Dihedral : 10.822 60.481 8704 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.28 % Allowed : 19.69 % Favored : 78.03 % 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: 1.91 (0.13), residues: 4718 helix: 2.45 (0.09), residues: 3248 sheet: None (None), residues: 0 loop : -1.60 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 29 TYR 0.015 0.001 TYR K 345 PHE 0.013 0.001 PHE K 141 TRP 0.029 0.002 TRP H 74 HIS 0.002 0.001 HIS N 134 Details of bonding type rmsd covalent geometry : bond 0.00237 (39242) covalent geometry : angle 0.55999 (53256) SS BOND : bond 0.00087 ( 28) SS BOND : angle 0.43255 ( 56) hydrogen bonds : bond 0.03204 ( 2367) hydrogen bonds : angle 3.60973 ( 7017) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 266 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8237 (tm-30) REVERT: B 5 GLN cc_start: 0.8895 (tt0) cc_final: 0.8655 (tm-30) REVERT: B 9 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8320 (tm-30) REVERT: B 29 ARG cc_start: 0.8011 (mmm-85) cc_final: 0.7744 (mmm-85) REVERT: C 9 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8183 (tm-30) REVERT: C 143 MET cc_start: 0.9065 (mtm) cc_final: 0.8786 (mtp) REVERT: D 5 GLN cc_start: 0.8671 (tp40) cc_final: 0.8305 (tm-30) REVERT: D 9 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8246 (tm-30) REVERT: D 31 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8505 (mt-10) REVERT: E 5 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8375 (tp40) REVERT: E 9 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8240 (tm-30) REVERT: F 5 GLN cc_start: 0.8546 (tp40) cc_final: 0.8305 (tp40) REVERT: F 9 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8318 (tm-30) REVERT: F 29 ARG cc_start: 0.8228 (mmm-85) cc_final: 0.7781 (mmm-85) REVERT: F 143 MET cc_start: 0.9167 (mtp) cc_final: 0.8836 (mtp) REVERT: F 147 ASP cc_start: 0.8931 (m-30) cc_final: 0.8710 (p0) REVERT: G 5 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8200 (tm-30) REVERT: G 9 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8215 (tm-30) REVERT: G 31 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8480 (mt-10) REVERT: G 143 MET cc_start: 0.9137 (mtp) cc_final: 0.8816 (mtp) REVERT: G 147 ASP cc_start: 0.8965 (m-30) cc_final: 0.8710 (p0) REVERT: H 5 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7816 (tm-30) REVERT: H 9 GLU cc_start: 0.8409 (tm-30) cc_final: 0.7802 (tm-30) REVERT: H 352 GLU cc_start: 0.9497 (tm-30) cc_final: 0.8836 (mp0) REVERT: I 9 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7800 (tm-30) REVERT: I 138 ASP cc_start: 0.8054 (m-30) cc_final: 0.7775 (m-30) REVERT: I 215 SER cc_start: 0.9239 (m) cc_final: 0.9038 (p) REVERT: J 9 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7787 (tm-30) REVERT: J 138 ASP cc_start: 0.7922 (m-30) cc_final: 0.7669 (m-30) REVERT: J 150 TYR cc_start: 0.6732 (t80) cc_final: 0.6526 (t80) REVERT: K 9 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7798 (tm-30) REVERT: K 57 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8388 (pm20) REVERT: K 138 ASP cc_start: 0.8013 (m-30) cc_final: 0.7781 (m-30) REVERT: K 215 SER cc_start: 0.9224 (m) cc_final: 0.8920 (p) REVERT: K 219 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8591 (mp) REVERT: L 9 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7792 (tm-30) REVERT: L 143 MET cc_start: 0.9031 (mtm) cc_final: 0.8748 (mtm) REVERT: L 215 SER cc_start: 0.9221 (m) cc_final: 0.9016 (p) REVERT: M 5 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7836 (tm-30) REVERT: M 9 GLU cc_start: 0.8483 (tm-30) cc_final: 0.7850 (tm-30) REVERT: M 57 GLU cc_start: 0.8730 (pm20) cc_final: 0.8334 (pm20) REVERT: M 352 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8520 (pm20) REVERT: N 9 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7843 (tm-30) REVERT: N 56 GLN cc_start: 0.8494 (pp30) cc_final: 0.8283 (pp30) outliers start: 80 outliers final: 57 residues