Starting phenix.real_space_refine on Tue Sep 15 11:24:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wbn_21594/09_2026/6wbn_21594.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wbn_21594/09_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_21594/09_2026/6wbn_21594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wbn_21594/09_2026/6wbn_21594.map" model { file = "/net/cci-nas-00/data/ceres_data/6wbn_21594/09_2026/6wbn_21594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wbn_21594/09_2026/6wbn_21594.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6wbn_21594/09_2026/6wbn_21594.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wbn_21594/09_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 6.97, per 1000 atoms: 0.18 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: 3.30 Conformation dependent library (CDL) restraints added in 1.6 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: 0.68 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: 7.02 Time building geometry restraints manager: 4.31 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: 22288 33.84 - 67.67: 882 67.67 - 101.51: 28 101.51 - 135.35: 28 135.35 - 169.19: 14 Dihedral angle restraints: 23240 sinusoidal: 9030 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 23237 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: 3.940 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: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 30.530 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 17.116 169.187 13916 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/Z covalent geometry : bond 0.00986 / 0.45 (39242) covalent geometry : angle 0.87641 / 0.46 (53256) SS BOND : bond 0.00162 / 0.10 ( 28) SS BOND : angle 0.72476 / 0.52 ( 56) hydrogen bonds : bond 0.12113 / 8.07 ( 2367) hydrogen bonds : angle 5.35271 / 3.93 ( 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 : 1.272 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: 0.8122 time to fit residues: 389.0485 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 : 1.271 ------------------------------------------------------------------------------- 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... 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 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: 79 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.108940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.071695 restraints weight = 84608.277| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.61 r_work: 0.3036 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 39270 Z= 0.124 Angle : 0.580 7.480 53312 Z= 0.289 Chirality : 0.040 0.124 6314 Planarity : 0.004 0.035 6230 Dihedral : 14.509 136.459 6660 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.27 % Allowed : 14.94 % Favored : 81.79 % 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: 0.80 (0.12), residues: 4718 helix: 1.63 (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 0.008 0.001 ARG B 254 TYR 0.017 0.001 TYR E 345 PHE 0.010 0.001 PHE H 54 TRP 0.009 0.001 TRP J 104 HIS 0.004 0.002 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (39242) covalent geometry : angle 0.57994 / 0.29 (53256) SS BOND : bond 0.00194 / 0.13 ( 28) SS BOND : angle 0.26244 / 0.19 ( 56) hydrogen bonds : bond 0.03872 / 2.58 ( 2367) hydrogen bonds : angle 4.09151 / 2.97 ( 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 : 1.447 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: 0.8397 (tm-30) cc_final: 0.8066 (tm-30) REVERT: A 140 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8207 (ptpp) REVERT: B 5 GLN cc_start: 0.8970 (tt0) cc_final: 0.8685 (tm-30) REVERT: B 9 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8205 (tm-30) REVERT: C 5 GLN cc_start: 0.8855 (tt0) cc_final: 0.8627 (tp40) REVERT: C 9 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8175 (tm-30) REVERT: D 9 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8102 (tm-30) REVERT: E 5 GLN cc_start: 0.8971 (tt0) cc_final: 0.8722 (tp40) REVERT: E 9 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8165 (tm-30) REVERT: F 5 GLN cc_start: 0.8908 (mt0) cc_final: 0.8675 (tp40) REVERT: F 9 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8226 (tm-30) REVERT: G 9 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8208 (tm-30) REVERT: H 5 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7854 (tm-30) REVERT: H 9 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7886 (tm-30) REVERT: I 5 GLN cc_start: 0.8636 (mt0) cc_final: 0.8233 (tm-30) REVERT: I 9 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7921 (tm-30) REVERT: I 256 ASP cc_start: 0.8776 (t0) cc_final: 0.8576 (t0) REVERT: J 9 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7858 (tm-30) REVERT: K 5 GLN cc_start: 0.8546 (mt0) cc_final: 0.8248 (tm-30) REVERT: K 9 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7972 (tm-30) REVERT: K 143 MET cc_start: 0.8878 (mtm) cc_final: 0.8668 (mtm) REVERT: L 9 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7888 (tm-30) REVERT: L 143 MET cc_start: 0.8658 (mtp) cc_final: 0.8344 (mtm) REVERT: M 5 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7847 (tm-30) REVERT: M 9 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7868 (tm-30) REVERT: M 57 GLU cc_start: 0.8475 (pm20) cc_final: 0.8166 (pm20) REVERT: N 5 GLN cc_start: 0.8644 (mt0) cc_final: 0.8223 (tm-30) REVERT: N 9 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7979 (tm-30) outliers start: 115 outliers final: 40 residues processed: 379 average time/residue: 0.6570 time to fit residues: 304.1841 Evaluate side-chains 321 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 280 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 31 GLU 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 246 CYS 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: 5.9990 chunk 190 optimal weight: 7.9990 chunk 399 optimal weight: 7.9990 chunk 445 optimal weight: 8.9990 chunk 209 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 312 optimal weight: 0.4980 chunk 129 