Starting phenix.real_space_refine on Sat Sep 12 07:57:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6lyg_30016/09_2026/6lyg_30016.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lyg_30016/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6lyg_30016/09_2026/6lyg_30016.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6lyg_30016/09_2026/6lyg_30016.cif" model { file = "/net/cci-nas-00/data/ceres_data/6lyg_30016/09_2026/6lyg_30016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lyg_30016/09_2026/6lyg_30016.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lyg_30016/09_2026/6lyg_30016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lyg_30016/09_2026/6lyg_30016.map" } 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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 3.45, 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: 1.26 Conformation dependent library (CDL) restraints added in 715.9 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: 0.32 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: 2.26 Time building geometry restraints manager: 1.72 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: 8095 17.00 - 34.00: 629 34.00 - 51.00: 140 51.00 - 67.99: 48 67.99 - 84.99: 24 Dihedral angle restraints: 8936 sinusoidal: 3432 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 8933 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: 0.05 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: 1.240 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.320 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 14.396 84.992 5288 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/Z covalent geometry : bond 0.00366 / 0.17 (15024) covalent geometry : angle 0.57975 / 0.36 (20352) SS BOND : bond 0.00165 / 0.12 ( 16) SS BOND : angle 0.84466 / 0.67 ( 32) hydrogen bonds : bond 0.11933 / 7.60 ( 1049) hydrogen bonds : angle 4.57574 / 3.35 ( 3147) link_NAG-ASN : bond 0.00416 / 0.28 ( 8) link_NAG-ASN : angle 3.35034 / 2.59 ( 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 : 0.596 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: 0.1539 time to fit residues: 108.0645 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 : 0.568 ------------------------------------------------------------------------------- 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... A 236 HIS C 236 HIS E 236 HIS G 236 HIS H 236 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.157925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.100349 restraints weight = 18249.674| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.33 r_work: 0.2863 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 15048 Z= 0.295 Angle : 0.651 5.903 20408 Z= 0.336 Chirality : 0.043 0.150 2336 Planarity : 0.005 0.051 2504 Dihedral : 3.831 16.149 1976 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.22 % Allowed : 19.67 % Favored : 77.11 % 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: 1.48 (0.20), residues: 1792 helix: 1.83 (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 0.010 0.002 PHE F 124 TRP 0.009 0.001 TRP G 81 HIS 0.005 0.002 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00752 / 0.29 (15024) covalent geometry : angle 0.63900 / 0.33 (20352) SS BOND : bond 0.00697 / 0.52 ( 16) SS BOND : angle 1.88348 / 1.45 ( 32) hydrogen bonds : bond 0.05646 / 3.76 ( 1049) hydrogen bonds : angle 3.68802 / 2.69 ( 3147) link_NAG-ASN : bond 0.00550 / 0.37 ( 8) link_NAG-ASN : angle 3.05689 / 2.36 ( 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 404 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 355 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.6824 (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: 0.8864 (mmm) REVERT: A 71 ASN cc_start: 0.9025 (t0) cc_final: 0.8705 (t0) REVERT: A 105 ARG cc_start: 0.8791 (mpt180) cc_final: 0.8568 (tpp-160) REVERT: A 143 GLN cc_start: 0.7710 (mm110) cc_final: 0.7465 (mm110) REVERT: A 147 GLN cc_start: 0.7504 (mm110) cc_final: 0.7182 (mm110) REVERT: A 148 LYS cc_start: 0.8377 (mppt) cc_final: 0.7740 (ttmt) REVERT: A 165 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7920 (mp0) REVERT: A 227 LYS cc_start: 0.7330 (tmtt) cc_final: 0.7092 (tptt) REVERT: A 240 PHE cc_start: 0.8046 (m-80) cc_final: 0.7788 (m-80) REVERT: B 46 ASP cc_start: 0.9196 (m-30) cc_final: 0.8791 (m-30) REVERT: B 105 ARG cc_start: 0.8875 (mpt180) cc_final: 0.8667 (tpp-160) REVERT: B 124 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8573 (t80) REVERT: B 148 LYS cc_start: 0.8440 (mmtm) cc_final: 0.7883 (tttt) REVERT: B 165 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7866 (mp0) REVERT: B 227 LYS cc_start: 0.7319 (tmtt) cc_final: 0.7072 (tptt) REVERT: C 32 GLN cc_start: 