Starting phenix.real_space_refine on Wed Mar 4 15:40:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lyg_30016/03_2026/6lyg_30016.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lyg_30016/03_2026/6lyg_30016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lyg_30016/03_2026/6lyg_30016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lyg_30016/03_2026/6lyg_30016.map" model { file = "/net/cci-nas-00/data/ceres_data/6lyg_30016/03_2026/6lyg_30016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lyg_30016/03_2026/6lyg_30016.cif" } resolution = 3.1 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= 0.003 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: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 9552 2.51 5 N 2384 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14688 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "F" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "G" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "H" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.31, per 1000 atoms: 0.23 Number of scatterers: 14688 At special positions: 0 Unit cell: (122.694, 122.694, 102.414, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 2632 8.00 N 2384 7.00 C 9552 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 159 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 159 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 159 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 159 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 159 " 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 139 " " NAG B1001 " - " ASN B 139 " " NAG C1001 " - " ASN C 139 " " NAG D1001 " - " ASN D 139 " " NAG E1001 " - " ASN E 139 " " NAG F1001 " - " ASN F 139 " " NAG G1001 " - " ASN G 139 " " NAG H1001 " - " ASN H 139 " Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 704.1 milliseconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3600 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 0 sheets defined 78.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 47 through 70 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 73 through 83 removed outlier: 3.628A pdb=" N LEU A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 107 Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'A' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 204 Processing helix chain 'A' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE A 240 " --> pdb=" O HIS A 236 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 18 Processing helix chain 'B' and resid 25 through 36 Processing helix chain 'B' and resid 47 through 70 Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 73 through 83 removed outlier: 3.629A pdb=" N LEU B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 107 Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 129 Processing helix chain 'B' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 204 Processing helix chain 'B' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE B 240 " --> pdb=" O HIS B 236 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 18 Processing helix chain 'C' and resid 25 through 36 Processing helix chain 'C' and resid 47 through 70 Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 73 through 83 removed outlier: 3.628A pdb=" N LEU C 77 " --> pdb=" O ASN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 107 removed outlier: 4.232A pdb=" N ARG C 96 " --> pdb=" O PRO C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 129 Processing helix chain 'C' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE C 153 " --> pdb=" O GLU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 204 Processing helix chain 'C' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE C 240 " --> pdb=" O HIS C 236 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 18 Processing helix chain 'D' and resid 25 through 36 Processing helix chain 'D' and resid 47 through 70 Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 73 through 83 removed outlier: 3.628A pdb=" N LEU D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 107 removed outlier: 4.232A pdb=" N ARG D 96 " --> pdb=" O PRO D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 129 Processing helix chain 'D' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE D 153 " --> pdb=" O GLU D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 204 Processing helix chain 'D' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE D 240 " --> pdb=" O HIS D 236 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 18 Processing helix chain 'E' and resid 25 through 36 Processing helix chain 'E' and resid 47 through 70 Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 73 through 83 removed outlier: 3.628A pdb=" N LEU E 77 " --> pdb=" O ASN E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 107 removed outlier: 4.232A pdb=" N ARG E 96 " --> pdb=" O PRO E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 129 Processing helix chain 'E' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE E 153 " --> pdb=" O GLU E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 204 Processing helix chain 'E' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER E 239 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE E 240 " --> pdb=" O HIS E 236 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN E 246 " --> pdb=" O LYS E 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 18 Processing helix chain 'F' and resid 25 through 36 Processing helix chain 'F' and resid 47 through 70 Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 73 through 83 removed outlier: 3.629A pdb=" N LEU F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 107 removed outlier: 4.232A pdb=" N ARG F 96 " --> pdb=" O PRO F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA F 111 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 129 Processing helix chain 'F' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS F 152 " --> pdb=" O LYS F 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE F 153 " --> pdb=" O GLU F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 204 Processing helix chain 'F' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER F 239 " --> pdb=" O GLU F 235 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE F 240 " --> pdb=" O HIS F 236 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 18 Processing helix chain 'G' and resid 25 through 36 Processing helix chain 'G' and resid 47 through 70 Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 73 through 83 removed outlier: 3.628A pdb=" N LEU G 77 " --> pdb=" O ASN G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 107 removed outlier: 4.232A pdb=" N ARG G 96 " --> pdb=" O PRO G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA G 111 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 129 Processing helix chain 'G' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS G 152 " --> pdb=" O LYS G 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE G 153 " --> pdb=" O GLU G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 204 Processing helix chain 'G' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU G 213 " --> pdb=" O GLN G 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER G 239 " --> pdb=" O GLU G 235 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE G 240 " --> pdb=" O HIS G 236 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN G 246 " --> pdb=" O LYS G 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 18 Processing helix chain 'H' and resid 25 through 36 Processing helix chain 'H' and resid 47 through 70 Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 73 through 83 removed outlier: 3.628A pdb=" N LEU H 77 " --> pdb=" O ASN H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 107 removed outlier: 4.232A pdb=" N ARG H 96 " --> pdb=" O PRO H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA H 111 " --> pdb=" O LEU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 129 Processing helix chain 'H' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS H 152 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE H 153 " --> pdb=" O GLU H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 204 Processing helix chain 'H' and resid 209 through 246 removed outlier: 3.565A pdb=" N LEU H 213 " --> pdb=" O GLN H 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER H 239 " --> pdb=" O GLU H 235 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE H 240 " --> pdb=" O HIS H 236 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN H 246 " --> pdb=" O LYS H 242 " (cutoff:3.500A) 1049 hydrogen bonds defined for protein. 