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 264 GLN C 89 GLN C 264 GLN D 264 GLN F 89 GLN H 353 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 264 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.106353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.068710 restraints weight = 85529.825| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.61 r_work: 0.2961 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 39270 Z= 0.159 Angle : 0.564 9.638 53312 Z= 0.281 Chirality : 0.040 0.156 6314 Planarity : 0.004 0.035 6230 Dihedral : 12.025 103.812 6660 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.07 % Allowed : 17.19 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.13), residues: 4718 helix: 2.06 (0.09), residues: 3248 sheet: None (None), residues: 0 loop : -1.87 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 152 TYR 0.019 0.001 TYR E 345 PHE 0.011 0.001 PHE N 54 TRP 0.007 0.001 TRP G 104 HIS 0.002 0.001 HIS J 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (39242) covalent geometry : angle 0.56458 / 0.28 (53256) SS BOND : bond 0.00134 / 0.09 ( 28) SS BOND : angle 0.38497 / 0.27 ( 56) hydrogen bonds : bond 0.03899 / 2.62 ( 2367) hydrogen bonds : angle 3.94317 / 2.86 ( 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 398 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 290 time to evaluate : 1.450 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: 0.8588 (tm-30) cc_final: 0.8177 (tm-30) REVERT: B 5 GLN cc_start: 0.8940 (tt0) cc_final: 0.8712 (tm-30) REVERT: B 9 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8304 (tm-30) REVERT: B 29 ARG cc_start: 0.7945 (mmm-85) cc_final: 0.7531 (mmt90) REVERT: B 143 MET cc_start: 0.9020 (mtm) cc_final: 0.8808 (mtp) REVERT: C 9 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8227 (tm-30) REVERT: C 143 MET cc_start: 0.8932 (mtm) cc_final: 0.8688 (mtp) REVERT: D 5 GLN cc_start: 0.8600 (tp40) cc_final: 0.8295 (tm-30) REVERT: D 9 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8201 (tm-30) REVERT: D 29 ARG cc_start: 0.7876 (mmm-85) cc_final: 0.7658 (mmm-85) REVERT: E 9 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8248 (tm-30) REVERT: E 29 ARG cc_start: 0.7933 (mmm-85) cc_final: 0.7570 (mmm-85) REVERT: F 9 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8295 (tm-30) REVERT: F 29 ARG cc_start: 0.8002 (mmm-85) cc_final: 0.7796 (mmm-85) REVERT: F 196 VAL cc_start: 0.8132 (OUTLIER) cc_final: 0.7879 (p) REVERT: G 5 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8208 (tp40) REVERT: G 9 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8231 (tm-30) REVERT: H 5 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7797 (tm-30) REVERT: H 9 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7858 (tm-30) REVERT: I 9 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7849 (tm-30) REVERT: I 89 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8531 (mt0) REVERT: I 152 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.6192 (mtm110) REVERT: J 9 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7803 (tm-30) REVERT: K 9 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7854 (tm-30) REVERT: K 89 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8540 (mt0) REVERT: L 9 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7882 (tm-30) REVERT: L 89 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8451 (mt0) REVERT: L 143 MET cc_start: 0.8668 (mtp) cc_final: 0.8403 (mtm) REVERT: L 152 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6265 (mtm110) REVERT: M 5 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7895 (tm-30) REVERT: M 9 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7846 (tm-30) REVERT: N 9 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7911 (tm-30) outliers start: 108 outliers final: 44 residues processed: 359 average time/residue: 0.7158 time to fit residues: 310.4070 Evaluate side-chains 311 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 261 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 88 VAL 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 D residue 88 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS 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 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 196 VAL Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 89 GLN 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 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 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: 8.9990 chunk 178 optimal weight: 0.9990 chunk 379 optimal weight: 2.9990 chunk 360 optimal weight: 7.9990 chunk 445 optimal weight: 3.9990 chunk 257 optimal weight: 0.9990 chunk 454 optimal weight: 0.0970 chunk 254 optimal weight: 5.9990 chunk 206 optimal weight: 0.0170 chunk 255 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 overall best weight: 1.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 264 GLN C 89 GLN D 89 GLN D 264 GLN F 89 GLN I 89 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN M 89 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.107730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.070789 restraints weight = 84839.858| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.62 r_work: 0.3023 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 39270 Z= 0.114 Angle : 0.529 8.261 53312 Z= 0.262 Chirality : 0.039 0.127 6314 Planarity : 0.004 0.035 6230 Dihedral : 10.702 98.045 6660 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.31 % Allowed : 18.50 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.13), residues: 4718 helix: 2.30 (0.09), residues: 3248 sheet: None (None), residues: 0 loop : -1.78 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 254 TYR 0.018 0.001 TYR D 345 PHE 0.010 0.001 PHE C 129 TRP 0.007 0.001 TRP M 104 HIS 0.001 0.001 HIS K 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (39242) covalent geometry : angle 0.52930 / 0.26 (53256) SS BOND : bond 0.00088 / 0.06 ( 28) SS BOND : angle 0.32760 / 0.23 ( 56) hydrogen bonds : bond 0.03325 / 2.22 ( 2367) hydrogen bonds : angle 3.76409 / 2.73 ( 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 381 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 300 time to evaluate : 1.480 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: 0.8710 (tm-30) cc_final: 0.8237 (tm-30) REVERT: B 5 GLN cc_start: 0.8931 (tt0) cc_final: 0.8677 (tm-30) REVERT: B 9 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8269 (tm-30) REVERT: B 143 MET cc_start: 0.9025 (mtm) cc_final: 0.8796 (mtp) REVERT: C 9 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8191 (tm-30) REVERT: C 143 MET cc_start: 0.8908 (mtm) cc_final: 0.8698 (mtp) REVERT: D 5 GLN cc_start: 0.8613 (tp40) cc_final: 0.8250 (tm-30) REVERT: D 9 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8176 (tm-30) REVERT: E 5 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8325 (tp40) REVERT: E 9 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8300 (tm-30) REVERT: F 5 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8264 (tp40) REVERT: F 9 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8304 (tm-30) REVERT: F 89 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8494 (mt0) REVERT: G 5 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8198 (tm-30) REVERT: G 9 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8187 (tm-30) REVERT: G 143 MET cc_start: 0.9042 (mtp) cc_final: 0.8760 (mtp) REVERT: G 147 ASP cc_start: 0.8973 (m-30) cc_final: 0.8758 (p0) REVERT: H 5 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7762 (tm-30) REVERT: H 9 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7817 (tm-30) REVERT: H 215 SER cc_start: 0.9171 (m) cc_final: 0.8933 (p) REVERT: I 9 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7830 (tm-30) REVERT: I 138 ASP cc_start: 0.7843 (m-30) cc_final: 0.7561 (m-30) REVERT: I 152 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.6125 (mtm110) REVERT: J 9 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7763 (tm-30) REVERT: K 9 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7772 (tm-30) REVERT: K 89 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8574 (mt0) REVERT: K 138 ASP cc_start: 0.7832 (m-30) cc_final: 0.7595 (m-30) REVERT: L 9 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7835 (tm-30) REVERT: L 143 MET cc_start: 0.8721 (mtp) cc_final: 0.8415 (mtm) REVERT: L 152 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6346 (mtm110) REVERT: M 5 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7822 (tm-30) REVERT: M 9 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7853 (tm-30) REVERT: M 57 GLU cc_start: 0.8631 (pm20) cc_final: 0.8251 (pm20) REVERT: N 9 GLU cc_start: 0.8414 (tm-30) cc_final: 0.7899 (tm-30) REVERT: N 89 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8237 (mt0) outliers start: 81 outliers final: 24 residues processed: 354 average time/residue: 0.7130 time to fit residues: 304.8363 Evaluate side-chains 296 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 267 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 246 CYS 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 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 196 VAL 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 196 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 189 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 471 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 328 optimal weight: 6.9990 chunk 208 optimal weight: 0.8980 chunk 366 optimal weight: 10.0000 chunk 243 optimal weight: 7.9990 chunk 226 optimal weight: 0.2980 chunk 248 optimal weight: 2.9990 chunk 403 optimal weight: 7.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 GLN C 264 GLN F 89 GLN G 264 GLN H 264 GLN I 89 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN K 353 ASN L 89 GLN N 89 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.105588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.068139 restraints weight = 85622.751| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.61 r_work: 0.2943 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 39270 Z= 0.182 Angle : 0.574 9.090 53312 Z= 0.285 Chirality : 0.040 0.144 6314 Planarity : 0.004 0.034 6230 Dihedral : 10.646 92.232 6650 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.90 % Allowed : 18.47 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.13), residues: 4718 helix: 2.30 (0.09), residues: 3262 sheet: None (None), residues: 0 loop : -1.75 (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 F 345 PHE 0.013 0.001 PHE E 67 TRP 0.019 0.002 TRP G 74 HIS 0.002 0.001 HIS K 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (39242) covalent geometry : angle 0.57399 / 0.29 (53256) SS BOND : bond 0.00155 / 0.10 ( 28) SS BOND : angle 0.44947 / 0.31 ( 56) hydrogen bonds : bond 0.03828 / 2.57 ( 2367) hydrogen bonds : angle 3.90992 / 2.83 ( 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 385 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 283 time to evaluate : 1.463 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: 0.8762 (tm-30) cc_final: 0.8250 (tm-30) REVERT: B 5 GLN cc_start: 0.8936 (tt0) cc_final: 0.8699 (tm-30) REVERT: B 9 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8282 (tm-30) REVERT: B 143 MET cc_start: 0.9067 (mtm) cc_final: 0.8836 (mtp) REVERT: C 9 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8179 (tm-30) REVERT: C 143 MET cc_start: 0.9009 (mtm) cc_final: 0.8748 (mtp) REVERT: C 353 ASN cc_start: 0.9105 (OUTLIER) cc_final: 0.8591 (t0) REVERT: D 5 GLN cc_start: 0.8678 (tp40) cc_final: 0.8316 (tm-30) REVERT: D 9 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8272 (tm-30) REVERT: E 5 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8362 (tp40) REVERT: E 9 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8335 (tm-30) REVERT: E 29 ARG cc_start: 0.7978 (mmm-85) cc_final: 0.7590 (mmm-85) REVERT: E 89 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8338 (mt0) REVERT: E 353 ASN cc_start: 0.8997 (OUTLIER) cc_final: 0.8552 (t0) REVERT: F 9 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8337 (tm-30) REVERT: F 29 ARG cc_start: 0.8059 (mmm-85) cc_final: 0.7780 (mmm-85) REVERT: F 147 ASP cc_start: 0.8987 (m-30) cc_final: 0.8780 (p0) REVERT: G 5 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8242 (tm-30) REVERT: G 9 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8268 (tm-30) REVERT: G 143 MET cc_start: 0.9095 (mtp) cc_final: 0.8829 (mtp) REVERT: G 353 ASN cc_start: 0.9059 (OUTLIER) cc_final: 0.8556 (t0) REVERT: H 5 GLN cc_start: 0.8297 (tm-30) cc_final: 0.7832 (tm-30) REVERT: H 9 GLU cc_start: 0.8445 (tm-30) cc_final: 0.7869 (tm-30) REVERT: I 9 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7887 (tm-30) REVERT: I 152 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6130 (mtm110) REVERT: J 9 GLU cc_start: 0.8406 (tm-30) cc_final: 0.7816 (tm-30) REVERT: J 138 ASP cc_start: 0.7964 (m-30) cc_final: 0.7726 (m-30) REVERT: K 9 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7862 (tm-30) REVERT: K 138 ASP cc_start: 0.7971 (m-30) cc_final: 0.7724 (m-30) REVERT: L 9 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7872 (tm-30) REVERT: L 143 MET cc_start: 0.8757 (mtp) cc_final: 0.8517 (mtm) REVERT: L 152 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6344 (mtm110) REVERT: M 5 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7862 (tm-30) REVERT: M 9 GLU cc_start: 0.8454 (tm-30) cc_final: 0.7879 (tm-30) REVERT: M 354 ILE cc_start: 0.7937 (mm) cc_final: 0.7691 (mt) REVERT: N 9 GLU cc_start: 0.8478 (tm-30) cc_final: 0.7945 (tm-30) outliers start: 102 outliers final: 49 residues processed: 352 average time/residue: 0.7253 time to fit residues: 310.1720 Evaluate side-chains 316 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 261 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 353 ASN 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 89 GLN Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain F residue 57 GLU 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 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain H residue 56 GLN 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 I residue 37 MET 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 3 ILE Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 246 CYS Chi-restraints excluded: chain K residue 3 ILE 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 56 GLN Chi-restraints excluded: chain L residue 57 GLU 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 M residue 57 GLU 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=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: 5.9990 chunk 403 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 28 optimal weight: 50.0000 chunk 397 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 424 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN C 89 GLN C 264 GLN E 264 GLN I 89 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN L 89 GLN N 89 GLN N 264 GLN N 353 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.105308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.067908 restraints weight = 85869.137| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.61 r_work: 0.2937 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2997 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= 0.184 Angle : 0.578 9.814 53312 Z= 0.287 Chirality : 0.040 0.141 6314 Planarity : 0.004 0.034 6230 Dihedral : 10.467 90.648 6650 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.50 % Allowed : 18.07 % Favored : 78.43 % 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: 2.27 (0.09), residues: 3276 sheet: None (None), residues: 0 loop : -1.76 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 29 TYR 0.016 0.001 TYR E 345 PHE 0.019 0.001 PHE M 244 TRP 0.026 0.002 TRP F 74 HIS 0.002 0.001 HIS K 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 (39242) covalent geometry : angle 0.57815 / 0.29 (53256) SS BOND : bond 0.00171 / 0.11 ( 28) SS BOND : angle 0.44218 / 0.30 ( 56) hydrogen bonds : bond 0.03784 / 2.54 ( 2367) hydrogen bonds : angle 3.87991 / 2.81 ( 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 392 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 269 time to evaluate : 1.371 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: 0.8775 (tm-30) cc_final: 0.8239 (tm-30) REVERT: B 5 GLN cc_start: 0.8937 (tt0) cc_final: 0.8718 (tm-30) REVERT: B 9 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8256 (tm-30) REVERT: B 29 ARG cc_start: 0.8122 (mmm-85) cc_final: 0.7501 (mmt90) REVERT: B 143 MET cc_start: 0.9108 (mtm) cc_final: 0.8731 (mtp) REVERT: C 9 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8171 (tm-30) REVERT: C 31 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8464 (mt-10) REVERT: C 143 MET cc_start: 0.9015 (mtm) cc_final: 0.8730 (mtp) REVERT: C 353 ASN cc_start: 0.9104 (OUTLIER) cc_final: 0.8627 (t0) REVERT: D 5 GLN cc_start: 0.8702 (tp40) cc_final: 0.8344 (tm-30) REVERT: D 9 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8243 (tm-30) REVERT: D 31 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8540 (mt-10) REVERT: E 5 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8424 (tp40) REVERT: E 9 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8339 (tm-30) REVERT: E 29 ARG cc_start: 0.8049 (mmm-85) cc_final: 0.7632 (mmm-85) REVERT: E 337 GLU cc_start: 0.8630 (tp30) cc_final: 0.8408 (tp30) REVERT: E 353 ASN cc_start: 0.9033 (OUTLIER) cc_final: 0.8556 (t0) REVERT: F 5 GLN cc_start: 0.8621 (tp40) cc_final: 0.8278 (tp40) REVERT: F 9 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8363 (tm-30) REVERT: F 29 ARG cc_start: 0.8082 (mmm-85) cc_final: 0.7759 (mmm-85) REVERT: F 147 ASP cc_start: 0.9000 (m-30) cc_final: 0.8785 (p0) REVERT: G 5 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8238 (tm-30) REVERT: G 9 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8240 (tm-30) REVERT: G 31 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8482 (mt-10) REVERT: G 268 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8938 (mm) REVERT: H 5 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7834 (tm-30) REVERT: H 9 GLU cc_start: 0.8458 (tm-30) cc_final: 0.7880 (tm-30) REVERT: H 215 SER cc_start: 0.9231 (m) cc_final: 0.9012 (p) REVERT: I 9 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7869 (tm-30) REVERT: J 9 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7819 (tm-30) REVERT: J 138 ASP cc_start: 0.7985 (m-30) cc_final: 0.7746 (m-30) REVERT: K 9 GLU cc_start: 0.8447 (tm-30) cc_final: 0.7820 (tm-30) REVERT: K 138 ASP cc_start: 0.8023 (m-30) cc_final: 0.7752 (m-30) REVERT: L 9 GLU cc_start: 0.8439 (tm-30) cc_final: 0.7867 (tm-30) REVERT: L 143 MET cc_start: 0.8747 (mtp) cc_final: 0.8492 (mtm) REVERT: L 152 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6327 (mtm110) REVERT: M 5 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7912 (tm-30) REVERT: M 9 GLU cc_start: 0.8474 (tm-30) cc_final: 0.7854 (tm-30) REVERT: M 57 GLU cc_start: 0.8709 (pm20) cc_final: 0.8307 (pm20) REVERT: M 354 ILE cc_start: 0.7946 (mm) cc_final: 0.7690 (mt) REVERT: N 9 GLU cc_start: 0.8474 (tm-30) cc_final: 0.7916 (tm-30) REVERT: N 138 ASP cc_start: 0.7935 (m-30) cc_final: 0.7722 (m-30) outliers start: 123 outliers final: 61 residues processed: 361 average time/residue: 0.6943 time to fit residues: 305.8822 Evaluate side-chains 327 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 261 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 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 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 246 CYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain D residue 57 GLU 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 57 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain F residue 57 GLU 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 246 CYS Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain H residue 56 GLN 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 285 VAL Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 56 GLN 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 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 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 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 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: 10.0000 chunk 370 optimal weight: 0.9980 chunk 352 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 65 optimal weight: 20.0000 chunk 304 optimal weight: 1.9990 chunk 264 optimal weight: 0.9980 chunk 443 optimal weight: 5.9990 chunk 462 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 GLN E 264 GLN F 264 GLN I 89 GLN I 353 ASN J 89 GLN N 89 GLN N 264 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.106652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.069727 restraints weight = 85399.676| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.63 r_work: 0.2991 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 39270 Z= 0.118 Angle : 0.545 10.563 53312 Z= 0.269 Chirality : 0.039 0.126 6314 Planarity : 0.004 0.035 6230 Dihedral : 9.848 87.743 6650 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.48 % Allowed : 18.81 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.13), residues: 4718 helix: 2.39 (0.09), residues: 3262 sheet: None (None), residues: 0 loop : -1.77 (0.16), residues: 1456 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 0.009 0.001 PHE F 129 TRP 0.034 0.001 TRP E 74 HIS 0.002 0.001 HIS M 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (39242) covalent geometry : angle 0.54472 / 0.27 (53256) SS BOND : bond 0.00098 / 0.06 ( 28) SS BOND : angle 0.35125 / 0.24 ( 56) hydrogen bonds : bond 0.03302 / 2.22 ( 2367) hydrogen bonds : angle 3.72226 / 2.69 ( 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 374 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 287 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8254 (tm-30) REVERT: B 5 GLN cc_start: 0.8916 (tt0) cc_final: 0.8673 (tm-30) REVERT: B 9 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8283 (tm-30) REVERT: B 29 ARG cc_start: 0.8122 (mmm-85) cc_final: 0.7532 (mmt90) REVERT: B 74 TRP cc_start: 0.8831 (t60) cc_final: 0.8480 (t-100) REVERT: C 9 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8201 (tm-30) REVERT: C 143 MET cc_start: 0.9004 (mtm) cc_final: 0.8767 (mtp) REVERT: D 5 GLN cc_start: 0.8683 (tp40) cc_final: 0.8320 (tm-30) REVERT: D 9 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8245 (tm-30) REVERT: D 31 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8474 (mt-10) REVERT: E 5 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8318 (tp40) REVERT: E 9 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8336 (tm-30) REVERT: E 29 ARG cc_start: 0.7947 (mmm-85) cc_final: 0.7553 (mmm-85) REVERT: F 5 GLN cc_start: 0.8577 (tp40) cc_final: 0.8215 (tp40) REVERT: F 9 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8342 (tm-30) REVERT: F 29 ARG cc_start: 0.7973 (mmm-85) cc_final: 0.7678 (mmm-85) REVERT: F 143 MET cc_start: 0.9147 (mtp) cc_final: 0.8782 (mtp) REVERT: F 147 ASP cc_start: 0.8979 (m-30) cc_final: 0.8749 (p0) REVERT: G 5 GLN cc_start: 0.8472 (tm-30) cc_final: 0.8211 (tm-30) REVERT: G 9 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8228 (tm-30) REVERT: G 31 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8478 (mt-10) REVERT: G 37 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8468 (ttt) REVERT: H 5 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7774 (tm-30) REVERT: H 9 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7823 (tm-30) REVERT: H 215 SER cc_start: 0.9132 (m) cc_final: 0.8922 (p) REVERT: I 9 GLU cc_start: 0.8375 (tm-30) cc_final: 0.7808 (tm-30) REVERT: J 9 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7737 (tm-30) REVERT: J 138 ASP cc_start: 0.7897 (m-30) cc_final: 0.7604 (m-30) REVERT: J 215 SER cc_start: 0.9123 (m) cc_final: 0.8918 (p) REVERT: K 9 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7822 (tm-30) REVERT: K 138 ASP cc_start: 0.7998 (m-30) cc_final: 0.7765 (m-30) REVERT: L 9 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7829 (tm-30) REVERT: L 57 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8537 (pm20) REVERT: L 143 MET cc_start: 0.8741 (mtp) cc_final: 0.8541 (mtm) REVERT: L 215 SER cc_start: 0.9170 (m) cc_final: 0.8924 (p) REVERT: M 5 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7822 (tm-30) REVERT: M 9 GLU cc_start: 0.8497 (tm-30) cc_final: 0.7896 (tm-30) REVERT: M 57 GLU cc_start: 0.8674 (pm20) cc_final: 0.8265 (pm20) REVERT: N 9 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7856 (tm-30) REVERT: N 56 GLN cc_start: 0.8493 (pp30) cc_final: 0.8275 (pp30) REVERT: N 138 ASP cc_start: 0.7909 (m-30) cc_final: 0.7667 (m-30) outliers start: 87 outliers final: 42 residues processed: 349 average time/residue: 0.6754 time to fit residues: 288.6991 Evaluate side-chains 299 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 255 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 246 CYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 57 GLU 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 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 37 MET Chi-restraints excluded: chain E residue 246 CYS 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 196 VAL Chi-restraints excluded: chain G residue 246 CYS 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 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 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 57 GLU 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 196 VAL Chi-restraints excluded: chain M residue 246 CYS 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: 7.9990 chunk 26 optimal weight: 1.9990 chunk 444 optimal weight: 0.8980 chunk 329 optimal weight: 4.9990 chunk 190 optimal weight: 7.9990 chunk 376 optimal weight: 0.0270 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 289 optimal weight: 9.9990 chunk 316 optimal weight: 3.9990 chunk 305 optimal weight: 20.0000 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 GLN C 264 GLN I 89 GLN N 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.105664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.068674 restraints weight = 85504.411| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.58 r_work: 0.2962 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 39270 Z= 0.151 Angle : 0.576 10.917 53312 Z= 0.282 Chirality : 0.040 0.130 6314 Planarity : 0.004 0.034 6230 Dihedral : 9.843 85.601 6650 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.73 % Allowed : 19.12 % Favored : 78.14 % 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: 1.79 (0.13), residues: 4718 helix: 2.39 (0.09), residues: 3262 sheet: None (None), residues: 0 loop : -1.76 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.017 0.001 TYR B 345 PHE 0.014 0.001 PHE K 141 TRP 0.036 0.002 TRP H 74 HIS 0.002 0.001 HIS H 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (39242) covalent geometry : angle 0.57573 / 0.28 (53256) SS BOND : bond 0.00138 / 0.09 ( 28) SS BOND : angle 0.45536 / 0.32 ( 56) hydrogen bonds : bond 0.03555 / 2.39 ( 2367) hydrogen bonds : angle 3.76994 / 2.73 ( 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 357 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 261 time to evaluate : 1.382 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: 0.8809 (tm-30) cc_final: 0.8258 (tm-30) REVERT: A 37 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8358 (ttt) REVERT: B 5 GLN cc_start: 0.8911 (tt0) cc_final: 0.8664 (tm-30) REVERT: B 9 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8300 (tm-30) REVERT: B 29 ARG cc_start: 0.8174 (mmm-85) cc_final: 0.7620 (mmt90) REVERT: B 74 TRP cc_start: 0.8835 (t60) cc_final: 0.8512 (t-100) REVERT: C 9 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8165 (tm-30) REVERT: C 143 MET cc_start: 0.9039 (mtm) cc_final: 0.8803 (mtp) REVERT: D 5 GLN cc_start: 0.8695 (tp40) cc_final: 0.8362 (tm-30) REVERT: D 9 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8249 (tm-30) REVERT: D 31 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8495 (mt-10) REVERT: E 5 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8347 (tp40) REVERT: E 9 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8327 (tm-30) REVERT: E 29 ARG cc_start: 0.8028 (mmm-85) cc_final: 0.7623 (mmm-85) REVERT: F 5 GLN cc_start: 0.8627 (tp40) cc_final: 0.8264 (tp40) REVERT: F 9 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8339 (tm-30) REVERT: F 29 ARG cc_start: 0.8085 (mmm-85) cc_final: 0.7783 (mmm-85) REVERT: F 147 ASP cc_start: 0.8985 (m-30) cc_final: 0.8761 (p0) REVERT: G 5 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8199 (tm-30) REVERT: G 9 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8229 (tm-30) REVERT: G 31 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8462 (mt-10) REVERT: G 143 MET cc_start: 0.9029 (mtp) cc_final: 0.8753 (mtp) REVERT: H 5 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7745 (tm-30) REVERT: H 9 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7852 (tm-30) REVERT: I 9 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7831 (tm-30) REVERT: I 57 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8536 (pm20) REVERT: J 9 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7739 (tm-30) REVERT: J 138 ASP cc_start: 0.7916 (m-30) cc_final: 0.7672 (m-30) REVERT: K 9 GLU cc_start: 0.8413 (tm-30) cc_final: 0.7826 (tm-30) REVERT: K 138 ASP cc_start: 0.8003 (m-30) cc_final: 0.7756 (m-30) REVERT: L 9 GLU cc_start: 0.8398 (tm-30) cc_final: 0.7833 (tm-30) REVERT: L 146 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7846 (tp) REVERT: M 5 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7838 (tm-30) REVERT: M 9 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7859 (tm-30) REVERT: M 57 GLU cc_start: 0.8697 (pm20) cc_final: 0.8322 (pm20) REVERT: M 352 GLU cc_start: 0.9009 (pm20) cc_final: 0.8523 (pm20) REVERT: N 9 GLU cc_start: 0.8441 (tm-30) cc_final: 0.7868 (tm-30) outliers start: 96 outliers final: 57 residues processed: 329 average time/residue: 0.6594 time to fit residues: 266.5629 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 : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 146 LEU 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 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 