0.6825 (tm-30) cc_final: 0.6358 (tp40) REVERT: C 46 ASP cc_start: 0.9228 (m-30) cc_final: 0.8986 (m-30) REVERT: C 70 MET cc_start: 0.9069 (mmm) cc_final: 0.8863 (mmm) REVERT: C 71 ASN cc_start: 0.9020 (t0) cc_final: 0.8700 (t0) REVERT: C 105 ARG cc_start: 0.8794 (mpt180) cc_final: 0.8572 (tpp-160) REVERT: C 143 GLN cc_start: 0.7699 (mm110) cc_final: 0.7452 (mm110) REVERT: C 147 GLN cc_start: 0.7498 (mm110) cc_final: 0.7176 (mm110) REVERT: C 148 LYS cc_start: 0.8379 (mppt) cc_final: 0.7741 (ttmt) REVERT: C 165 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7908 (mp0) REVERT: C 227 LYS cc_start: 0.7324 (tmtt) cc_final: 0.7091 (tptt) REVERT: C 240 PHE cc_start: 0.8045 (m-80) cc_final: 0.7784 (m-80) REVERT: D 46 ASP cc_start: 0.9209 (m-30) cc_final: 0.8804 (m-30) REVERT: D 105 ARG cc_start: 0.8879 (mpt180) cc_final: 0.8673 (tpp-160) REVERT: D 124 PHE cc_start: 0.9159 (OUTLIER) cc_final: 0.8573 (t80) REVERT: D 148 LYS cc_start: 0.8445 (mmtm) cc_final: 0.7837 (tttt) REVERT: D 165 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7867 (mp0) REVERT: E 32 GLN cc_start: 0.6832 (tm-30) cc_final: 0.6363 (tp40) REVERT: E 46 ASP cc_start: 0.9228 (m-30) cc_final: 0.8987 (m-30) REVERT: E 70 MET cc_start: 0.9073 (mmm) cc_final: 0.8867 (mmm) REVERT: E 71 ASN cc_start: 0.9020 (t0) cc_final: 0.8700 (t0) REVERT: E 105 ARG cc_start: 0.8785 (mpt180) cc_final: 0.8561 (tpp-160) REVERT: E 143 GLN cc_start: 0.7706 (mm110) cc_final: 0.7458 (mm110) REVERT: E 147 GLN cc_start: 0.7511 (mm110) cc_final: 0.7189 (mm110) REVERT: E 148 LYS cc_start: 0.8379 (mppt) cc_final: 0.7743 (ttmt) REVERT: E 165 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7928 (mp0) REVERT: E 227 LYS cc_start: 0.7326 (tmtt) cc_final: 0.7088 (tptt) REVERT: E 240 PHE cc_start: 0.8045 (m-80) cc_final: 0.7786 (m-80) REVERT: F 46 ASP cc_start: 0.9200 (m-30) cc_final: 0.8794 (m-30) REVERT: F 105 ARG cc_start: 0.8874 (mpt180) cc_final: 0.8669 (tpp-160) REVERT: F 124 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8578 (t80) REVERT: F 148 LYS cc_start: 0.8404 (mppt) cc_final: 0.7963 (tttt) REVERT: F 165 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7863 (mp0) REVERT: G 32 GLN cc_start: 0.6840 (tm-30) cc_final: 0.6372 (tp40) REVERT: G 46 ASP cc_start: 0.9228 (m-30) cc_final: 0.8984 (m-30) REVERT: G 70 MET cc_start: 0.9066 (mmm) cc_final: 0.8864 (mmm) REVERT: G 71 ASN cc_start: 0.9020 (t0) cc_final: 0.8699 (t0) REVERT: G 105 ARG cc_start: 0.8786 (mpt180) cc_final: 0.8564 (tpp-160) REVERT: G 143 GLN cc_start: 0.7714 (mm110) cc_final: 0.7466 (mm110) REVERT: G 147 GLN cc_start: 0.7511 (mm110) cc_final: 0.7189 (mm110) REVERT: G 148 LYS cc_start: 0.8373 (mppt) cc_final: 0.7738 (ttmt) REVERT: G 165 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7933 (mp0) REVERT: G 227 LYS cc_start: 0.7339 (tmtt) cc_final: 0.7104 (tptt) REVERT: G 240 PHE cc_start: 0.8041 (m-80) cc_final: 0.7782 (m-80) REVERT: H 46 ASP cc_start: 0.9196 (m-30) cc_final: 0.8744 (m-30) REVERT: H 105 ARG cc_start: 0.8874 (mpt180) cc_final: 0.8668 (tpp-160) REVERT: H 124 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8570 (t80) REVERT: H 148 LYS cc_start: 0.8416 (mppt) cc_final: 0.7967 (tttt) REVERT: H 165 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7868 (mp0) REVERT: H 227 LYS cc_start: 0.7320 (tmtt) cc_final: 0.7075 (tptt) outliers start: 49 outliers final: 20 residues processed: 377 average time/residue: 0.1359 time to fit residues: 73.5150 Evaluate side-chains 366 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 342 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU 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 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 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 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: 3.9990 chunk 98 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN B 71 ASN C 71 ASN D 71 ASN E 71 ASN F 71 ASN G 71 ASN H 71 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.160801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.103530 restraints weight = 18354.562| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.36 r_work: 0.2920 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15048 Z= 0.151 Angle : 0.529 5.673 20408 Z= 0.275 Chirality : 0.038 0.126 2336 Planarity : 0.004 0.047 2504 Dihedral : 3.689 17.206 1976 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.12 % Allowed : 21.38 % Favored : 77.50 % 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: 2.37 (0.20), residues: 1792 helix: 2.44 (0.13), residues: 1408 sheet: None (None), residues: 0 loop : -1.96 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 176 TYR 0.022 0.002 TYR E 142 PHE 0.008 0.001 PHE E 124 TRP 0.005 0.001 