3147 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4495 1.34 - 1.46: 3261 1.46 - 1.58: 7092 1.58 - 1.69: 0 1.69 - 1.81: 176 Bond restraints: 15024 Sorted by residual: bond pdb=" N ALA G 93 " pdb=" CA ALA G 93 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.81e+00 bond pdb=" N ALA B 93 " pdb=" CA ALA B 93 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.27e-02 6.20e+03 4.65e+00 bond pdb=" N ALA E 93 " pdb=" CA ALA E 93 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.23e-02 6.61e+03 4.62e+00 bond pdb=" N ALA C 93 " pdb=" CA ALA C 93 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.23e-02 6.61e+03 4.62e+00 bond pdb=" N ALA H 93 " pdb=" CA ALA H 93 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.60e+00 ... (remaining 15019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 19842 1.52 - 3.04: 381 3.04 - 4.56: 77 4.56 - 6.08: 44 6.08 - 7.60: 8 Bond angle restraints: 20352 Sorted by residual: angle pdb=" N ALA H 93 " pdb=" CA ALA H 93 " pdb=" C ALA H 93 " ideal model delta sigma weight residual 111.36 118.96 -7.60 1.09e+00 8.42e-01 4.86e+01 angle pdb=" N ALA D 93 " pdb=" CA ALA D 93 " pdb=" C ALA D 93 " ideal model delta sigma weight residual 111.36 118.96 -7.60 1.09e+00 8.42e-01 4.86e+01 angle pdb=" N ALA E 93 " pdb=" CA ALA E 93 " pdb=" C ALA E 93 " ideal model delta sigma weight residual 111.36 118.95 -7.59 1.09e+00 8.42e-01 4.85e+01 angle pdb=" N ALA C 93 " pdb=" CA ALA C 93 " pdb=" C ALA C 93 " ideal model delta sigma weight residual 111.36 118.95 -7.59 1.09e+00 8.42e-01 4.85e+01 angle pdb=" N ALA F 93 " pdb=" CA ALA F 93 " pdb=" C ALA F 93 " ideal model delta sigma weight residual 111.36 118.95 -7.59 1.09e+00 8.42e-01 4.85e+01 ... (remaining 20347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 8231 17.00 - 34.00: 661 34.00 - 51.00: 140 51.00 - 67.99: 48 67.99 - 84.99: 24 Dihedral angle restraints: 9104 sinusoidal: 3600 harmonic: 5504 Sorted by residual: dihedral pdb=" CB CYS B 43 " pdb=" SG CYS B 43 " pdb=" SG CYS B 159 " pdb=" CB CYS B 159 " ideal model delta sinusoidal sigma weight residual 93.00 119.90 -26.90 1 1.00e+01 1.00e-02 1.04e+01 dihedral pdb=" CB CYS F 43 " pdb=" SG CYS F 43 " pdb=" SG CYS F 159 " pdb=" CB CYS F 159 " ideal model delta sinusoidal sigma weight residual 93.00 119.90 -26.90 1 1.00e+01 1.00e-02 1.04e+01 dihedral pdb=" CB CYS C 43 " pdb=" SG CYS C 43 " pdb=" SG CYS C 159 " pdb=" CB CYS C 159 " ideal model delta sinusoidal sigma weight residual 93.00 119.89 -26.89 1 1.00e+01 1.00e-02 1.04e+01 ... (remaining 9101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2068 0.059 - 0.118: 250 0.118 - 0.178: 3 0.178 - 0.237: 9 0.237 - 0.296: 6 Chirality restraints: 2336 Sorted by residual: chirality pdb=" CA ALA F 93 " pdb=" N ALA F 93 " pdb=" C ALA F 93 " pdb=" CB ALA F 93 " both_signs ideal model delta sigma weight residual False 2.48 2.19 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA ALA D 93 " pdb=" N ALA D 93 " pdb=" C ALA D 93 " pdb=" CB ALA D 93 " both_signs ideal model delta sigma weight residual False 2.48 2.19 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA ALA G 93 " pdb=" N ALA G 93 " pdb=" C ALA G 93 " pdb=" CB ALA G 93 " both_signs ideal model delta sigma weight residual False 2.48 2.19 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 2333 not shown) Planarity restraints: 2512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 59 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO D 60 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 60 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 60 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 59 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO B 60 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 60 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 60 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 59 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.32e+00 pdb=" N PRO A 60 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 60 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 60 " 0.026 5.00e-02 4.00e+02 ... (remaining 2509 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4363 2.82 - 3.34: 14844 3.34 - 3.86: 23737 3.86 - 4.38: 24593 4.38 - 4.90: 45157 Nonbonded interactions: 112694 Sorted by model distance: nonbonded pdb=" OH TYR H 68 " pdb=" OG1 THR H 103 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR F 68 " pdb=" OG1 THR F 103 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR B 68 " pdb=" OG1 THR B 103 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR A 68 " pdb=" OG1 THR A 103 " model vdw 2.300 3.040 nonbonded pdb=" OH TYR G 68 " pdb=" OG1 THR G 103 " model vdw 2.300 3.040 ... (remaining 112689 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.250 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 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 : 0.004 0.039 15048 Z= 0.172 Angle : 0.591 7.601 20408 Z= 0.360 Chirality : 0.042 0.296 2336 Planarity : 0.004 0.046 2504 Dihedral : 14.338 84.992 5456 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 17.89 % Favored : 82.11 % 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: -0.02 (0.19), residues: 1792 helix: 0.79 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -3.07 (0.27), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 201 TYR 0.008 0.001 TYR H 177 PHE 0.007 0.001 PHE H 64 TRP 0.008 0.001 TRP H 62 HIS 0.002 0.000 HIS H 220 Details of bonding type rmsd covalent geometry : bond 0.00366 (15024) covalent geometry : angle 0.57975 (20352) SS BOND : bond 0.00165 ( 16) SS BOND : angle 0.84466 ( 32) hydrogen bonds : bond 0.11933 ( 1049) hydrogen bonds : angle 4.57574 ( 3147) link_NAG-ASN : bond 0.00416 ( 8) link_NAG-ASN : angle 3.35034 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 0.554 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.5776 (tm-30) cc_final: 0.5486 (tp40) REVERT: A 46 ASP cc_start: 0.8746 (m-30) cc_final: 0.8390 (m-30) REVERT: A 71 ASN cc_start: 0.8435 (t0) cc_final: 0.8185 (t0) REVERT: A 79 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7484 (tp30) REVERT: A 82 LYS cc_start: 0.8306 (tttt) cc_final: 0.8049 (ttmt) REVERT: A 105 ARG cc_start: 0.7954 (mpt180) cc_final: 0.7695 (tpp-160) REVERT: A 148 LYS cc_start: 0.8429 (mppt) cc_final: 0.7630 (ttmm) REVERT: A 165 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7096 (mp0) REVERT: A 238 LYS cc_start: 0.6739 (mtmm) cc_final: 0.6464 (mtmt) REVERT: B 38 GLU cc_start: 0.8027 (tp30) cc_final: 0.7705 (tp30) REVERT: B 46 ASP cc_start: 0.8770 (m-30) cc_final: 0.8161 (m-30) REVERT: B 73 ASN cc_start: 0.8313 (p0) cc_final: 0.8043 (p0) REVERT: B 79 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7530 (tp30) REVERT: B 82 LYS cc_start: 0.8451 (tttt) cc_final: 0.7891 (tptp) REVERT: B 105 ARG cc_start: 0.7935 (mpt180) cc_final: 0.7673 (tpp-160) REVERT: B 165 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7219 (mp0) REVERT: B 220 HIS cc_start: 0.7986 (m-70) cc_final: 0.7698 (m170) REVERT: C 32 GLN cc_start: 0.5774 (tm-30) cc_final: 0.5486 (tp40) REVERT: C 46 ASP cc_start: 0.8746 (m-30) cc_final: 0.8390 (m-30) REVERT: C 71 ASN cc_start: 0.8436 (t0) cc_final: 0.8181 (t0) REVERT: C 79 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7491 (tp30) REVERT: C 82 LYS cc_start: 0.8308 (tttt) cc_final: 0.8050 (ttmt) REVERT: C 105 ARG cc_start: 0.7953 (mpt180) cc_final: 0.7694 (tpp-160) REVERT: C 148 LYS cc_start: 0.8431 (mppt) cc_final: 0.7633 (ttmm) REVERT: C 165 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7096 (mp0) REVERT: C 238 LYS cc_start: 0.6740 (mtmm) cc_final: 0.6469 (mtmt) REVERT: D 38 GLU cc_start: 0.8028 (tp30) cc_final: 0.7704 (tp30) REVERT: D 46 ASP cc_start: 0.8771 (m-30) cc_final: 0.8156 (m-30) REVERT: D 73 ASN cc_start: 0.8333 (p0) cc_final: 0.8087 (p0) REVERT: D 79 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7535 (tp30) REVERT: D 82 LYS cc_start: 0.8450 (tttt) cc_final: 0.7885 (tptp) REVERT: D 105 ARG cc_start: 0.7933 (mpt180) cc_final: 0.7672 (tpp-160) REVERT: D 165 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7012 (mt-10) REVERT: D 220 HIS cc_start: 0.7989 (m-70) cc_final: 0.7690 (m170) REVERT: E 32 GLN cc_start: 0.5773 (tm-30) cc_final: 0.5486 (tp40) REVERT: E 46 ASP cc_start: 0.8746 (m-30) cc_final: 0.8391 (m-30) REVERT: E 71 ASN cc_start: 0.8437 (t0) cc_final: 0.8183 (t0) REVERT: E 79 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7496 (tp30) REVERT: E 82 LYS cc_start: 0.8308 (tttt) cc_final: 0.8046 (ttmt) REVERT: E 105 ARG cc_start: 0.7953 (mpt180) cc_final: 0.7696 (tpp-160) REVERT: E 148 LYS cc_start: 0.8429 (mppt) cc_final: 0.7631 (ttmm) REVERT: E 165 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7096 (mp0) REVERT: E 238 LYS cc_start: 0.6739 (mtmm) cc_final: 0.6467 (mtmt) REVERT: F 38 GLU cc_start: 0.8023 (tp30) cc_final: 0.7698 (tp30) REVERT: F 46 ASP cc_start: 0.8761 (m-30) cc_final: 0.8157 (m-30) REVERT: F 73 ASN cc_start: 0.8333 (p0) cc_final: 0.8084 (p0) REVERT: F 79 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7539 (tp30) REVERT: F 82 LYS cc_start: 0.8450 (tttt) cc_final: 0.7887 (tptp) REVERT: F 105 ARG cc_start: 0.7921 (mpt180) cc_final: 0.7661 (tpp-160) REVERT: F 148 LYS cc_start: 0.8462 (mppt) cc_final: 0.7848 (tttt) REVERT: F 165 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7020 (mt-10) REVERT: G 32 GLN cc_start: 0.5776 (tm-30) cc_final: 0.5485 (tp40) REVERT: G 46 ASP cc_start: 0.8745 (m-30) cc_final: 0.8389 (m-30) REVERT: G 71 ASN cc_start: 0.8438 (t0) cc_final: 0.8183 (t0) REVERT: G 79 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7494 (tp30) REVERT: G 82 LYS cc_start: 0.8307 (tttt) cc_final: 0.8049 (ttmt) REVERT: G 105 ARG cc_start: 0.7953 (mpt180) cc_final: 0.7696 (tpp-160) REVERT: G 148 LYS cc_start: 0.8430 (mppt) cc_final: 0.7631 (ttmm) REVERT: G 165 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7097 (mp0) REVERT: G 238 LYS cc_start: 0.6740 (mtmm) cc_final: 0.6470 (mtmt) REVERT: H 38 GLU cc_start: 0.8023 (tp30) cc_final: 0.7703 (tp30) REVERT: H 46 ASP cc_start: 0.8760 (m-30) cc_final: 0.8155 (m-30) REVERT: H 73 ASN cc_start: 0.8330 (p0) cc_final: 0.8083 (p0) REVERT: H 79 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7538 (tp30) REVERT: H 82 LYS cc_start: 0.8448 (tttt) cc_final: 0.7885 (tptp) REVERT: H 105 ARG cc_start: 0.7923 (mpt180) cc_final: 0.7663 (tpp-160) REVERT: H 148 LYS cc_start: 0.8463 (mppt) cc_final: 0.7850 (tttt) REVERT: H 165 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7017 (mt-10) outliers start: 0 outliers final: 0 residues processed: 509 average time/residue: 0.1494 time to fit residues: 103.8161 Evaluate side-chains 339 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS B 236 HIS C 236 HIS D 236 HIS E 236 HIS F 236 HIS G 236 HIS H 236 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.158022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.100439 