196 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 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 57 GLU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 297 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 196 VAL Chi-restraints excluded: chain G residue 246 CYS 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 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 57 GLU 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 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 57 GLU 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 196 VAL Chi-restraints excluded: chain M residue 246 CYS 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: 50.0000 chunk 282 optimal weight: 2.9990 chunk 472 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 421 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 233 optimal weight: 9.9990 chunk 464 optimal weight: 3.9990 chunk 399 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 264 GLN C 264 GLN I 89 GLN N 89 GLN N 264 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.104365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.066946 restraints weight = 86482.483| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.61 r_work: 0.2923 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3447 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= 0.210 Angle : 0.625 11.036 53312 Z= 0.308 Chirality : 0.041 0.207 6314 Planarity : 0.004 0.033 6230 Dihedral : 10.179 84.607 6650 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.76 % Allowed : 19.27 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.13), residues: 4718 helix: 2.36 (0.09), residues: 3248 sheet: None (None), residues: 0 loop : -1.66 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 75 TYR 0.017 0.001 TYR A 345 PHE 0.014 0.001 PHE H 67 TRP 0.040 0.002 TRP H 74 HIS 0.002 0.001 HIS N 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (39242) covalent geometry : angle 0.62462 / 0.31 (53256) SS BOND : bond 0.00188 / 0.12 ( 28) SS BOND : angle 0.52965 / 0.37 ( 56) hydrogen bonds : bond 0.03916 / 2.64 ( 2367) hydrogen bonds : angle 3.89793 / 2.83 ( 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 335 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 238 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8237 (tm-30) REVERT: A 37 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8381 (ttt) REVERT: B 5 GLN cc_start: 0.8911 (tt0) cc_final: 0.8673 (tm-30) REVERT: B 9 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8251 (tm-30) REVERT: B 29 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.7821 (mmt90) REVERT: C 9 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8166 (tm-30) REVERT: C 31 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8620 (mt-10) REVERT: C 143 MET cc_start: 0.9033 (mtm) cc_final: 0.8791 (mtp) REVERT: D 5 GLN cc_start: 0.8723 (tp40) cc_final: 0.8388 (tm-30) REVERT: D 9 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8226 (tm-30) REVERT: D 31 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8445 (mt-10) REVERT: E 5 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8488 (tm-30) REVERT: E 9 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8295 (tm-30) REVERT: E 37 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8482 (ttt) REVERT: F 5 GLN cc_start: 0.8675 (tp40) cc_final: 0.8308 (tp40) REVERT: F 9 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8323 (tm-30) REVERT: F 29 ARG cc_start: 0.8157 (mmm-85) cc_final: 0.7890 (mmm-85) REVERT: F 147 ASP cc_start: 0.8968 (m-30) cc_final: 0.8756 (p0) REVERT: G 5 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8262 (tm-30) REVERT: G 9 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8229 (tm-30) REVERT: G 31 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8481 (mt-10) REVERT: H 5 GLN cc_start: 0.8251 (tm-30) cc_final: 0.7780 (tm-30) REVERT: H 9 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7852 (tm-30) REVERT: I 9 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7813 (tm-30) REVERT: J 9 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7767 (tm-30) REVERT: J 138 ASP cc_start: 0.7965 (m-30) cc_final: 0.7693 (m-30) REVERT: K 9 GLU cc_start: 0.8424 (tm-30) cc_final: 0.7842 (tm-30) REVERT: K 57 GLU cc_start: 0.8759 (pm20) cc_final: 0.8351 (pm20) REVERT: K 138 ASP cc_start: 0.8067 (m-30) cc_final: 0.7825 (m-30) REVERT: L 9 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7813 (tm-30) REVERT: L 57 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8579 (pm20) REVERT: L 143 MET cc_start: 0.9026 (mtm) cc_final: 0.8762 (mtm) REVERT: M 5 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7840 (tm-30) REVERT: M 9 GLU cc_start: 0.8477 (tm-30) cc_final: 0.7824 (tm-30) REVERT: M 57 GLU cc_start: 0.8776 (pm20) cc_final: 0.8370 (pm20) REVERT: M 352 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8731 (pm20) REVERT: N 9 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7839 (tm-30) outliers start: 97 outliers final: 58 residues processed: 315 average time/residue: 0.6728 time to fit residues: 259.0928 Evaluate side-chains 289 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 227 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET 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 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 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 196 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 209 LEU 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 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 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 196 VAL 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 56 GLN 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 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 268 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 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 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 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: 3.9990 chunk 108 optimal weight: 0.9980 chunk 70 optimal weight: 