TRP G 81 HIS 0.003 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.15 (15024) covalent geometry : angle 0.51809 / 0.27 (20352) SS BOND : bond 0.00393 / 0.29 ( 16) SS BOND : angle 1.20089 / 0.93 ( 32) hydrogen bonds : bond 0.04565 / 3.05 ( 1049) hydrogen bonds : angle 3.37166 / 2.46 ( 3147) link_NAG-ASN : bond 0.00250 / 0.18 ( 8) link_NAG-ASN : angle 2.91399 / 2.27 ( 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 431 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 414 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: 0.6936 (tm-30) cc_final: 0.6492 (tp40) REVERT: A 46 ASP cc_start: 0.9237 (m-30) cc_final: 0.9005 (m-30) REVERT: A 71 ASN cc_start: 0.9004 (OUTLIER) cc_final: 0.8558 (t0) REVERT: A 79 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7589 (tp30) REVERT: A 105 ARG cc_start: 0.8703 (mpt180) cc_final: 0.8487 (tpp-160) REVERT: A 143 GLN cc_start: 0.8004 (mm110) cc_final: 0.7634 (mm110) REVERT: A 147 GLN cc_start: 0.7429 (mm110) cc_final: 0.7156 (mm110) REVERT: A 148 LYS cc_start: 0.8306 (mppt) cc_final: 0.7751 (ttmm) REVERT: A 165 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7525 (mt-10) REVERT: A 227 LYS cc_start: 0.7341 (tmtt) cc_final: 0.7125 (tptt) REVERT: A 240 PHE cc_start: 0.7961 (m-80) cc_final: 0.7624 (m-80) REVERT: B 46 ASP cc_start: 0.9167 (m-30) cc_final: 0.8777 (m-30) REVERT: B 73 ASN cc_start: 0.8876 (p0) cc_final: 0.8485 (p0) REVERT: B 79 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7701 (tp30) REVERT: B 105 ARG cc_start: 0.8807 (mpt180) cc_final: 0.8599 (tpp-160) REVERT: B 124 PHE cc_start: 0.9122 (OUTLIER) cc_final: 0.8522 (t80) REVERT: B 148 LYS cc_start: 0.8357 (mmtm) cc_final: 0.7891 (tttt) REVERT: B 165 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7911 (mp0) REVERT: B 167 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7959 (mp0) REVERT: B 227 LYS cc_start: 0.7314 (tmtt) cc_final: 0.7074 (tptt) REVERT: C 32 GLN cc_start: 0.6943 (tm-30) cc_final: 0.6501 (tp40) REVERT: C 46 ASP cc_start: 0.9240 (m-30) cc_final: 0.9009 (m-30) REVERT: C 71 ASN cc_start: 0.9005 (OUTLIER) cc_final: 0.8559 (t0) REVERT: C 79 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7586 (tp30) REVERT: C 105 ARG cc_start: 0.8702 (mpt180) cc_final: 0.8487 (tpp-160) REVERT: C 143 GLN cc_start: 0.8010 (mm110) cc_final: 0.7636 (mm110) REVERT: C 147 GLN cc_start: 0.7435 (mm110) cc_final: 0.7163 (mm110) REVERT: C 148 LYS cc_start: 0.8300 (mppt) cc_final: 0.7747 (ttmm) REVERT: C 165 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7514 (mt-10) REVERT: C 227 LYS cc_start: 0.7348 (tmtt) cc_final: 0.7130 (tptt) REVERT: C 240 PHE cc_start: 0.7963 (m-80) cc_final: 0.7626 (m-80) REVERT: D 46 ASP cc_start: 0.9179 (m-30) cc_final: 0.8784 (m-30) REVERT: D 73 ASN cc_start: 0.8881 (p0) cc_final: 0.8495 (p0) REVERT: D 79 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7687 (tp30) REVERT: D 105 ARG cc_start: 0.8807 (mpt180) cc_final: 0.8600 (tpp-160) REVERT: D 124 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8536 (t80) REVERT: D 148 LYS cc_start: 0.8382 (mmtm) cc_final: 0.7857 (tttt) REVERT: D 165 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7908 (mp0) REVERT: D 167 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8009 (mp0) REVERT: E 32 GLN cc_start: 0.6947 (tm-30) cc_final: 0.6505 (tp40) REVERT: E 46 ASP cc_start: 0.9241 (m-30) cc_final: 0.9010 (m-30) REVERT: E 71 ASN cc_start: 0.8999 (OUTLIER) cc_final: 0.8552 (t0) REVERT: E 79 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7593 (tp30) REVERT: E 105 ARG cc_start: 0.8698 (mpt180) cc_final: 0.8483 (tpp-160) REVERT: E 143 GLN cc_start: 0.8018 (mm110) cc_final: 0.7642 (mm110) REVERT: E 147 GLN cc_start: 0.7430 (mm110) cc_final: 0.7157 (mm110) REVERT: E 148 LYS cc_start: 0.8307 (mppt) cc_final: 0.7752 (ttmm) REVERT: E 165 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7526 (mt-10) REVERT: E 227 LYS cc_start: 0.7347 (tmtt) cc_final: 0.7129 (tptt) REVERT: E 240 PHE cc_start: 0.7959 (m-80) cc_final: 0.7623 (m-80) REVERT: F 46 ASP cc_start: 0.9180 (m-30) cc_final: 0.8789 (m-30) REVERT: F 73 ASN cc_start: 0.8879 (p0) cc_final: 0.8493 (p0) REVERT: F 79 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7688 (tp30) REVERT: F 105 ARG cc_start: 0.8800 (mpt180) cc_final: 0.8594 (tpp-160) REVERT: F 124 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8533 (t80) REVERT: F 148 LYS cc_start: 0.8363 (mppt) cc_final: 0.7985 (tttt) REVERT: F 165 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7929 (mp0) REVERT: F 167 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8040 (mp0) REVERT: G 32 GLN cc_start: 0.6940 (tm-30) cc_final: 0.6497 (tp40) REVERT: G 46 ASP cc_start: 0.9235 (m-30) cc_final: 0.9005 (m-30) REVERT: G 71 ASN cc_start: 0.9001 (OUTLIER) cc_final: 0.8555 (t0) REVERT: G 79 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7597 (tp30) REVERT: G 105 ARG cc_start: 0.8696 (mpt180) cc_final: 0.8484 (tpp-160) REVERT: G 143 GLN cc_start: 0.8014 (mm110) cc_final: 0.7641 (mm110) REVERT: G 147 GLN cc_start: 0.7440 (mm110) cc_final: 0.7167 (mm110) REVERT: G 148 LYS cc_start: 0.8298 (mppt) cc_final: 0.7749 (ttmm) REVERT: G 165 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7530 (mt-10) REVERT: G 227 LYS cc_start: 0.7338 (tmtt) cc_final: 0.7122 (tptt) REVERT: G 240 PHE cc_start: 0.7961 (m-80) cc_final: 0.7621 (m-80) REVERT: H 46 ASP cc_start: 0.9168 (m-30) cc_final: 0.8778 (m-30) REVERT: H 73 ASN cc_start: 0.8876 (p0) cc_final: 0.8489 (p0) REVERT: H 79 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7639 (tp30) REVERT: H 105 ARG cc_start: 0.8806 (mpt180) cc_final: 0.8600 (tpp-160) REVERT: H 124 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8535 (t80) REVERT: H 148 LYS cc_start: 0.8360 (mppt) cc_final: 0.7983 (tttt) REVERT: H 165 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7911 (mp0) REVERT: H 167 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8068 (mp0) REVERT: H 227 LYS cc_start: 0.7300 (tmtt) cc_final: 0.7064 (tptt) outliers start: 17 outliers final: 4 residues processed: 418 average time/residue: 0.1325 time to fit residues: 79.7870 Evaluate side-chains 375 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 363 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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: 0.6980 chunk 35 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.162598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.105327 restraints weight = 18268.825| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.37 r_work: 0.2941 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2590 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= 0.120 Angle : 0.504 5.470 20408 Z= 0.262 Chirality : 0.036 0.123 2336 Planarity : 0.004 0.045 2504 Dihedral : 3.601 17.167 1976 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.58 % Allowed : 20.99 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.20), residues: 1792 helix: 2.68 (0.13), residues: 1408 sheet: None (None), residues: 0 loop : -1.79 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 204 TYR 0.015 0.001 TYR E 142 PHE 0.007 0.001 PHE G 124 TRP 0.006 0.001 TRP F 62 HIS 0.003 0.001 HIS F 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (15024) covalent geometry : angle 0.49367 / 0.26 (20352) SS BOND : bond 0.00301 / 0.22 ( 16) SS BOND : angle 0.97125 / 0.75 ( 32) hydrogen bonds : bond 0.04120 / 2.76 ( 1049) hydrogen bonds : angle 3.22697 / 2.36 ( 3147) link_NAG-ASN : bond 0.00033 / 0.02 ( 8) link_NAG-ASN : angle 2.81672 / 2.19 ( 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 385 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 361 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.6929 (tm-30) cc_final: 0.6540 (tp40) REVERT: A 46 ASP cc_start: 0.9062 (m-30) cc_final: 0.8834 (m-30) REVERT: A 79 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7509 (tp30) REVERT: A 105 ARG cc_start: 0.8563 (mpt180) cc_final: 0.8358 (tpp-160) REVERT: A 143 GLN cc_start: 0.7924 (mm110) cc_final: 0.7595 (mm110) REVERT: A 147 GLN cc_start: 0.7361 (mm110) cc_final: 0.7129 (mm110) REVERT: A 148 LYS cc_start: 0.8062 (mppt) cc_final: 0.7611 (ttmm) REVERT: A 165 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7287 (mt-10) REVERT: A 227 LYS cc_start: 0.7352 (tmtt) cc_final: 0.7151 (tptt) REVERT: B 46 ASP cc_start: 0.8991 (m-30) cc_final: 0.8627 (m-30) REVERT: B 73 ASN cc_start: 0.8792 (p0) cc_final: 0.8363 (p0) REVERT: B 105 ARG cc_start: 0.8698 (mpt180) cc_final: 0.8475 (tpp-160) REVERT: B 148 LYS cc_start: 0.8143 (mmtm) cc_final: 0.7859 (tttt) REVERT: B 165 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7485 (mt-10) REVERT: B 227 LYS cc_start: 0.7282 (tmtt) cc_final: 0.7072 (tptt) REVERT: C 32 GLN cc_start: 0.6925 (tm-30) cc_final: 0.6537 (tp40) REVERT: C 46 ASP cc_start: 0.9065 (m-30) cc_final: 0.8835 (m-30) REVERT: C 79 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7508 (tp30) REVERT: C 105 ARG cc_start: 0.8560 (mpt180) cc_final: 0.8357 (tpp-160) REVERT: C 143 GLN cc_start: 0.7924 (mm110) cc_final: 0.7594 (mm110) REVERT: C 147 GLN cc_start: 0.7372 (mm110) cc_final: 0.7137 (mm110) REVERT: C 148 LYS cc_start: 0.8064 (mppt) cc_final: 0.7611 (ttmm) REVERT: C 165 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7283 (mt-10) REVERT: C 227 LYS cc_start: 0.7355 (tmtt) cc_final: 0.7153 (tptt) REVERT: D 46 ASP cc_start: 0.8995 (m-30) cc_final: 0.8594 (m-30) REVERT: D 73 ASN cc_start: 0.8795 (p0) cc_final: 0.8365 (p0) REVERT: D 105 ARG cc_start: 0.8703 (mpt180) cc_final: 0.8482 (tpp-160) REVERT: D 148 LYS cc_start: 0.8185 (mmtm) cc_final: 0.7842 (tttt) REVERT: D 165 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7491 (mt-10) REVERT: E 32 GLN cc_start: 0.6930 (tm-30) cc_final: 0.6542 (tp40) REVERT: E 46 ASP cc_start: 0.9056 (m-30) cc_final: 0.8827 (m-30) REVERT: E 79 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7507 (tp30) REVERT: E 105 ARG cc_start: 0.8558 (mpt180) cc_final: 0.8355 (tpp-160) REVERT: E 143 GLN cc_start: 0.7932 (mm110) cc_final: 0.7599 (mm110) REVERT: E 147 GLN cc_start: 0.7371 (mm110) cc_final: 0.7140 (mm110) REVERT: E 148 LYS cc_start: 0.8059 (mppt) cc_final: 0.7610 (ttmm) REVERT: E 165 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7301 (mt-10) REVERT: F 46 ASP cc_start: 0.8994 (m-30) cc_final: 0.8629 (m-30) REVERT: F 73 ASN cc_start: 0.8794 (p0) cc_final: 0.8364 (p0) REVERT: F 105 ARG cc_start: 0.8693 (mpt180) cc_final: 0.8474 (tpp-160) REVERT: F 148 LYS cc_start: 0.8167 (mppt) cc_final: 0.7916 (tttt) REVERT: F 164 GLU cc_start: 0.7964 (pm20) cc_final: 0.7354 (pm20) REVERT: F 165 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7727 (mp0) REVERT: G 32 GLN cc_start: 0.6923 (tm-30) cc_final: 0.6534 (tp40) REVERT: G 46 ASP cc_start: 0.9050 (m-30) cc_final: 0.8823 (m-30) REVERT: G 79 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7511 (tp30) REVERT: G 105 ARG cc_start: 0.8557 (mpt180) cc_final: 0.8354 (tpp-160) REVERT: G 143 GLN cc_start: 0.7929 (mm110) cc_final: 0.7601 (mm110) REVERT: G 147 GLN cc_start: 0.7368 (mm110) cc_final: 0.7135 (mm110) REVERT: G 148 LYS cc_start: 0.8055 (mppt) cc_final: 0.7608 (ttmm) REVERT: G 165 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7288 (mt-10) REVERT: G 227 LYS cc_start: 0.7352 (tmtt) cc_final: 0.7152 (tptt) REVERT: H 46 ASP cc_start: 0.8987 (m-30) cc_final: 0.8624 (m-30) REVERT: H 73 ASN cc_start: 0.8791 (p0) cc_final: 0.8361 (p0) REVERT: H 105 ARG cc_start: 0.8697 (mpt180) cc_final: 0.8476 (tpp-160) REVERT: H 148 LYS cc_start: 0.8175 (mppt) cc_final: 0.7920 (tttt) REVERT: H 165 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7481 (mt-10) REVERT: H 227 LYS cc_start: 0.7281 (tmtt) cc_final: 0.7073 (tptt) outliers start: 24 outliers final: 6 residues processed: 371 average time/residue: 0.1383 time to fit residues: 73.0510 Evaluate side-chains 353 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 347 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 181 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 125 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 78 optimal weight: 0.7980 chunk 151 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN C 71 ASN E 71 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.162298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.105497 restraints weight = 18248.512| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.34 r_work: 0.2956 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2706 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= 0.125 Angle : 0.508 5.566 20408 Z= 0.264 Chirality : 0.036 0.125 2336 Planarity : 0.004 0.046 2504 Dihedral : 3.554 17.086 1976 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.45 % Allowed : 20.26 % Favored : 78.29 % 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: 2.96 (0.20), residues: 1792 helix: 2.83 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.72 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 204 TYR 0.015 0.001 TYR E 142 PHE 0.007 0.001 PHE E 124 TRP 0.006 0.001 TRP F 62 HIS 0.003 0.001 HIS F 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (15024) covalent geometry : angle 0.49924 / 0.26 (20352) SS BOND : bond 0.00335 / 0.25 ( 16) SS BOND : angle 1.00976 / 0.79 ( 32) hydrogen bonds : bond 0.03964 / 2.65 ( 1049) hydrogen bonds : angle 3.14934 / 2.30 ( 3147) link_NAG-ASN : bond 0.00104 / 0.06 ( 8) link_NAG-ASN : angle 2.67011 / 2.07 ( 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 403 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 381 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.6805 (tm-30) cc_final: 0.6457 (tp40) REVERT: A 46 ASP cc_start: 0.9044 (m-30) cc_final: 0.8823 (m-30) REVERT: A 71 ASN cc_start: 0.8807 (t0) cc_final: 0.8541 (t0) REVERT: A 79 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7516 (tp30) REVERT: A 105 ARG cc_start: 0.8588 (mpt180) cc_final: 0.8373 (tpp-160) REVERT: A 143 GLN cc_start: 0.7920 (mm110) cc_final: 0.7585 (mm-40) REVERT: A 147 GLN cc_start: 0.7454 (mm110) cc_final: 0.7185 (mm110) REVERT: A 148 LYS cc_start: 0.8041 (mppt) cc_final: 0.7560 (ttmm) REVERT: A 165 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7326 (mt-10) REVERT: B 46 ASP cc_start: 