processed: 334 average time/residue: 0.6498 time to fit residues: 267.8965 Evaluate side-chains 302 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 242 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain J residue 278 VAL Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 352 GLU Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 246 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 355 optimal weight: 9.9990 chunk 282 optimal weight: 3.9990 chunk 472 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 421 optimal weight: 0.0980 chunk 91 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 chunk 464 optimal weight: 0.0040 chunk 399 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 overall best weight: 1.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 GLN D 264 GLN J 353 ASN K 89 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.106019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.069513 restraints weight = 85801.420| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.57 r_work: 0.2993 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 39270 Z= 0.121 Angle : 0.570 13.550 53312 Z= 0.277 Chirality : 0.039 0.354 6314 Planarity : 0.004 0.034 6230 Dihedral : 10.728 63.100 8701 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.31 % Allowed : 19.83 % Favored : 77.86 % 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: 1.95 (0.13), residues: 4718 helix: 2.48 (0.09), residues: 3248 sheet: None (None), residues: 0 loop : -1.59 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 29 TYR 0.016 0.001 TYR B 345 PHE 0.010 0.001 PHE J 141 TRP 0.040 0.002 TRP A 74 HIS 0.001 0.001 HIS J 134 Details of bonding type rmsd covalent geometry : bond 0.00275 (39242) covalent geometry : angle 0.57010 (53256) SS BOND : bond 0.00107 ( 28) SS BOND : angle 0.48284 ( 56) hydrogen bonds : bond 0.03275 ( 2367) hydrogen bonds : angle 3.61189 ( 7017) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 245 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8300 (tm-30) REVERT: B 5 GLN cc_start: 0.8894 (tt0) cc_final: 0.8656 (tm-30) REVERT: B 9 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8297 (tm-30) REVERT: B 29 ARG cc_start: 0.8028 (mmm-85) cc_final: 0.7736 (mmm-85) REVERT: C 9 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8200 (tm-30) REVERT: C 143 MET cc_start: 0.9063 (mtm) cc_final: 0.8670 (mtp) REVERT: D 5 GLN cc_start: 0.8698 (tp40) cc_final: 0.8362 (tm-30) REVERT: D 9 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8272 (tm-30) REVERT: D 31 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8488 (mt-10) REVERT: E 5 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8386 (tp40) REVERT: E 9 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8306 (tm-30) REVERT: F 5 GLN cc_start: 0.8572 (tp40) cc_final: 0.8279 (tp40) REVERT: F 9 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8348 (tm-30) REVERT: F 29 ARG cc_start: 0.8249 (mmm-85) cc_final: 0.7816 (mmm-85) REVERT: F 143 MET cc_start: 0.9158 (mtp) cc_final: 0.8806 (mtp) REVERT: F 147 ASP cc_start: 0.8955 (m-30) cc_final: 0.8735 (p0) REVERT: G 5 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8211 (tm-30) REVERT: G 9 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8282 (tm-30) REVERT: G 31 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8481 (mt-10) REVERT: G 143 MET cc_start: 0.9151 (mtp) cc_final: 0.8810 (mtp) REVERT: G 147 ASP cc_start: 0.8970 (m-30) cc_final: 0.8697 (p0) REVERT: H 5 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7750 (tm-30) REVERT: H 9 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7848 (tm-30) REVERT: H 352 GLU cc_start: 0.9459 (tm-30) cc_final: 0.8798 (mp0) REVERT: I 9 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7826 (tm-30) REVERT: I 138 ASP cc_start: 0.8046 (m-30) cc_final: 0.7782 (m-30) REVERT: J 9 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7832 (tm-30) REVERT: J 138 ASP