30.0000 chunk 307 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 179 optimal weight: 0.0030 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 361 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 89 GLN L 353 ASN N 89 GLN N 264 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.105767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.069131 restraints weight = 85166.586| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.56 r_work: 0.2979 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39270 Z= 0.123 Angle : 0.582 15.049 53312 Z= 0.284 Chirality : 0.040 0.293 6314 Planarity : 0.004 0.035 6230 Dihedral : 9.585 82.371 6650 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.62 % Allowed : 20.40 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.13), residues: 4718 helix: 2.41 (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 B 75 TYR 0.015 0.001 TYR A 345 PHE 0.010 0.001 PHE H 141 TRP 0.029 0.002 TRP H 74 HIS 0.002 0.001 HIS I 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (39242) covalent geometry : angle 0.58194 / 0.28 (53256) SS BOND : bond 0.00107 / 0.07 ( 28) SS BOND : angle 0.43445 / 0.30 ( 56) hydrogen bonds : bond 0.03397 / 2.28 ( 2367) hydrogen bonds : angle 3.73027 / 2.70 ( 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 298 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 241 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8257 (tm-30) REVERT: A 37 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8328 (ttt) REVERT: B 5 GLN cc_start: 0.8910 (tt0) cc_final: 0.8665 (tm-30) REVERT: B 9 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8274 (tm-30) REVERT: B 29 ARG cc_start: 0.8250 (mmm-85) cc_final: 0.7654 (mmt90) REVERT: C 9 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8158 (tm-30) REVERT: C 31 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8610 (mt-10) REVERT: C 143 MET cc_start: 0.9050 (mtm) cc_final: 0.8810 (mtp) REVERT: D 5 GLN cc_start: 0.8706 (tp40) cc_final: 0.8356 (tm-30) REVERT: D 9 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8246 (tm-30) REVERT: D 31 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8442 (mt-10) REVERT: E 5 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8437 (tm-30) REVERT: E 9 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8316 (tm-30) REVERT: E 29 ARG cc_start: 0.8129 (mmm-85) cc_final: 0.7492 (mtt180) REVERT: F 5 GLN cc_start: 0.8637 (tp40) cc_final: 0.8253 (tp40) REVERT: F 9 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8336 (tm-30) REVERT: F 29 ARG cc_start: 0.8094 (mmm-85) cc_final: 0.7827 (mmm-85) REVERT: F 147 ASP cc_start: 0.8895 (m-30) cc_final: 0.8688 (p0) REVERT: G 5 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8191 (tm-30) REVERT: G 9 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8199 (tm-30) REVERT: G 31 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8473 (mt-10) REVERT: H 5 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7731 (tm-30) REVERT: H 9 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7853 (tm-30) REVERT: I 9 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7818 (tm-30) REVERT: J 9 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7794 (tm-30) REVERT: J 138 ASP cc_start: 0.7941 (m-30) cc_final: 0.7706 (m-30) REVERT: K 9 GLU cc_start: 0.8428 (tm-30) cc_final: 0.7832 (tm-30) REVERT: K 57 GLU cc_start: 0.8753 (pm20) cc_final: 0.8353 (pm20) REVERT: K 138 ASP cc_start: 0.8039 (m-30) cc_final: 0.7816 (m-30) REVERT: L 9 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7829 (tm-30) REVERT: L 57 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8531 (pm20) REVERT: M 5 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7813 (tm-30) REVERT: M 9 GLU cc_start: 0.8503 (tm-30) cc_final: 0.7895 (tm-30) REVERT: M 57 GLU cc_start: 0.8776 (pm20) cc_final: 0.8378 (pm20) REVERT: M 352 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8679 (pm20) REVERT: N 9 GLU cc_start: 0.8445 (tm-30) cc_final: 0.7862 (tm-30) outliers start: 57 outliers final: 42 residues processed: 288 average time/residue: 0.6775 time to fit residues: 239.0073 Evaluate side-chains 281 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 236 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 342 VAL 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 57 GLU 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 D residue 342 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 297 VAL 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 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 414 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 427 optimal weight: 3.9990 chunk 353 optimal weight: 0.7980 chunk 267 optimal weight: 6.9990 chunk 249 optimal weight: 3.9990 chunk 361 optimal weight: 0.9990 chunk 419 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 464 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 353 ASN I 89 GLN N 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.105457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.068890 restraints weight = 85298.303| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.60 r_work: 0.2974 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39270 Z= 0.135 Angle : 0.587 14.162 53312 Z= 0.286 Chirality : 0.040 0.366 6314 Planarity : 0.004 0.034 6230 Dihedral : 9.427 79.302 6650 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.94 % Allowed : 20.18 % 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: 1.90 (0.13), residues: 4718 helix: 2.44 (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 0.002 0.000 ARG B 29 TYR 0.016 0.001 TYR G 345 PHE 0.010 0.001 PHE H 141 TRP 0.029 0.002 TRP H 74 HIS 0.001 0.001 HIS L 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (39242) covalent geometry : angle 0.58706 / 0.29 (53256) SS BOND : bond 0.00117 / 0.07 ( 28) SS BOND : angle 0.44955 / 0.31 ( 56) hydrogen bonds : bond 0.03432 / 2.31 ( 2367) hydrogen bonds : angle 3.73482 / 2.71 ( 7017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10857.01 seconds wall clock time: 185 minutes 58.47 seconds (11158.47 seconds total)