0.8985 (m-30) cc_final: 0.8630 (m-30) REVERT: B 73 ASN cc_start: 0.8802 (p0) cc_final: 0.8390 (p0) REVERT: B 79 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7651 (tp30) REVERT: B 105 ARG cc_start: 0.8712 (mpt180) cc_final: 0.8481 (tpp-160) REVERT: B 124 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8371 (t80) REVERT: B 148 LYS cc_start: 0.8102 (mmtm) cc_final: 0.7847 (tttt) REVERT: B 165 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7781 (mp0) REVERT: B 167 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8082 (mp0) REVERT: B 220 HIS cc_start: 0.8319 (m-70) cc_final: 0.8107 (m170) REVERT: C 32 GLN cc_start: 0.6812 (tm-30) cc_final: 0.6461 (tp40) REVERT: C 46 ASP cc_start: 0.9052 (m-30) cc_final: 0.8832 (m-30) REVERT: C 71 ASN cc_start: 0.8805 (t0) cc_final: 0.8540 (t0) REVERT: C 79 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7522 (tp30) REVERT: C 105 ARG cc_start: 0.8601 (mpt180) cc_final: 0.8387 (tpp-160) REVERT: C 143 GLN cc_start: 0.7915 (mm110) cc_final: 0.7581 (mm-40) REVERT: C 147 GLN cc_start: 0.7471 (mm110) cc_final: 0.7198 (mm110) REVERT: C 148 LYS cc_start: 0.8048 (mppt) cc_final: 0.7561 (ttmm) REVERT: C 165 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7321 (mt-10) REVERT: D 46 ASP cc_start: 0.8995 (m-30) cc_final: 0.8596 (m-30) REVERT: D 73 ASN cc_start: 0.8808 (p0) cc_final: 0.8398 (p0) REVERT: D 79 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7607 (tp30) REVERT: D 105 ARG cc_start: 0.8714 (mpt180) cc_final: 0.8485 (tpp-160) REVERT: D 124 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8392 (t80) REVERT: D 148 LYS cc_start: 0.8122 (mmtm) cc_final: 0.7815 (tttt) REVERT: D 165 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7780 (mp0) REVERT: D 167 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8079 (mp0) REVERT: D 220 HIS cc_start: 0.8342 (m-70) cc_final: 0.8141 (m170) REVERT: E 32 GLN cc_start: 0.6816 (tm-30) cc_final: 0.6466 (tp40) REVERT: E 46 ASP cc_start: 0.9052 (m-30) cc_final: 0.8833 (m-30) REVERT: E 71 ASN cc_start: 0.8810 (t0) cc_final: 0.8547 (t0) REVERT: E 79 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7515 (tp30) REVERT: E 105 ARG cc_start: 0.8600 (mpt180) cc_final: 0.8387 (tpp-160) REVERT: E 143 GLN cc_start: 0.7928 (mm110) cc_final: 0.7591 (mm-40) REVERT: E 147 GLN cc_start: 0.7472 (mm110) cc_final: 0.7199 (mm110) REVERT: E 148 LYS cc_start: 0.8047 (mppt) cc_final: 0.7561 (ttmm) REVERT: E 165 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7329 (mt-10) REVERT: F 46 ASP cc_start: 0.8992 (m-30) cc_final: 0.8637 (m-30) REVERT: F 73 ASN cc_start: 0.8805 (p0) cc_final: 0.8395 (p0) REVERT: F 79 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7590 (tp30) REVERT: F 105 ARG cc_start: 0.8706 (mpt180) cc_final: 0.8476 (tpp-160) REVERT: F 124 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8394 (t80) REVERT: F 147 GLN cc_start: 0.7670 (mm110) cc_final: 0.7377 (mm110) REVERT: F 148 LYS cc_start: 0.8178 (mppt) cc_final: 0.7898 (tttt) REVERT: F 164 GLU cc_start: 0.7848 (pm20) cc_final: 0.7524 (pm20) REVERT: F 165 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7630 (mp0) REVERT: F 220 HIS cc_start: 0.8358 (m-70) cc_final: 0.8155 (m170) REVERT: G 32 GLN cc_start: 0.6795 (tm-30) cc_final: 0.6450 (tp40) REVERT: G 46 ASP cc_start: 0.9038 (m-30) cc_final: 0.8820 (m-30) REVERT: G 79 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7520 (tp30) REVERT: G 105 ARG cc_start: 0.8639 (mpt180) cc_final: 0.8426 (tpp-160) REVERT: G 143 GLN cc_start: 0.7916 (mm110) cc_final: 0.7583 (mm-40) REVERT: G 147 GLN cc_start: 0.7469 (mm110) cc_final: 0.7199 (mm110) REVERT: G 148 LYS cc_start: 0.8038 (mppt) cc_final: 0.7559 (ttmm) REVERT: G 165 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7317 (mt-10) REVERT: H 46 ASP cc_start: 0.8969 (m-30) cc_final: 0.8615 (m-30) REVERT: H 73 ASN cc_start: 0.8806 (p0) cc_final: 0.8395 (p0) REVERT: H 79 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7650 (tp30) REVERT: H 105 ARG cc_start: 0.8708 (mpt180) cc_final: 0.8478 (tpp-160) REVERT: H 124 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8395 (t80) REVERT: H 147 GLN cc_start: 0.7710 (mm110) cc_final: 0.7428 (mm110) REVERT: H 148 LYS cc_start: 0.8174 (mppt) cc_final: 0.7921 (tttt) REVERT: H 165 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7780 (mp0) REVERT: H 167 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8087 (mp0) outliers start: 22 outliers final: 9 residues processed: 389 average time/residue: 0.1300 time to fit residues: 72.3277 Evaluate side-chains 379 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 366 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 F residue 181 LEU Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 