cc_start: 0.7917 (m-30) cc_final: 0.7712 (m-30) REVERT: J 150 TYR cc_start: 0.6771 (t80) cc_final: 0.6553 (t80) REVERT: K 9 GLU cc_start: 0.8431 (tm-30) cc_final: 0.7856 (tm-30) REVERT: K 57 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8334 (pm20) REVERT: K 138 ASP cc_start: 0.8046 (m-30) cc_final: 0.7821 (m-30) REVERT: K 215 SER cc_start: 0.9223 (m) cc_final: 0.8955 (p) REVERT: L 9 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7811 (tm-30) REVERT: L 143 MET cc_start: 0.9047 (mtm) cc_final: 0.8758 (mtm) REVERT: M 5 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7851 (tm-30) REVERT: M 9 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7861 (tm-30) REVERT: M 57 GLU cc_start: 0.8725 (pm20) cc_final: 0.8356 (pm20) REVERT: M 352 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8472 (pm20) REVERT: N 9 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7863 (tm-30) outliers start: 81 outliers final: 55 residues processed: 311 average time/residue: 0.6761 time to fit residues: 258.0314 Evaluate side-chains 291 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 234 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain H residue 278 VAL Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain J residue 278 VAL Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain K residue 278 VAL Chi-restraints excluded: chain L residue 37 MET Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 352 GLU Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 246 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 3 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 70 optimal weight: 0.0030 chunk 307 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 361 optimal weight: 0.9990 chunk 186 optimal weight: 20.0000 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 353 ASN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.107033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.070847 restraints weight = 85121.037| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.60 r_work: 0.3033 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 39270 Z= 0.106 Angle : 0.560 13.065 53312 Z= 0.271 Chirality : 0.039 0.351 6314 Planarity : 0.004 0.034 6230 Dihedral : 10.300 67.083 8698 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.76 % Allowed : 20.35 % Favored : 77.89 % 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: 1.97 (0.13), residues: 4718 helix: 2.52 (0.09), residues: 3248 sheet: -1.11 (0.52), residues: 98 loop : -1.64 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 29 TYR 0.015 0.001 TYR D 345 PHE 0.008 0.001 PHE K 141 TRP 0.032 0.002 TRP A 74 HIS 0.001 0.001 HIS J 106 Details of bonding type rmsd covalent geometry : bond 0.00231 (39242) covalent geometry : angle 0.56060 (53256) SS BOND : bond 0.00082 ( 28) SS BOND : angle 0.44472 ( 56) hydrogen bonds : bond 0.03006 ( 2367) hydrogen bonds : angle 3.53600 ( 7017) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9436 Ramachandran restraints generated. 4718 Oldfield, 0 Emsley, 4718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 246 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8334 (tm-30) REVERT: B 5 GLN cc_start: 0.8871 (tt0) cc_final: 0.8652 (tm-30) REVERT: B 9 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8340 (tm-30) REVERT: B 29 ARG cc_start: 0.7987 (mmm-85) cc_final: 0.7744 (mmm-85) REVERT: C 9 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8237 (tm-30) REVERT: D 5 GLN cc_start: 0.8705 (tp40) cc_final: 0.8368 (tm-30) REVERT: D 9 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8307 (tm-30) REVERT: D 31 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8480 (mt-10) REVERT: E 5 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8345 (tp40) REVERT: E 9 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8337 (tm-30) REVERT: F 5 GLN cc_start: 0.8548 (tp40) cc_final: 0.8251 (tp40) REVERT: F 9 