restraints weight = 18233.995| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.33 r_work: 0.2858 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 15048 Z= 0.292 Angle : 0.644 5.904 20408 Z= 0.333 Chirality : 0.042 0.150 2336 Planarity : 0.005 0.051 2504 Dihedral : 4.353 21.100 2144 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 3.22 % Allowed : 19.54 % Favored : 77.24 % 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: 1.47 (0.20), residues: 1792 helix: 1.82 (0.13), residues: 1408 sheet: None (None), residues: 0 loop : -2.35 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.009 0.002 TYR F 177 PHE 0.011 0.002 PHE H 124 TRP 0.008 0.001 TRP G 81 HIS 0.006 0.002 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00747 (15024) covalent geometry : angle 0.63147 (20352) SS BOND : bond 0.00678 ( 16) SS BOND : angle 1.80500 ( 32) hydrogen bonds : bond 0.05672 ( 1049) hydrogen bonds : angle 3.68752 ( 3147) link_NAG-ASN : bond 0.00591 ( 8) link_NAG-ASN : angle 3.26326 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 352 time to evaluate : 0.481 Fit side-chains REVERT: A 32 GLN cc_start: 0.6823 (tm-30) cc_final: 0.6354 (tp40) REVERT: A 46 ASP cc_start: 0.9230 (m-30) cc_final: 0.8988 (m-30) REVERT: A 70 MET cc_start: 0.9069 (mmm) cc_final: 0.8866 (mmm) REVERT: A 71 ASN cc_start: 0.9020 (t0) cc_final: 0.8698 (t0) REVERT: A 105 ARG cc_start: 0.8786 (mpt180) cc_final: 0.8563 (tpp-160) REVERT: A 143 GLN cc_start: 0.7666 (mm110) cc_final: 0.7434 (mm110) REVERT: A 147 GLN cc_start: 0.7505 (mm110) cc_final: 0.7185 (mm110) REVERT: A 148 LYS cc_start: 0.8379 (mppt) cc_final: 0.7742 (ttmt) REVERT: A 165 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7922 (mp0) REVERT: A 227 LYS cc_start: 0.7329 (tmtt) cc_final: 0.7092 (tptt) REVERT: A 240 PHE cc_start: 0.8045 (m-80) cc_final: 0.7787 (m-80) REVERT: B 46 ASP cc_start: 0.9199 (m-30) cc_final: 0.8795 (m-30) REVERT: B 105 ARG cc_start: 0.8870 (mpt180) cc_final: 0.8661 (tpp-160) REVERT: B 124 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8576 (t80) REVERT: B 148 LYS cc_start: 0.8442 (mmtm) cc_final: 0.7888 (tttt) REVERT: B 165 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7863 (mp0) REVERT: B 227 LYS cc_start: 0.7324 (tmtt) cc_final: 0.7083 (tptt) REVERT: C 32 GLN cc_start: 0.6827 (tm-30) cc_final: 0.6358 (tp40) REVERT: C 46 ASP cc_start: 0.9231 (m-30) cc_final: 0.8989 (m-30) REVERT: C 70 MET cc_start: 0.9068 (mmm) cc_final: 0.8866 (mmm) REVERT: C 71 ASN cc_start: 0.9019 (t0) cc_final: 0.8695 (t0) REVERT: C 105 ARG cc_start: 0.8790 (mpt180) cc_final: 0.8568 (tpp-160) REVERT: C 143 GLN cc_start: 0.7657 (mm110) cc_final: 0.7425 (mm110) REVERT: C 147 GLN cc_start: 0.7501 (mm110) cc_final: 0.7181 (mm110) REVERT: C 148 LYS cc_start: 0.8380 (mppt) cc_final: 0.7743 (ttmt) REVERT: C 165 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7907 (mp0) REVERT: C 227 LYS cc_start: 0.7322 (tmtt) cc_final: 0.7090 (tptt) REVERT: C 240 PHE cc_start: 0.8045 (m-80) cc_final: 0.7785 (m-80) REVERT: D 46 ASP cc_start: 0.9212 (m-30) cc_final: 0.8761 (m-30) REVERT: D 105 ARG cc_start: 0.8873 (mpt180) cc_final: 0.8667 (tpp-160) REVERT: D 124 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8573 (t80) REVERT: D 148 LYS cc_start: 0.8449 (mmtm) cc_final: 0.7844 (tttt) REVERT: D 165 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7863 (mp0) REVERT: E 32 GLN cc_start: 0.6836 (tm-30) cc_final: 0.6366 (tp40) REVERT: E 46 ASP cc_start: 0.9228 (m-30) cc_final: 0.8987 (m-30) REVERT: E 70 MET cc_start: 0.9070 (mmm) cc_final: 0.8867 (mmm) REVERT: E 71 ASN cc_start: 0.9016 (t0) cc_final: 0.8693 (t0) REVERT: E 105 ARG cc_start: 0.8782 (mpt180) cc_final: 0.8557 (tpp-160) REVERT: E 143 GLN cc_start: 0.7665 (mm110) cc_final: 0.7431 (mm110) REVERT: E 147 GLN cc_start: 0.7511 (mm110) cc_final: 0.7192 (mm110) REVERT: E 148 LYS cc_start: 0.8381 (mppt) cc_final: 0.7746 (ttmt) REVERT: E 165 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7927 (mp0) REVERT: E 227 LYS cc_start: 0.7323 (tmtt) cc_final: 0.7088 (tptt) REVERT: E 240 PHE cc_start: 0.8042 (m-80) cc_final: 0.7784 (m-80) REVERT: F 46 ASP cc_start: 0.9204 (m-30) cc_final: 0.8800 (m-30) REVERT: F 105 ARG cc_start: 0.8870 (mpt180) cc_final: 0.8664 (tpp-160) REVERT: F 124 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8581 (t80) REVERT: F 148 LYS cc_start: 0.8405 (mppt) cc_final: 0.7966 (tttt) REVERT: F 165 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7859 (mp0) REVERT: G 32 GLN cc_start: 0.6842 (tm-30) cc_final: 0.6373 (tp40) REVERT: G 46 ASP cc_start: 0.9230 (m-30) cc_final: 0.8990 (m-30) REVERT: G 70 MET cc_start: 0.9067 (mmm) cc_final: 0.8864 (mmm) REVERT: G 71 ASN cc_start: 0.9016 (t0) cc_final: 0.8693 (t0) REVERT: G 105 ARG cc_start: 0.8785 (mpt180) cc_final: 0.8563 (tpp-160) REVERT: G 143 GLN cc_start: 0.7671 (mm110) cc_final: 0.7437 (mm110) REVERT: G 147 GLN cc_start: 0.7508 (mm110) cc_final: 0.7189 (mm110) REVERT: G 148 LYS cc_start: 0.8375 (mppt) cc_final: 0.7741 (ttmt) REVERT: G 165 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7934 (mp0) REVERT: G 227 LYS cc_start: 0.7325 (tmtt) cc_final: 0.7089 (tptt) REVERT: G 240 PHE cc_start: 0.8040 (m-80) cc_final: 0.7781 (m-80) REVERT: H 46 ASP cc_start: 0.9198 (m-30) cc_final: 0.8748 (m-30) REVERT: H 105 ARG cc_start: 0.8868 (mpt180) cc_final: 0.8661 (tpp-160) REVERT: H 124 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8578 (t80) REVERT: H 148 LYS cc_start: 0.8408 (mppt) cc_final: 0.7974 (tttt) REVERT: H 165 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7862 (mp0) REVERT: H 227 LYS cc_start: 0.7324 (tmtt) cc_final: 0.7085 (tptt) outliers start: 49 outliers final: 24 residues processed: 374 average time/residue: 0.1411 time to fit residues: 74.6110 Evaluate side-chains 369 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 341 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 124 PHE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 200 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 60 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 71 ASN C 71 ASN D 71 ASN E 71 ASN F 71 ASN ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 ASN H 71 ASN ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.162067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.104755 restraints weight = 18352.256| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.36 r_work: 0.2946 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15048 Z= 0.129 Angle : 0.513 5.569 20408 Z= 0.267 Chirality : 0.037 0.122 2336 Planarity : 0.004 0.045 2504 Dihedral : 3.930 17.257 2144 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.12 % Allowed : 21.71 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.20), residues: 1792 helix: 2.48 (0.13), residues: 1408 sheet: None (None), residues: 0 loop : -2.02 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 176 TYR 0.022 0.001 TYR G 142 PHE 0.007 0.001 PHE A 124 TRP 0.006 0.001 TRP B 62 HIS 0.003 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00306 (15024) covalent geometry : angle 0.50334 (20352) SS BOND : bond 0.00318 ( 16) SS BOND : angle 1.05726 ( 32) hydrogen bonds : bond 0.04325 ( 1049) hydrogen bonds : angle 3.28804 ( 3147) link_NAG-ASN : bond 0.00359 ( 8) link_NAG-ASN : angle 2.79524 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 412 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.6899 (tm-30) cc_final: 0.6499 (tp40) REVERT: A 46 ASP cc_start: 0.9047 (m-30) cc_final: 0.8805 (m-30) REVERT: A 71 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8476 (t0) REVERT: A 79 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7470 (tp30) REVERT: A 105 ARG cc_start: 0.8536 (mpt180) cc_final: 0.8323 (tpp-160) REVERT: A 143 GLN cc_start: 0.7954 (mm110) cc_final: 0.7634 (mm110) REVERT: A 147 GLN cc_start: 0.7427 (mm110) cc_final: 0.7180 (mm110) REVERT: A 148 LYS cc_start: 0.8183 (mppt) cc_final: 0.7720 (ttmm) REVERT: A 165 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7255 (mt-10) REVERT: A 240 PHE cc_start: 0.7959 (m-80) cc_final: 0.7604 (m-80) REVERT: B 46 ASP cc_start: 0.8986 (m-30) cc_final: 0.8578 (m-30) REVERT: B 73 ASN cc_start: 0.8870 (p0) cc_final: 0.8487 (p0) REVERT: B 79 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7590 (tp30) REVERT: B 105 ARG cc_start: 0.8704 (mpt180) cc_final: 0.8483 (tpp-160) REVERT: B 124 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8416 (t80) REVERT: B 148 LYS cc_start: 0.8220 (mmtm) cc_final: 0.7885 (tttt) REVERT: B 165 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7803 (mp0) REVERT: B 167 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7901 (mp0) REVERT: B 227 LYS cc_start: 0.7304 (tmtt) cc_final: 0.7089 (tptt) REVERT: C 32 GLN cc_start: 0.6904 (tm-30) cc_final: 0.6504 (tp40) REVERT: C 46 ASP cc_start: 0.9050 (m-30) cc_final: 0.8808 (m-30) REVERT: C 71 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8471 (t0) REVERT: C 79 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7467 (tp30) REVERT: C 105 ARG cc_start: 0.8535 (mpt180) cc_final: 0.8325 (tpp-160) REVERT: C 143 GLN cc_start: 0.7958 (mm110) cc_final: 0.7633 (mm110) REVERT: C 147 GLN cc_start: 0.7431 (mm110) cc_final: 0.7184 (mm110) REVERT: C 148 LYS cc_start: 0.8179 (mppt) cc_final: 0.7717 (ttmm) REVERT: C 165 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7250 (mt-10) REVERT: C 240 PHE cc_start: 0.7962 (m-80) cc_final: 0.7607 (m-80) REVERT: D 46 ASP cc_start: 0.8995 (m-30) cc_final: 0.8589 (m-30) REVERT: D 73 ASN cc_start: 0.8872 (p0) cc_final: 0.8483 (p0) REVERT: D 79 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7626 (tp30) REVERT: D 105 ARG cc_start: 0.8667 (mpt180) cc_final: 0.8451 (tpp-160) REVERT: D 124 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8417 (t80) REVERT: D 148 LYS cc_start: 0.8254 (mmtm) cc_final: 0.7846 (tttt) REVERT: D 165 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7806 (mp0) REVERT: D 167 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7867 (mp0) REVERT: E 32 GLN cc_start: 0.6906 (tm-30) cc_final: 0.6507 (tp40) REVERT: E 46 ASP cc_start: 0.9045 (m-30) cc_final: 0.8804 (m-30) REVERT: E 71 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8473 (t0) REVERT: E 79 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7472 (tp30) REVERT: E 105 ARG cc_start: 0.8537 (mpt180) cc_final: 0.8327 (tpp-160) REVERT: E 143 GLN cc_start: 0.7958 (mm110) cc_final: 0.7632 (mm110) REVERT: E 147 GLN cc_start: 0.7430 (mm110) cc_final: 0.7184 (mm110) REVERT: E 148 LYS cc_start: 0.8181 (mppt) cc_final: 0.7719 (ttmm) REVERT: E 165 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7266 (mt-10) REVERT: E 240 PHE cc_start: 0.7959 (m-80) cc_final: 0.7605 (m-80) REVERT: F 46 ASP cc_start: 0.8999 (m-30) cc_final: 0.8594 (m-30) REVERT: F 73 ASN cc_start: 0.8872 (p0) cc_final: 0.8480 (p0) REVERT: F 79 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7586 (tp30) REVERT: F 105 ARG cc_start: 0.8656 (mpt180) cc_final: 0.8439 (tpp-160) REVERT: F 124 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.8421 (t80) REVERT: F 148 LYS cc_start: 0.8264 (mppt) cc_final: 0.7973 (tttt) REVERT: F 165 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7813 (mp0) REVERT: F 167 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7957 (mp0) REVERT: G 32 GLN cc_start: 0.6902 (tm-30) cc_final: 0.6505 (tp40) REVERT: G 46 ASP cc_start: 0.9047 (m-30) cc_final: 0.8807 (m-30) REVERT: G 71 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8470 (t0) REVERT: G 79 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7479 (tp30) REVERT: G 105 ARG cc_start: 0.8539 (mpt180) cc_final: 0.8328 (tpp-160) REVERT: G 143 GLN cc_start: 0.7987 (mm110) cc_final: 0.7659 (mm110) REVERT: G 147 GLN cc_start: 0.7430 (mm110) cc_final: 0.7183 (mm110) REVERT: G 148 LYS cc_start: 0.8179 (mppt) cc_final: 0.7718 (ttmm) REVERT: G 165 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7255 (mt-10) REVERT: G 240 PHE cc_start: 0.7959 (m-80) cc_final: 0.7605 (m-80) REVERT: H 46 ASP cc_start: 0.8993 (m-30) cc_final: 0.8587 (m-30) REVERT: H 73 ASN cc_start: 0.8868 (p0) cc_final: 0.8476 (p0) REVERT: H 79 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7595 (tp30) REVERT: H 105 ARG cc_start: 0.8659 (mpt180) cc_final: 0.8441 (tpp-160) REVERT: H 124 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8419 (t80) REVERT: H 148 LYS cc_start: 0.8257 (mppt) cc_final: 0.7965 (tttt) REVERT: H 165 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7801 (mp0) REVERT: H 167 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8016 (mp0) REVERT: H 227 LYS cc_start: 0.7301 (tmtt) cc_final: 0.7088 (tptt) outliers start: 17 outliers final: 4 residues processed: 416 average time/residue: 0.1349 time to fit residues: 80.1621 Evaluate side-chains 364 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 352 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain G residue 71 ASN Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 124 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 167 optimal weight: 0.0000 chunk 35 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.162977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.105356 restraints weight = 18282.818| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.39 r_work: 0.2950 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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 0.037 15048 Z= 0.116 Angle : 0.506 5.430 20408 Z= 0.263 Chirality : 0.036 0.122 2336 Planarity : 0.004 0.045 2504 Dihedral : 3.660 16.778 2144 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.51 % Allowed : 20.92 % Favored : 77.57 % 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: 2.76 (0.20), residues: 1792 helix: 2.73 (0.13), residues: 1408 sheet: None (None), residues: 0 loop : -1.87 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 204 TYR 0.017 0.001 TYR C 142 PHE 0.005 0.001 PHE A 124 TRP 0.006 0.001 TRP H 62 HIS 0.003 0.001 HIS F 236 Details of bonding type rmsd covalent geometry : bond 0.00272 (15024) covalent geometry : angle 0.49646 (20352) SS BOND : bond 0.00278 ( 16) SS BOND : angle 0.91159 ( 32) hydrogen bonds : bond 0.03975 ( 1049) hydrogen bonds : angle 3.16084 ( 3147) link_NAG-ASN : bond 0.00076 ( 8) link_NAG-ASN : angle 2.73326 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 356 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.6823 (tm-30) cc_final: 0.6437 (tp40) REVERT: A 46 ASP cc_start: 0.9058 (m-30) cc_final: 0.8832 (m-30) REVERT: A 79 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7502 (tp30) REVERT: A 105 ARG cc_start: 0.8543 (mpt180) cc_final: 0.8343 (tpp-160) REVERT: A 143 GLN cc_start: 0.7918 (mm110) cc_final: 0.7591 (mm110) REVERT: A 147 GLN cc_start: 0.7348 (mm110) cc_final: 0.7121 (mm110) REVERT: A 148 LYS cc_start: 0.8064 (mppt) cc_final: 0.7601 (ttmm) REVERT: A 165 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7569 (mp0) REVERT: A 240 PHE cc_start: 0.7972 (m-80) cc_final: 0.7540 (m-80) REVERT: B 46 ASP cc_start: 0.8987 (m-30) cc_final: 0.8624 (m-30) REVERT: B 73 ASN cc_start: 0.8786 (p0) cc_final: 0.8358 (p0) REVERT: B 79 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7532 (tp30) REVERT: B 105 ARG cc_start: 0.8686 (mpt180) cc_final: 0.8467 (tpp-160) REVERT: B 148 LYS cc_start: 0.8122 (mmtm) cc_final: 0.7854 (tttt) REVERT: B 164 GLU cc_start: 0.7961 (pm20) cc_final: 0.7351 (pm20) REVERT: B 165 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7687 (mp0) REVERT: B 227 LYS cc_start: 0.7286 (tmtt) cc_final: 0.7081 (tptt) REVERT: C 32 GLN cc_start: 0.6823 (tm-30) cc_final: 0.6438 (tp40) REVERT: C 46 ASP cc_start: 0.9061 (m-30) cc_final: 0.8833 (m-30) REVERT: C 79 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7511 (tp30) REVERT: C 143 GLN cc_start: 0.7925 (mm110) cc_final: 0.7594 (mm110) REVERT: C 147 GLN cc_start: 0.7366 (mm110) cc_final: 0.7136 (mm110) REVERT: C 148 LYS cc_start: 0.8073 (mppt) cc_final: 0.7604 (ttmm) REVERT: C 165 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7272 (mt-10) REVERT: C 240 PHE cc_start: 0.7971 (m-80) cc_final: 0.7539 (m-80) REVERT: D 46 ASP cc_start: 0.8998 (m-30) cc_final: 0.8637 (m-30) REVERT: D 73 ASN cc_start: 0.8783 (p0) cc_final: 0.8374 (p0) REVERT: D 105 ARG cc_start: 0.8689 (mpt180) cc_final: 0.8472 (tpp-160) REVERT: D 148 LYS cc_start: 0.8172 (mmtm) cc_final: 0.7844 (tttt) REVERT: D 164 GLU cc_start: 0.7978 (pm20) cc_final: 0.7382 (pm20) REVERT: D 165 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7670 (mp0) REVERT: E 32 GLN cc_start: 0.6827 (tm-30) cc_final: 0.6445 (tp40) REVERT: E 46 ASP cc_start: 0.9056 (m-30) cc_final: 0.8829 (m-30) REVERT: E 79 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7508 (tp30) REVERT: E 143 GLN cc_start: 0.7933 (mm110) cc_final: 0.7601 (mm110) REVERT: E 147 GLN cc_start: 0.7357 (mm110) cc_final: 0.7130 (mm110) REVERT: E 148 LYS cc_start: 0.8064 (mppt) cc_final: 0.7600 (ttmm) REVERT: E 165 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7284 (mt-10) REVERT: E 240 PHE cc_start: 0.7971 (m-80) cc_final: 0.7539 (m-80) REVERT: F 46 ASP cc_start: 0.9008 (m-30) cc_final: 0.8645 (m-30) REVERT: F 73 ASN cc_start: 0.8776 (p0) cc_final: 0.8368 (p0) REVERT: F 79 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7548 (tp30) REVERT: F 105 ARG cc_start: 0.8638 (mpt180) cc_final: 0.8423 (tpp-160) REVERT: F 148 LYS cc_start: 0.8203 (mppt) cc_final: 0.7944 (tttt) REVERT: F 165 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7496 (mt-10) REVERT: G 32 GLN cc_start: 0.6824 (tm-30) cc_final: 0.6437 (tp40) REVERT: G 46 ASP cc_start: 0.9047 (m-30) cc_final: 0.8821 (m-30) REVERT: G 79 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7501 (tp30) REVERT: G 143 GLN cc_start: 0.7921 (mm110) cc_final: 0.7584 (mm110) REVERT: G 147 GLN cc_start: 0.7346 (mm110) cc_final: 0.7117 (mm110) REVERT: G 148 LYS cc_start: 0.8053 (mppt) cc_final: 0.7598 (ttmm) REVERT: G 165 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7566 (mp0) REVERT: G 240 PHE cc_start: 0.7972 (m-80) cc_final: 0.7540 (m-80) REVERT: H 46 ASP cc_start: 0.8993 (m-30) cc_final: 0.8631 (m-30) REVERT: H 73 ASN cc_start: 0.8783 (p0) cc_final: 0.8375 (p0) REVERT: H 105 ARG cc_start: 0.8677 (mpt180) cc_final: 0.8460 (tpp-160) REVERT: H 148 LYS cc_start: 0.8200 (mppt) cc_final: 0.7937 (tttt) REVERT: H 164 GLU cc_start: 0.7974 (pm20) cc_final: 0.7362 (pm20) REVERT: H 165 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7674 (mp0) REVERT: H 227 LYS cc_start: 0.7281 (tmtt) cc_final: 0.7077 (tptt) outliers start: 23 outliers final: 7 residues processed: 368 average time/residue: 0.1294 time to fit residues: 67.8747 Evaluate side-chains 349 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 342 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 98 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 125 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 155 optimal weight: 0.5980 chunk 147 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 151 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 GLN D 104 GLN F 104 GLN H 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.162418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.104839 restraints weight = 18313.367| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.38 r_work: 0.2965 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15048 Z= 0.116 Angle : 0.490 5.590 20408 Z= 0.255 Chirality : 0.036 0.124 2336 Planarity : 0.004 0.050 2504 Dihedral : 3.487 16.668 2144 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.32 % Allowed : 20.07 % Favored : 78.62 % 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: 3.02 (0.20), residues: 1792 helix: 2.89 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.78 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 83 TYR 0.015 0.001 TYR G 142 PHE 0.006 0.001 PHE E 124 TRP 0.006 0.001 TRP H 62 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00279 (15024) covalent geometry : angle 0.48289 (20352) SS BOND : bond 0.00282 ( 16) SS BOND : angle 0.87165 ( 32) hydrogen bonds : bond 0.03780 ( 1049) hydrogen bonds : angle 3.07749 ( 3147) link_NAG-ASN : bond 0.00068 ( 8) link_NAG-ASN : angle 2.37562 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 354 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.6766 (tm-30) cc_final: 0.6409 (tp40) REVERT: A 46 ASP cc_start: 0.9059 (m-30) cc_final: 0.8840 (m-30) REVERT: A 79 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7512 (tp30) REVERT: A 105 ARG cc_start: 0.8629 (mpt180) cc_final: 0.8413 (tpp-160) REVERT: A 133 ASP cc_start: 0.9048 (t70) cc_final: 0.8845 (t0) REVERT: A 148 LYS cc_start: 0.8020 (mppt) cc_final: 0.7609 (ttmm) REVERT: A 164 GLU cc_start: 0.7889 (pm20) cc_final: 0.7391 (pm20) REVERT: A 165 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7514 (mp0) REVERT: B 46 ASP cc_start: 0.8995 (m-30) cc_final: 0.8638 (m-30) REVERT: B 73 ASN cc_start: 0.8791 (p0) cc_final: 0.8381 (p0) REVERT: B 79 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7498 (tp30) REVERT: B 105 ARG cc_start: 0.8702 (mpt180) cc_final: 0.8477 (tpp-160) REVERT: B 124 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8352 (t80) REVERT: B 148 LYS cc_start: 0.8091 (mmtm) cc_final: 0.7849 (tttt) REVERT: B 164 GLU cc_start: 0.7846 (pm20) cc_final: 0.7510 (pm20) REVERT: B 165 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7613 (mp0) REVERT: C 32 GLN cc_start: 0.6769 (tm-30) cc_final: 0.6409 (tp40) REVERT: C 46 ASP cc_start: 0.9063 (m-30) cc_final: 0.8844 (m-30) REVERT: C 79 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7497 (tp30) REVERT: C 133 ASP cc_start: 0.9045 (t70) cc_final: 0.8843 (t0) REVERT: C 148 LYS cc_start: 0.8024 (mppt) cc_final: 0.7612 (ttmm) REVERT: C 165 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7299 (mt-10) REVERT: D 46 ASP cc_start: 0.8992 (m-30) cc_final: 0.8632 (m-30) REVERT: D 73 ASN cc_start: 0.8774 (p0) cc_final: 0.8352 (p0) REVERT: D 79 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7531 (tp30) REVERT: D 105 ARG cc_start: 0.8704 (mpt180) cc_final: 0.8484 (tpp-160) REVERT: D 124 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8357 (t80) REVERT: D 148 LYS cc_start: 0.8089 (mmtm) cc_final: 0.7802 (tttt) REVERT: D 164 GLU cc_start: 0.7853 (pm20) cc_final: 0.7515 (pm20) REVERT: D 165 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7616 (mp0) REVERT: E 32 GLN cc_start: 0.6772 (tm-30) cc_final: 0.6415 (tp40) REVERT: E 46 ASP cc_start: 0.9065 (m-30) cc_final: 0.8844 (m-30) REVERT: E 79 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7498 (tp30) REVERT: E 133 ASP cc_start: 0.9051 (t70) cc_final: 0.8846 (t0) REVERT: E 148 LYS cc_start: 0.8022 (mppt) cc_final: 0.7611 (ttmm) REVERT: E 165 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7314 (mt-10) REVERT: F 46 ASP cc_start: 0.9006 (m-30) cc_final: 0.8649 (m-30) REVERT: F 73 ASN cc_start: 0.8769 (p0) cc_final: 0.8347 (p0) REVERT: F 79 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7526 (tp30) REVERT: F 105 ARG cc_start: 0.8699 (mpt180) cc_final: 0.8479 (tpp-160) REVERT: F 124 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8358 (t80) REVERT: F 147 GLN cc_start: 0.7704 (mm110) cc_final: 0.7429 (mm110) REVERT: F 148 LYS cc_start: 0.8146 (mppt) cc_final: 0.7902 (tttt) REVERT: F 164 GLU cc_start: 0.8045 (pm20) cc_final: 0.7137 (pm20) REVERT: F 167 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8092 (mp0) REVERT: G 32 GLN cc_start: 0.6771 (tm-30) cc_final: 0.6414 (tp40) REVERT: G 46 ASP cc_start: 0.9051 (m-30) cc_final: 0.8831 (m-30) REVERT: G 79 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7498 (tp30) REVERT: G 148 LYS cc_start: 0.8011 (mppt) cc_final: 0.7609 (ttmm) REVERT: G 164 GLU cc_start: 0.7888 (pm20) cc_final: 0.7396 (pm20) REVERT: G 165 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7514 (mp0) REVERT: H 46 ASP cc_start: 0.8989 (m-30) cc_final: 0.8633 (m-30) REVERT: H 73 ASN cc_start: 0.8824 (p0) cc_final: 0.8388 (p0) REVERT: H 79 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7492 (tp30) REVERT: H 105 ARG cc_start: 0.8702 (mpt180) cc_final: 0.8480 (tpp-160) REVERT: H 124 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8361 (t80) REVERT: H 147 GLN cc_start: 0.7700 (mm110) cc_final: 0.7424 (mm110) REVERT: H 148 LYS cc_start: 0.8150 (mppt) cc_final: 0.7907 (tttt) REVERT: H 165 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7749 (mp0) outliers start: 20 outliers final: 8 residues processed: 363 average time/residue: 0.1354 time to fit residues: 69.1186 Evaluate side-chains 357 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 345 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 124 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 121 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 123 optimal weight: 0.0000 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 50.0000 chunk 170 optimal weight: 0.3980 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.163159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.105269 restraints weight = 18195.324| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.38 r_work: 0.2956 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15048 Z= 0.123 Angle : 0.495 5.499 20408 Z= 0.257 Chirality : 0.037 0.124 2336 Planarity : 0.004 0.046 2504 Dihedral : 3.470 16.569 2144 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.18 % Allowed : 20.66 % Favored : 78.16 % 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: 3.13 (0.20), residues: 1792 helix: 2.93 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.59 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.022 0.001 TYR G 142 PHE 0.006 0.001 PHE G 124 TRP 0.005 0.001 TRP D 62 HIS 0.005 0.001 HIS G 220 Details of bonding type rmsd covalent geometry : bond 0.00300 (15024) covalent geometry : angle 0.48846 (20352) SS BOND : bond 0.00333 ( 16) SS BOND : angle 1.00083 ( 32) hydrogen bonds : bond 0.03804 ( 1049) hydrogen bonds : angle 3.07011 ( 3147) link_NAG-ASN : bond 0.00054 ( 8) link_NAG-ASN : angle 2.21457 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 355 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.6761 (tm-30) cc_final: 0.6411 (tp40) REVERT: A 46 ASP cc_start: 0.9048 (m-30) cc_final: 0.8832 (m-30) REVERT: A 79 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7520 (tp30) REVERT: A 105 ARG cc_start: 0.8666 (mpt180) cc_final: 0.8444 (tpp-160) REVERT: A 143 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7595 (mm110) REVERT: A 147 GLN cc_start: 0.7582 (mm110) cc_final: 0.7228 (mm110) REVERT: A 148 LYS cc_start: 0.8026 (mppt) cc_final: 0.7607 (ttmm) REVERT: A 164 GLU cc_start: 0.7867 (pm20) cc_final: 0.7619 (pm20) REVERT: A 165 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7298 (mt-10) REVERT: B 46 ASP cc_start: 0.8993 (m-30) cc_final: 0.8633 (m-30) REVERT: B 73 ASN cc_start: 0.8795 (p0) cc_final: 0.8363 (p0) REVERT: B 79 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7508 (tp30) REVERT: B 105 ARG cc_start: 0.8708 (mpt180) cc_final: 0.8470 (tpp-160) REVERT: B 124 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.8362 (t80) REVERT: B 143 GLN cc_start: 0.8015 (mm110) cc_final: 0.7677 (mm-40) REVERT: B 147 GLN cc_start: 0.7868 (mm110) cc_final: 0.7445 (mm110) REVERT: B 165 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7733 (mp0) REVERT: C 32 GLN cc_start: 0.6765 (tm-30) cc_final: 0.6420 (tp40) REVERT: C 46 ASP cc_start: 0.9045 (m-30) cc_final: 0.8830 (m-30) REVERT: C 79 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7531 (tp30) REVERT: C 133 ASP cc_start: 0.9032 (t70) cc_final: 0.8831 (t0) REVERT: C 143 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7605 (mm110) REVERT: C 147 GLN cc_start: 0.7599 (mm110) cc_final: 0.7244 (mm110) REVERT: C 148 LYS cc_start: 0.8043 (mppt) cc_final: 0.7612 (ttmm) REVERT: C 165 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7594 (mp0) REVERT: D 46 ASP cc_start: 0.8984 (m-30) cc_final: 0.8621 (m-30) REVERT: D 73 ASN cc_start: 0.8806 (p0) cc_final: 0.8359 (p0) REVERT: D 79 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7503 (tp30) REVERT: D 105 ARG cc_start: 0.8711 (mpt180) cc_final: 0.8477 (tpp-160) REVERT: D 124 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8368 (t80) REVERT: D 147 GLN cc_start: 0.7858 (mm110) cc_final: 0.7419 (mm110) REVERT: D 148 LYS cc_start: 0.8071 (mmtm) cc_final: 0.7815 (tttt) REVERT: D 165 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7734 (mp0) REVERT: E 32 GLN cc_start: 0.6771 (tm-30) cc_final: 0.6425 (tp40) REVERT: E 46 ASP cc_start: 0.9066 (m-30) cc_final: 0.8848 (m-30) REVERT: E 79 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7528 (tp30) REVERT: E 133 ASP cc_start: 0.9032 (t70) cc_final: 0.8831 (t0) REVERT: E 143 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7611 (mm110) REVERT: E 147 GLN cc_start: 0.7594 (mm110) cc_final: 0.7238 (mm110) REVERT: E 148 LYS cc_start: 0.8035 (mppt) cc_final: 0.7609 (ttmm) REVERT: E 165 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7612 (mp0) REVERT: F 46 ASP cc_start: 0.9014 (m-30) cc_final: 0.8655 (m-30) REVERT: F 73 ASN cc_start: 0.8806 (p0) cc_final: 0.8358 (p0) REVERT: F 79 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7508 (tp30) REVERT: F 105 ARG cc_start: 0.8704 (mpt180) cc_final: 0.8469 (tpp-160) REVERT: F 124 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8373 (t80) REVERT: F 147 GLN cc_start: 0.7676 (mm110) cc_final: 0.7409 (mm110) REVERT: F 148 LYS cc_start: 0.8114 (mppt) cc_final: 0.7871 (tttt) REVERT: F 167 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8087 (mp0) REVERT: G 32 GLN cc_start: 0.6772 (tm-30) cc_final: 0.6424 (tp40) REVERT: G 46 ASP cc_start: 0.9049 (m-30) cc_final: 0.8832 (m-30) REVERT: G 79 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7527 (tp30) REVERT: G 133 ASP cc_start: 0.9020 (t70) cc_final: 0.8786 (t0) REVERT: G 143 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7607 (mm110) REVERT: G 147 GLN cc_start: 0.7583 (mm110) cc_final: 0.7231 (mm110) REVERT: G 148 LYS cc_start: 0.8023 (mppt) cc_final: 0.7608 (ttmm) REVERT: G 164 GLU cc_start: 0.7871 (pm20) cc_final: 0.7630 (pm20) REVERT: G 165 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7299 (mt-10) REVERT: H 46 ASP cc_start: 0.8994 (m-30) cc_final: 0.8635 (m-30) REVERT: H 73 ASN cc_start: 0.8821 (p0) cc_final: 0.8384 (p0) REVERT: H 79 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7500 (tp30) REVERT: H 105 ARG cc_start: 0.8704 (mpt180) cc_final: 0.8468 (tpp-160) REVERT: H 124 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8376 (t80) REVERT: H 147 GLN cc_start: 0.7669 (mm110) cc_final: 0.7404 (mm110) REVERT: H 148 LYS cc_start: 0.8114 (mppt) cc_final: 0.7872 (tttt) REVERT: H 165 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7466 (mt-10) REVERT: H 167 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8076 (mp0) outliers start: 18 outliers final: 8 residues processed: 363 average time/residue: 0.1311 time to fit residues: 67.6341 Evaluate side-chains 373 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 361 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 124 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 45 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 179 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 125 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 138 optimal weight: 70.0000 chunk 148 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN C 143 GLN E 143 GLN G 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.163861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.106162 restraints weight = 18177.751| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.36 r_work: 0.2959 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15048 Z= 0.120 Angle : 0.487 6.113 20408 Z= 0.253 Chirality : 0.037 0.124 2336 Planarity : 0.004 0.046 2504 Dihedral : 3.411 16.519 2144 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.25 % Allowed : 20.39 % Favored : 78.36 % 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: 3.24 (0.20), residues: 1792 helix: 2.99 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.45 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.018 0.001 TYR G 142 PHE 0.006 0.001 PHE G 124 TRP 0.004 0.001 TRP H 62 HIS 0.004 0.001 HIS G 220 Details of bonding type rmsd covalent geometry : bond 0.00294 (15024) covalent geometry : angle 0.47998 (20352) SS BOND : bond 0.00328 ( 16) SS BOND : angle 0.97092 ( 32) hydrogen bonds : bond 0.03766 ( 1049) hydrogen bonds : angle 3.03925 ( 3147) link_NAG-ASN : bond 0.00042 ( 8) link_NAG-ASN : angle 2.29658 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 384 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.6765 (tm-30) cc_final: 0.6429 (tp40) REVERT: A 46 ASP cc_start: 0.9049 (m-30) cc_final: 0.8837 (m-30) REVERT: A 73 ASN cc_start: 0.8588 (p0) cc_final: 0.8315 (p0) REVERT: A 79 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7522 (tp30) REVERT: A 80 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8316 (mm-30) REVERT: A 105 ARG cc_start: 0.8671 (mpt180) cc_final: 0.8429 (tpp-160) REVERT: A 147 GLN cc_start: 0.7565 (mm110) cc_final: 0.7262 (mm110) REVERT: A 148 LYS cc_start: 0.8033 (mppt) cc_final: 0.7601 (ttmm) REVERT: A 164 GLU cc_start: 0.7913 (pm20) cc_final: 0.7676 (pm20) REVERT: A 165 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7264 (mt-10) REVERT: A 167 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8042 (mp0) REVERT: B 46 ASP cc_start: 0.8991 (m-30) cc_final: 0.8633 (m-30) REVERT: B 73 ASN cc_start: 0.8773 (p0) cc_final: 0.8313 (p0) REVERT: B 79 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7513 (tp30) REVERT: B 105 ARG cc_start: 0.8714 (mpt180) cc_final: 0.8470 (tpp-160) REVERT: B 124 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8378 (t80) REVERT: B 143 GLN cc_start: 0.8118 (mm110) cc_final: 0.7797 (mm-40) REVERT: B 164 GLU cc_start: 0.7788 (pm20) cc_final: 0.7575 (pm20) REVERT: B 165 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7509 (mt-10) REVERT: B 167 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8079 (mp0) REVERT: C 32 GLN cc_start: 0.6767 (tm-30) cc_final: 0.6428 (tp40) REVERT: C 46 ASP cc_start: 0.9049 (m-30) cc_final: 0.8837 (m-30) REVERT: C 73 ASN cc_start: 0.8585 (p0) cc_final: 0.8314 (p0) REVERT: C 79 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7525 (tp30) REVERT: C 147 GLN cc_start: 0.7582 (mm110) cc_final: 0.7273 (mm110) REVERT: C 148 LYS cc_start: 0.8045 (mppt) cc_final: 0.7604 (ttmm) REVERT: C 165 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7612 (mp0) REVERT: D 46 ASP cc_start: 0.8984 (m-30) cc_final: 0.8623 (m-30) REVERT: D 73 ASN cc_start: 0.8784 (p0) cc_final: 0.8339 (p0) REVERT: D 79 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7505 (tp30) REVERT: D 105 ARG cc_start: 0.8724 (mpt180) cc_final: 0.8487 (tpp-160) REVERT: D 124 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8382 (t80) REVERT: D 143 GLN cc_start: 0.8100 (mm110) cc_final: 0.7567 (mm-40) REVERT: D 147 GLN cc_start: 0.7896 (mm110) cc_final: 0.7474 (mm110) REVERT: D 148 LYS cc_start: 0.8012 (mmtm) cc_final: 0.7797 (tttt) REVERT: D 165 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7519 (mt-10) REVERT: D 167 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8080 (mp0) REVERT: E 32 GLN cc_start: 0.6774 (tm-30) cc_final: 0.6440 (tp40) REVERT: E 46 ASP cc_start: 0.9066 (m-30) cc_final: 0.8852 (m-30) REVERT: E 73 ASN cc_start: 0.8581 (p0) cc_final: 0.8309 (p0) REVERT: E 79 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7524 (tp30) REVERT: E 147 GLN cc_start: 0.7575 (mm110) cc_final: 0.7267 (mm110) REVERT: E 148 LYS cc_start: 0.8042 (mppt) cc_final: 0.7604 (ttmm) REVERT: E 165 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7632 (mp0) REVERT: F 46 ASP cc_start: 0.9009 (m-30) cc_final: 0.8650 (m-30) REVERT: F 73 ASN cc_start: 0.8784 (p0) cc_final: 0.8339 (p0) REVERT: F 79 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7505 (tp30) REVERT: F 105 ARG cc_start: 0.8715 (mpt180) cc_final: 0.8482 (tpp-160) REVERT: F 124 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.8384 (t80) REVERT: F 147 GLN cc_start: 0.7683 (mm110) cc_final: 0.7439 (mm110) REVERT: F 148 LYS cc_start: 0.8087 (mppt) cc_final: 0.7850 (tttt) REVERT: G 32 GLN cc_start: 0.6796 (tm-30) cc_final: 0.6469 (tp40) REVERT: G 46 ASP cc_start: 0.9046 (m-30) cc_final: 0.8833 (m-30) REVERT: G 79 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7523 (tp30) REVERT: G 133 ASP cc_start: 0.9007 (t70) cc_final: 0.8778 (t0) REVERT: G 147 GLN cc_start: 0.7566 (mm110) cc_final: 0.7261 (mm110) REVERT: G 148 LYS cc_start: 0.8029 (mppt) cc_final: 0.7598 (ttmm) REVERT: G 164 GLU cc_start: 0.7908 (pm20) cc_final: 0.7672 (pm20) REVERT: G 165 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7266 (mt-10) REVERT: G 167 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8035 (mp0) REVERT: H 46 ASP cc_start: 0.8991 (m-30) cc_final: 0.8632 (m-30) REVERT: H 73 ASN cc_start: 0.8820 (p0) cc_final: 0.8380 (p0) REVERT: H 79 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7481 (tp30) REVERT: H 105 ARG cc_start: 0.8710 (mpt180) cc_final: 0.8477 (tpp-160) REVERT: H 124 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8389 (t80) REVERT: H 147 GLN cc_start: 0.7672 (mm110) cc_final: 0.7431 (mm110) REVERT: H 148 LYS cc_start: 0.8084 (mppt) cc_final: 0.7834 (tttt) REVERT: H 167 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8093 (mp0) outliers start: 19 outliers final: 10 residues processed: 388 average time/residue: 0.1301 time to fit residues: 72.0289 Evaluate side-chains 381 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 367 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 124 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 58 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 178 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.163458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.104965 restraints weight = 18236.020| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.38 r_work: 0.2949 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15048 Z= 0.135 Angle : 0.515 6.150 20408 Z= 0.267 Chirality : 0.037 0.125 2336 Planarity : 0.004 0.047 2504 Dihedral : 3.421 16.516 2144 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.18 % Allowed : 20.13 % Favored : 78.68 % 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: 3.27 (0.20), residues: 1792 helix: 3.00 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.35 (0.35), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 83 TYR 0.015 0.001 TYR E 142 PHE 0.007 0.001 PHE B 124 TRP 0.003 0.001 TRP D 62 HIS 0.005 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00339 (15024) covalent geometry : angle 0.50723 (20352) SS BOND : bond 0.00367 ( 16) SS BOND : angle 1.02139 ( 32) hydrogen bonds : bond 0.03895 ( 1049) hydrogen bonds : angle 3.07120 ( 3147) link_NAG-ASN : bond 0.00074 ( 8) link_NAG-ASN : angle 2.36506 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 369 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.6664 (tm-30) cc_final: 