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8346 (tm-30) REVERT: F 29 ARG cc_start: 0.8150 (mmm-85) cc_final: 0.7748 (mmm-85) REVERT: F 143 MET cc_start: 0.9158 (mtp) cc_final: 0.8851 (mtp) REVERT: F 147 ASP cc_start: 0.8946 (m-30) cc_final: 0.8719 (p0) REVERT: G 5 GLN cc_start: 0.8476 (tm-30) cc_final: 0.8244 (tm-30) REVERT: G 9 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8306 (tm-30) REVERT: G 31 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8439 (mt-10) REVERT: G 143 MET cc_start: 0.9146 (mtp) cc_final: 0.8782 (mtp) REVERT: G 147 ASP cc_start: 0.8973 (m-30) cc_final: 0.8698 (p0) REVERT: H 5 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7752 (tm-30) REVERT: H 9 GLU cc_start: 0.8462 (tm-30) cc_final: 0.7882 (tm-30) REVERT: H 352 GLU cc_start: 0.9431 (tm-30) cc_final: 0.8807 (mp0) REVERT: I 5 GLN cc_start: 0.8533 (tt0) cc_final: 0.8104 (tm-30) REVERT: I 9 GLU cc_start: 0.8436 (tm-30) cc_final: 0.7870 (tm-30) REVERT: I 56 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8617 (pp30) REVERT: I 138 ASP cc_start: 0.8055 (m-30) cc_final: 0.7780 (m-30) REVERT: J 9 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7786 (tm-30) REVERT: K 9 GLU cc_start: 0.8481 (tm-30) cc_final: 0.7918 (tm-30) REVERT: K 57 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8312 (pm20) REVERT: K 138 ASP cc_start: 0.8034 (m-30) cc_final: 0.7825 (m-30) REVERT: L 9 GLU cc_start: 0.8406 (tm-30) cc_final: 0.7830 (tm-30) REVERT: L 143 MET cc_start: 0.9045 (mtm) cc_final: 0.8764 (mtm) REVERT: M 5 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7806 (tm-30) REVERT: M 9 GLU cc_start: 0.8555 (tm-30) cc_final: 0.7956 (tm-30) REVERT: M 352 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8372 (pm20) REVERT: N 9 GLU cc_start: 0.8471 (tm-30) cc_final: 0.7897 (tm-30) outliers start: 62 outliers final: 39 residues processed: 296 average time/residue: 0.6936 time to fit residues: 249.4095 Evaluate side-chains 272 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 231 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain H residue 278 VAL Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 246 CYS Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain J residue 278 VAL Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain K residue 278 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain M residue 352 GLU Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 414 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 427 optimal weight: 5.9990 chunk 353 optimal weight: 0.7980 chunk 267 optimal weight: 9.9990 chunk 249 optimal weight: 3.9990 chunk 361 optimal weight: 5.9990 chunk 419 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 464 optimal weight: 0.0020 chunk 224 optimal weight: 4.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.105848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.069253 restraints weight = 85335.882| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.61 r_work: 0.2992 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 39270 Z= 0.132 Angle : 0.582 14.390 53312 Z= 0.281 Chirality : 0.040 0.422 6314 Planarity : 0.004 0.033 6230 Dihedral : 10.413 67.974 8694 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.65 % Allowed : 20.69 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.13), residues: 4718 helix: 2.48 (0.09), residues: 3262 sheet: None (None), residues: 0 loop : -1.64 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 29 TYR 0.016 0.001 TYR A 345 PHE 0.009 0.001 PHE C 244 TRP 0.035 0.002 TRP B 74 HIS 0.001 0.000 HIS J 134 Details of bonding type rmsd covalent geometry : bond 0.00307 (39242) covalent geometry : angle 0.58220 (53256) SS BOND : bond 0.00120 ( 28) SS BOND : angle 0.51586 ( 56) hydrogen bonds : bond 0.03308 ( 2367) hydrogen bonds : angle 3.60480 ( 7017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11156.78 seconds wall clock time: 191 minutes 1.23 seconds (11461.23 seconds total)