0.6278 (tp40) REVERT: A 46 ASP cc_start: 0.9054 (m-30) cc_final: 0.8841 (m-30) REVERT: A 73 ASN cc_start: 0.8584 (p0) cc_final: 0.8201 (p0) REVERT: A 79 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7525 (tp30) REVERT: A 80 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8289 (mm-30) REVERT: A 105 ARG cc_start: 0.8688 (mpt180) cc_final: 0.8423 (tpp-160) REVERT: A 142 TYR cc_start: 0.8442 (m-80) cc_final: 0.8230 (m-80) REVERT: A 143 GLN cc_start: 0.7931 (mm110) cc_final: 0.7636 (mm-40) REVERT: A 147 GLN cc_start: 0.7596 (mm110) cc_final: 0.7308 (mm110) REVERT: A 148 LYS cc_start: 0.7998 (mppt) cc_final: 0.7567 (ttmm) REVERT: A 164 GLU cc_start: 0.7939 (pm20) cc_final: 0.7398 (pm20) REVERT: A 165 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7552 (mp0) REVERT: A 167 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8036 (mp0) REVERT: B 46 ASP cc_start: 0.8992 (m-30) cc_final: 0.8594 (m-30) REVERT: B 73 ASN cc_start: 0.8758 (p0) cc_final: 0.8188 (p0) REVERT: B 79 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7520 (tp30) REVERT: B 105 ARG cc_start: 0.8735 (mpt180) cc_final: 0.8470 (tpp-160) REVERT: B 124 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8418 (t80) REVERT: B 164 GLU cc_start: 0.7800 (pm20) cc_final: 0.7234 (pm20) REVERT: B 167 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8093 (mp0) REVERT: C 32 GLN cc_start: 0.6684 (tm-30) cc_final: 0.6294 (tp40) REVERT: C 46 ASP cc_start: 0.9051 (m-30) cc_final: 0.8839 (m-30) REVERT: C 73 ASN cc_start: 0.8576 (p0) cc_final: 0.8197 (p0) REVERT: C 79 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7520 (tp30) REVERT: C 142 TYR cc_start: 0.8327 (m-80) cc_final: 0.8048 (m-80) REVERT: C 143 GLN cc_start: 0.7906 (mm110) cc_final: 0.7571 (mm-40) REVERT: C 147 GLN cc_start: 0.7614 (mm110) cc_final: 0.7321 (mm110) REVERT: C 148 LYS cc_start: 0.8045 (mppt) cc_final: 0.7600 (ttmm) REVERT: C 165 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7621 (mp0) REVERT: D 46 ASP cc_start: 0.9002 (m-30) cc_final: 0.8601 (m-30) REVERT: D 73 ASN cc_start: 0.8777 (p0) cc_final: 0.8220 (p0) REVERT: D 79 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7532 (tp30) REVERT: D 105 ARG cc_start: 0.8722 (mpt180) cc_final: 0.8479 (tpp-160) REVERT: D 124 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8423 (t80) REVERT: D 147 GLN cc_start: 0.7915 (mm110) cc_final: 0.7502 (mm110) REVERT: D 167 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8086 (mp0) REVERT: E 32 GLN cc_start: 0.6682 (tm-30) cc_final: 0.6297 (tp40) REVERT: E 46 ASP cc_start: 0.9067 (m-30) cc_final: 0.8854 (m-30) REVERT: E 73 ASN cc_start: 0.8570 (p0) cc_final: 0.8191 (p0) REVERT: E 79 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7528 (tp30) REVERT: E 142 TYR cc_start: 0.8331 (m-80) cc_final: 0.8056 (m-80) REVERT: E 143 GLN cc_start: 0.7909 (mm110) cc_final: 0.7575 (mm-40) REVERT: E 147 GLN cc_start: 0.7606 (mm110) cc_final: 0.7319 (mm110) REVERT: E 148 LYS cc_start: 0.8036 (mppt) cc_final: 0.7597 (ttmm) REVERT: E 165 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7641 (mp0) REVERT: F 46 ASP cc_start: 0.9015 (m-30) cc_final: 0.8652 (m-30) REVERT: F 73 ASN cc_start: 0.8773 (p0) cc_final: 0.8218 (p0) REVERT: F 79 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7527 (tp30) REVERT: F 105 ARG cc_start: 0.8721 (mpt180) cc_final: 0.8477 (tpp-160) REVERT: F 124 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8425 (t80) REVERT: F 147 GLN cc_start: 0.7701 (mm110) cc_final: 0.7471 (mm110) REVERT: F 148 LYS cc_start: 0.8135 (mppt) cc_final: 0.7863 (tttt) REVERT: G 32 GLN cc_start: 0.6674 (tm-30) cc_final: 0.6289 (tp40) REVERT: G 46 ASP cc_start: 0.9059 (m-30) cc_final: 0.8846 (m-30) REVERT: G 73 ASN cc_start: 0.8541 (p0) cc_final: 0.8209 (p0) REVERT: G 79 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7530 (tp30) REVERT: G 133 ASP cc_start: 0.9003 (t70) cc_final: 0.8772 (t0) REVERT: G 142 TYR cc_start: 0.8447 (m-80) cc_final: 0.8242 (m-80) REVERT: G 143 GLN cc_start: 0.7944 (mm110) cc_final: 0.7646 (mm-40) REVERT: G 147 GLN cc_start: 0.7604 (mm110) cc_final: 0.7312 (mm110) REVERT: G 148 LYS cc_start: 0.7997 (mppt) cc_final: 0.7564 (ttmm) REVERT: G 164 GLU cc_start: 0.7941 (pm20) cc_final: 0.7398 (pm20) REVERT: G 165 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7545 (mp0) REVERT: G 167 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8024 (mp0) REVERT: H 46 ASP cc_start: 0.9006 (m-30) cc_final: 0.8641 (m-30) REVERT: H 73 ASN cc_start: 0.8752 (p0) cc_final: 0.8206 (p0) REVERT: H 105 ARG cc_start: 0.8718 (mpt180) cc_final: 0.8473 (tpp-160) REVERT: H 124 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8427 (t80) REVERT: H 147 GLN cc_start: 0.7693 (mm110) cc_final: 0.7459 (mm110) REVERT: H 148 LYS cc_start: 0.8096 (mppt) cc_final: 0.7837 (tttt) REVERT: H 165 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7731 (mt-10) outliers start: 18 outliers final: 14 residues processed: 373 average time/residue: 0.1330 time to fit residues: 70.3932 Evaluate side-chains 376 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 358 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 124 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 0.0370 chunk 129 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.163741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.105871 restraints weight = 18335.558| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.38 r_work: 0.2965 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15048 Z= 0.117 Angle : 0.508 6.687 20408 Z= 0.264 Chirality : 0.036 0.123 2336 Planarity : 0.004 0.046 2504 Dihedral : 3.379 16.645 2144 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.51 % Allowed : 19.74 % Favored : 78.75 % 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: 3.20 (0.20), residues: 1792 helix: 2.97 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -1.62 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 176 TYR 0.016 0.001 TYR G 142 PHE 0.006 0.001 PHE C 124 TRP 0.005 0.001 TRP H 62 HIS 0.005 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00285 (15024) covalent geometry : angle 0.50167 (20352) SS BOND : bond 0.00297 ( 16) SS BOND : angle 0.89859 ( 32) hydrogen bonds : bond 0.03668 ( 1049) hydrogen bonds : angle 3.01423 ( 3147) link_NAG-ASN : bond 0.00049 ( 8) link_NAG-ASN : angle 2.26920 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 367 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.6693 (tm-30) cc_final: 0.6252 (tp40) REVERT: A 46 ASP cc_start: 0.9047 (m-30) cc_final: 0.8837 (m-30) REVERT: A 73 ASN cc_start: 0.8528 (p0) cc_final: 0.8175 (p0) REVERT: A 79 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7501 (tp30) REVERT: A 105 ARG cc_start: 0.8688 (mpt180) cc_final: 0.8425 (tpp-160) REVERT: A 142 TYR cc_start: 0.8401 (m-80) cc_final: 0.8184 (m-80) REVERT: A 143 GLN cc_start: 0.7937 (mm110) cc_final: 0.7610 (mm-40) REVERT: A 147 GLN cc_start: 0.7666 (mm110) cc_final: 0.7394 (mm110) REVERT: A 148 LYS cc_start: 0.7995 (mppt) cc_final: 0.7576 (ttmm) REVERT: A 164 GLU cc_start: 0.7949 (pm20) cc_final: 0.7414 (pm20) REVERT: A 165 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7546 (mp0) REVERT: A 167 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8041 (mp0) REVERT: B 46 ASP cc_start: 0.8982 (m-30) cc_final: 0.8621 (m-30) REVERT: B 73 ASN cc_start: 0.8727 (p0) cc_final: 0.8158 (p0) REVERT: B 79 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7542 (tp30) REVERT: B 105 ARG cc_start: 0.8719 (mpt180) cc_final: 0.8474 (tpp-160) REVERT: B 124 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8381 (t80) REVERT: B 164 GLU cc_start: 0.7745 (pm20) cc_final: 0.7375 (pm20) REVERT: B 167 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8081 (mp0) REVERT: C 32 GLN cc_start: 0.6702 (tm-30) cc_final: 0.6330 (tp40) REVERT: C 46 ASP cc_start: 0.9051 (m-30) cc_final: 0.8841 (m-30) REVERT: C 73 ASN cc_start: 0.8525 (p0) cc_final: 0.8177 (p0) REVERT: C 79 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7514 (tp30) REVERT: C 142 TYR cc_start: 0.8279 (m-80) cc_final: 0.7992 (m-80) REVERT: C 143 GLN cc_start: 0.7954 (mm110) cc_final: 0.7634 (mm-40) REVERT: C 147 GLN cc_start: 0.7613 (mm110) cc_final: 0.7331 (mm110) REVERT: C 148 LYS cc_start: 0.7984 (mppt) cc_final: 0.7554 (ttmm) REVERT: C 165 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7591 (mp0) REVERT: D 46 ASP cc_start: 0.9000 (m-30) cc_final: 0.8636 (m-30) REVERT: D 73 ASN cc_start: 0.8698 (p0) cc_final: 0.8149 (p0) REVERT: D 79 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7526 (tp30) REVERT: D 105 ARG cc_start: 0.8714 (mpt180) cc_final: 0.8472 (tpp-160) REVERT: D 124 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8384 (t80) REVERT: E 32 GLN cc_start: 0.6698 (tm-30) cc_final: 0.6257 (tp40) REVERT: E 46 ASP cc_start: 0.9066 (m-30) cc_final: 0.8860 (m-30) REVERT: E 73 ASN cc_start: 0.8523 (p0) cc_final: 0.8170 (p0) REVERT: E 79 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7509 (tp30) REVERT: E 142 TYR cc_start: 0.8285 (m-80) cc_final: 0.8004 (m-80) REVERT: E 143 GLN cc_start: 0.7961 (mm110) cc_final: 0.7641 (mm-40) REVERT: E 147 GLN cc_start: 0.7610 (mm110) cc_final: 0.7329 (mm110) REVERT: E 148 LYS cc_start: 0.7987 (mppt) cc_final: 0.7558 (ttmm) REVERT: E 165 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7596 (mp0) REVERT: F 38 GLU cc_start: 0.8279 (tp30) cc_final: 0.8016 (tp30) REVERT: F 46 ASP cc_start: 0.9014 (m-30) cc_final: 0.8653 (m-30) REVERT: F 73 ASN cc_start: 0.8698 (p0) cc_final: 0.8151 (p0) REVERT: F 79 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7519 (tp30) REVERT: F 105 ARG cc_start: 0.8703 (mpt180) cc_final: 0.8466 (tpp-160) REVERT: F 124 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8385 (t80) REVERT: F 147 GLN cc_start: 0.7713 (mm110) cc_final: 0.7500 (mm110) REVERT: F 148 LYS cc_start: 0.8088 (mppt) cc_final: 0.7867 (tttt) REVERT: G 32 GLN cc_start: 0.6701 (tm-30) cc_final: 0.6261 (tp40) REVERT: G 46 ASP cc_start: 0.9048 (m-30) cc_final: 0.8840 (m-30) REVERT: G 73 ASN cc_start: 0.8501 (p0) cc_final: 0.8167 (p0) REVERT: G 79 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7504 (tp30) REVERT: G 133 ASP cc_start: 0.8990 (t70) cc_final: 0.8761 (t0) REVERT: G 142 TYR cc_start: 0.8363 (m-80) cc_final: 0.8147 (m-80) REVERT: G 143 GLN cc_start: 0.7990 (mm110) cc_final: 0.7679 (mm-40) REVERT: G 147 GLN cc_start: 0.7673 (mm110) cc_final: 0.7396 (mm110) REVERT: G 148 LYS cc_start: 0.8000 (mppt) cc_final: 0.7575 (ttmm) REVERT: G 164 GLU cc_start: 0.7940 (pm20) cc_final: 0.7408 (pm20) REVERT: G 165 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7543 (mp0) REVERT: G 167 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8032 (mp0) REVERT: H 46 ASP cc_start: 0.8993 (m-30) cc_final: 0.8633 (m-30) REVERT: H 73 ASN cc_start: 0.8734 (p0) cc_final: 0.8178 (p0) REVERT: H 105 ARG cc_start: 0.8708 (mpt180) cc_final: 0.8469 (tpp-160) REVERT: H 124 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8387 (t80) REVERT: H 147 GLN cc_start: 0.7717 (mm110) cc_final: 0.7504 (mm110) REVERT: H 148 LYS cc_start: 0.8117 (mppt) cc_final: 0.7851 (tttt) REVERT: H 165 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7741 (mt-10) REVERT: H 167 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8090 (mp0) outliers start: 23 outliers final: 15 residues processed: 375 average time/residue: 0.1315 time to fit residues: 70.7170 Evaluate side-chains 385 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 366 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 142 TYR Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 124 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 31 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 161 optimal weight: 50.0000 chunk 101 optimal weight: 0.0970 chunk 61 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.163355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.105048 restraints weight = 18228.423| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.36 r_work: 0.2944 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15048 Z= 0.144 Angle : 0.526 5.618 20408 Z= 0.273 Chirality : 0.037 0.126 2336 Planarity : 0.004 0.047 2504 Dihedral : 3.405 16.486 2144 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.32 % Allowed : 20.00 % Favored : 78.68 % 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: 3.18 (0.20), residues: 1792 helix: 2.95 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -1.59 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 176 TYR 0.015 0.001 TYR E 142 PHE 0.007 0.001 PHE F 124 TRP 0.004 0.001 TRP E 187 HIS 0.005 0.001 HIS C 220 Details of bonding type rmsd covalent geometry : bond 0.00366 (15024) covalent geometry : angle 0.51799 (20352) SS BOND : bond 0.00406 ( 16) SS BOND : angle 1.08133 ( 32) hydrogen bonds : bond 0.03977 ( 1049) hydrogen bonds : angle 3.09599 ( 3147) link_NAG-ASN : bond 0.00142 ( 8) link_NAG-ASN : angle 2.45308 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 364 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.6699 (tm-30) cc_final: 0.6314 (tp40) REVERT: A 46 ASP cc_start: 0.9043 (m-30) cc_final: 0.8829 (m-30) REVERT: A 73 ASN cc_start: 0.8544 (p0) cc_final: 0.8190 (p0) REVERT: A 79 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7517 (tp30) REVERT: A 105 ARG cc_start: 0.8726 (mpt180) cc_final: 0.8466 (tpp-160) REVERT: A 143 GLN cc_start: 0.8041 (mm110) cc_final: 0.7761 (mm-40) REVERT: A 147 GLN cc_start: 0.7691 (mm110) cc_final: 0.7437 (mm110) REVERT: A 148 LYS cc_start: 0.7994 (mppt) cc_final: 0.7585 (ttmm) REVERT: A 164 GLU cc_start: 0.7947 (pm20) cc_final: 0.7426 (pm20) REVERT: A 165 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7601 (mp0) REVERT: A 167 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8037 (mp0) REVERT: B 46 ASP cc_start: 0.8984 (m-30) cc_final: 0.8583 (m-30) REVERT: B 73 ASN cc_start: 0.8735 (p0) cc_final: 0.8191 (p0) REVERT: B 79 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7595 (tp30) REVERT: B 105 ARG cc_start: 0.8733 (mpt180) cc_final: 0.8477 (tpp-160) REVERT: B 124 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8428 (t80) REVERT: B 164 GLU cc_start: 0.7776 (pm20) cc_final: 0.7521 (pm20) REVERT: B 165 GLU cc_start: 0.7603 (mp0) cc_final: 0.7067 (mp0) REVERT: B 167 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8124 (mp0) REVERT: C 32 GLN cc_start: 0.6710 (tm-30) cc_final: 0.6326 (tp40) REVERT: C 46 ASP cc_start: 0.9043 (m-30) cc_final: 0.8828 (m-30) REVERT: C 73 ASN cc_start: 0.8541 (p0) cc_final: 0.8186 (p0) REVERT: C 79 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7516 (tp30) REVERT: C 142 TYR cc_start: 0.8294 (m-80) cc_final: 0.8020 (m-80) REVERT: C 143 GLN cc_start: 0.7982 (mm110) cc_final: 0.7668 (mm-40) REVERT: C 147 GLN cc_start: 0.7684 (mm110) cc_final: 0.7423 (mm110) REVERT: C 148 LYS cc_start: 0.8005 (mppt) cc_final: 0.7583 (ttmm) REVERT: C 165 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7669 (mp0) REVERT: D 46 ASP cc_start: 0.9000 (m-30) cc_final: 0.8600 (m-30) REVERT: D 73 ASN cc_start: 0.8747 (p0) cc_final: 0.8193 (p0) REVERT: D 79 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7574 (tp30) REVERT: D 105 ARG cc_start: 0.8738 (mpt180) cc_final: 0.8485 (tpp-160) REVERT: D 124 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.8435 (t80) REVERT: D 165 GLU cc_start: 0.7786 (mp0) cc_final: 0.7448 (mp0) REVERT: D 167 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8141 (mp0) REVERT: E 32 GLN cc_start: 0.6702 (tm-30) cc_final: 0.6320 (tp40) REVERT: E 46 ASP cc_start: 0.9066 (m-30) cc_final: 0.8851 (m-30) REVERT: E 73 ASN cc_start: 0.8539 (p0) cc_final: 0.8184 (p0) REVERT: E 79 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7503 (tp30) REVERT: E 142 TYR cc_start: 0.8303 (m-80) cc_final: 0.8037 (m-80) REVERT: E 143 GLN cc_start: 0.7985 (mm110) cc_final: 0.7668 (mm-40) REVERT: E 147 GLN cc_start: 0.7678 (mm110) cc_final: 0.7415 (mm110) REVERT: E 148 LYS cc_start: 0.8011 (mppt) cc_final: 0.7584 (ttmm) REVERT: E 165 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7681 (mp0) REVERT: F 38 GLU cc_start: 0.8284 (tp30) cc_final: 0.8020 (tp30) REVERT: F 46 ASP cc_start: 0.9024 (m-30) cc_final: 0.8628 (m-30) REVERT: F 73 ASN cc_start: 0.8705 (p0) cc_final: 0.8169 (p0) REVERT: F 79 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7539 (tp30) REVERT: F 105 ARG cc_start: 0.8731 (mpt180) cc_final: 0.8477 (tpp-160) REVERT: F 124 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8446 (t80) REVERT: F 147 GLN cc_start: 0.7765 (mm110) cc_final: 0.7564 (mm110) REVERT: F 148 LYS cc_start: 0.8102 (mppt) cc_final: 0.7850 (tttt) REVERT: G 32 GLN cc_start: 0.6692 (tm-30) cc_final: 0.6310 (tp40) REVERT: G 46 ASP cc_start: 0.9043 (m-30) cc_final: 0.8828 (m-30) REVERT: G 73 ASN cc_start: 0.8520 (p0) cc_final: 0.8179 (p0) REVERT: G 133 ASP cc_start: 0.8990 (t70) cc_final: 0.8771 (t0) REVERT: G 143 GLN cc_start: 0.8000 (mm110) cc_final: 0.7687 (mm-40) REVERT: G 147 GLN cc_start: 0.7691 (mm110) cc_final: 0.7429 (mm110) REVERT: G 148 LYS cc_start: 0.8006 (mppt) cc_final: 0.7586 (ttmm) REVERT: G 164 GLU cc_start: 0.7940 (pm20) cc_final: 0.7420 (pm20) REVERT: G 165 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7602 (mp0) REVERT: G 167 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8038 (mp0) REVERT: H 46 ASP cc_start: 0.9003 (m-30) cc_final: 0.8605 (m-30) REVERT: H 73 ASN cc_start: 0.8735 (p0) cc_final: 0.8172 (p0) REVERT: H 105 ARG cc_start: 0.8737 (mpt180) cc_final: 0.8482 (tpp-160) REVERT: H 124 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8444 (t80) REVERT: H 148 LYS cc_start: 0.8097 (mppt) cc_final: 0.7842 (tttt) REVERT: H 165 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7716 (mp0) REVERT: H 167 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8110 (mp0) outliers start: 20 outliers final: 13 residues processed: 368 average time/residue: 0.1372 time to fit residues: 71.4624 Evaluate side-chains 347 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 330 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 124 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 141 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 165 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 59 optimal weight: 0.0980 chunk 36 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.164335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.106350 restraints weight = 18304.853| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.38 r_work: 0.2977 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15048 Z= 0.111 Angle : 0.498 5.407 20408 Z= 0.258 Chirality : 0.036 0.122 2336 Planarity : 0.004 0.046 2504 Dihedral : 3.331 16.781 2144 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.05 % Allowed : 20.46 % Favored : 78.49 % 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: 3.32 (0.20), residues: 1792 helix: 3.01 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : -1.55 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 83 TYR 0.015 0.001 TYR D 142 PHE 0.006 0.001 PHE G 124 TRP 0.007 0.001 TRP B 62 HIS 0.005 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00265 (15024) covalent geometry : angle 0.49200 (20352) SS BOND : bond 0.00274 ( 16) SS BOND : angle 0.81957 ( 32) hydrogen bonds : bond 0.03513 ( 1049) hydrogen bonds : angle 2.97487 ( 3147) link_NAG-ASN : bond 0.00072 ( 8) link_NAG-ASN : angle 2.20195 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3585.10 seconds wall clock time: 62 minutes 1.31 seconds (3721.31 seconds total)