124 PHE Chi-restraints excluded: chain H residue 181 LEU 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: 1.9990 chunk 175 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 50.0000 chunk 170 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.162432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.104896 restraints weight = 18157.487| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.36 r_work: 0.2950 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15048 Z= 0.132 Angle : 0.516 5.624 20408 Z= 0.267 Chirality : 0.037 0.125 2336 Planarity : 0.004 0.046 2504 Dihedral : 3.546 16.982 1976 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.45 % Allowed : 20.00 % Favored : 78.55 % 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: 3.06 (0.20), residues: 1792 helix: 2.89 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.65 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 201 TYR 0.016 0.001 TYR A 142 PHE 0.007 0.001 PHE G 124 TRP 0.005 0.001 TRP F 62 HIS 0.003 0.001 HIS H 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.13 (15024) covalent geometry : angle 0.50633 / 0.26 (20352) SS BOND : bond 0.00351 / 0.26 ( 16) SS BOND : angle 1.03670 / 0.80 ( 32) hydrogen bonds : bond 0.03991 / 2.67 ( 1049) hydrogen bonds : angle 3.13697 / 2.29 ( 3147) link_NAG-ASN : bond 0.00087 / 0.06 ( 8) link_NAG-ASN : angle 2.69452 / 2.09 ( 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 386 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 364 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.6777 (tm-30) cc_final: 0.6428 (tp40) REVERT: A 46 ASP cc_start: 0.9056 (m-30) cc_final: 0.8837 (m-30) REVERT: A 71 ASN cc_start: 0.8779 (t0) cc_final: 0.8530 (t0) REVERT: A 79 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7526 (tp30) REVERT: A 105 ARG cc_start: 0.8656 (mpt180) cc_final: 0.8414 (tpp-160) REVERT: A 147 GLN cc_start: 0.7472 (mm110) cc_final: 0.7112 (mm110) REVERT: A 148 LYS cc_start: 0.8016 (mppt) cc_final: 0.7527 (ttmm) REVERT: A 165 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7332 (mt-10) REVERT: B 46 ASP cc_start: 0.8994 (m-30) cc_final: 0.8597 (m-30) REVERT: B 73 ASN cc_start: 0.8841 (p0) cc_final: 0.8393 (p0) REVERT: B 79 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7588 (tp30) REVERT: B 105 ARG cc_start: 0.8716 (mpt180) cc_final: 0.8471 (tpp-160) REVERT: B 124 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8408 (t80) REVERT: B 143 GLN cc_start: 0.7986 (mm110) cc_final: 0.7731 (mm-40) REVERT: B 147 GLN cc_start: 0.7857 (mm110) cc_final: 0.7428 (mm110) REVERT: B 148 LYS cc_start: 0.8043 (mmtm) cc_final: 0.7829 (tttt) REVERT: B 167 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8100 (mp0) REVERT: B 220 HIS cc_start: 0.8275 (m-70) cc_final: 0.8067 (m170) REVERT: C 32 GLN cc_start: 0.6779 (tm-30) cc_final: 0.6430 (tp40) REVERT: C 46 ASP cc_start: 0.9059 (m-30) cc_final: 0.8840 (m-30) REVERT: C 71 ASN cc_start: 0.8780 (t0) cc_final: 0.8528 (t0) REVERT: C 79 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7529 (tp30) REVERT: C 105 ARG cc_start: 0.8592 (mpt180) cc_final: 0.8356 (tpp-160) REVERT: C 147 GLN cc_start: 0.7485 (mm110) cc_final: 0.7125 (mm110) REVERT: C 148 LYS cc_start: 0.8022 (mppt) cc_final: 0.7530 (ttmm) REVERT: C 165 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7312 (mt-10) REVERT: D 46 ASP cc_start: 0.8999 (m-30) cc_final: 0.8595 (m-30) REVERT: D 73 ASN cc_start: 0.8844 (p0) cc_final: 0.8399 (p0) REVERT: D 79 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7590 (tp30) REVERT: D 105 ARG cc_start: 0.8719 (mpt180) cc_final: 0.8477 (tpp-160) REVERT: D 124 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8411 (t80) REVERT: D 143 GLN cc_start: 0.8050 (mm110) cc_final: 0.7793 (mm-40) REVERT: D 147 GLN cc_start: 0.7859 (mm110) cc_final: 0.7417 (mm110) REVERT: D 148 LYS cc_start: 0.8104 (mmtm) cc_final: 0.7823 (tttt) REVERT: D 167 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8089 (mp0) REVERT: E 32 GLN cc_start: 0.6784 (tm-30) cc_final: 0.6434 (tp40) REVERT: E 46 ASP cc_start: 0.9073 (m-30) cc_final: 0.8853 (m-30) REVERT: E 71 ASN cc_start: 0.8784 (t0) cc_final: 0.8534 (t0) REVERT: E 79 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7526 (tp30) REVERT: E 105 ARG cc_start: 0.8598 (mpt180) cc_final: 0.8359 (tpp-160) REVERT: E 147 GLN cc_start: 0.7483 (mm110) cc_final: 0.7126 (mm110) REVERT: E 148 LYS cc_start: 0.8016 (mppt) cc_final: 0.7525 (ttmm) REVERT: E 165 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7325 (mt-10) REVERT: F 46 ASP cc_start: 0.8998 (m-30) cc_final: 0.8602 (m-30) REVERT: F 73 ASN cc_start: 0.8840 (p0) cc_final: 0.8397 (p0) REVERT: F 79 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7571 (tp30) REVERT: F 105 ARG cc_start: 0.8712 (mpt180) cc_final: 0.8468 (tpp-160) REVERT: F 124 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8408 (t80) REVERT: F 147 GLN cc_start: 0.7683 (mm110) cc_final: 0.7409 (mm110) REVERT: F 148 LYS cc_start: 0.8126 (mppt) cc_final: 0.7870 (tttt) REVERT: F 165 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7774 (mp0) REVERT: F 220 HIS cc_start: 0.8310 (m-70) cc_final: 0.8107 (m170) REVERT: G 32 GLN cc_start: 0.6772 (tm-30) cc_final: 0.6427 (tp40) REVERT: G 46 ASP cc_start: 0.9061 (m-30) cc_final: 0.8842 (m-30) REVERT: G 79 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7531 (tp30) REVERT: G 105 ARG cc_start: 0.8666 (mpt180) cc_final: 0.8425 (tpp-160) REVERT: G 147 GLN cc_start: 0.7479 (mm110) cc_final: 0.7120 (mm110) REVERT: G 148 LYS cc_start: 0.8012 (mppt) cc_final: 0.7523 (ttmm) REVERT: G 165 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7327 (mt-10) REVERT: H 46 ASP cc_start: 0.8992 (m-30) cc_final: 0.8594 (m-30) REVERT: H 73 ASN cc_start: 0.8843 (p0) cc_final: 0.8400 (p0) REVERT: H 79 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7595 (tp30) REVERT: H 105 ARG cc_start: 0.8716 (mpt180) cc_final: 0.8473 (tpp-160) REVERT: H 124 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8406 (t80) REVERT: H 147 GLN cc_start: 0.7686 (mm110) cc_final: 0.7409 (mm110) REVERT: H 148 LYS cc_start: 0.8134 (mppt) cc_final: 0.7876 (tttt) REVERT: H 167 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8084 (mp0) outliers start: 22 outliers final: 14 residues processed: 372 average time/residue: 0.1326 time to fit residues: 70.8441 Evaluate side-chains 365 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 347 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 169 ILE 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 E residue 169 ILE Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 124 PHE Chi-restraints excluded: chain H residue 181 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 45 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 138 optimal weight: 70.0000 chunk 148 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.164258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.106191 restraints weight = 18080.994| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.36 r_work: 0.2963 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2957 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= 0.120 Angle : 0.501 5.507 20408 Z= 0.260 Chirality : 0.037 0.124 2336 Planarity : 0.004 0.046 2504 Dihedral : 3.533 16.981 1976 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.71 % Allowed : 19.54 % 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: 3.16 (0.20), residues: 1792 helix: 2.95 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.54 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 176 TYR 0.023 0.001 TYR G 142 PHE 0.007 0.001 PHE G 124 TRP 0.005 0.001 TRP H 62 HIS 0.003 0.001 HIS C 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (15024) covalent geometry : angle 0.49328 / 0.26 (20352) SS BOND : bond 0.00315 / 0.23 ( 16) SS BOND : angle 0.95178 / 0.74 ( 32) hydrogen bonds : bond 0.03800 / 2.54 ( 1049) hydrogen bonds : angle 3.06820 / 2.24 ( 3147) link_NAG-ASN : bond 0.00059 / 0.04 ( 8) link_NAG-ASN : angle 2.37706 / 1.80 ( 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 364 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 338 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 32 GLN cc_start: 0.6818 (tm-30) cc_final: 0.6456 (tp40) REVERT: A 46 ASP cc_start: 0.9051 (m-30) cc_final: 0.8836 (m-30) REVERT: A 71 ASN cc_start: 0.8802 (t0) cc_final: 0.8600 (t0) REVERT: A 79 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7521 (tp30) REVERT: A 105 ARG cc_start: 0.8689 (mpt180) cc_final: 0.8429 (tpp-160) REVERT: A 148 LYS cc_start: 0.7998 (mppt) cc_final: 0.7533 (ttmm) REVERT: A 165 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7326 (mt-10) REVERT: B 46 ASP cc_start: 0.8994 (m-30) cc_final: 0.8599 (m-30) REVERT: B 73 ASN cc_start: 0.8812 (p0) cc_final: 0.8354 (p0) REVERT: B 79 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7547 (tp30) REVERT: B 105 ARG cc_start: 0.8716 (mpt180) cc_final: 0.8473 (tpp-160) REVERT: B 124 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8401 (t80) REVERT: B 143 GLN cc_start: 0.7985 (mm110) cc_final: 0.7758 (mm-40) REVERT: B 147 GLN cc_start: 0.7885 (mm110) cc_final: 0.7465 (mm110) REVERT: C 32 GLN cc_start: 0.6821 (tm-30) cc_final: 0.6453 (tp40) REVERT: C 46 ASP cc_start: 0.9059 (m-30) cc_final: 0.8845 (m-30) REVERT: C 71 ASN cc_start: 0.8802 (t0) cc_final: 0.8598 (t0) REVERT: C 79 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7528 (tp30) REVERT: C 105 ARG cc_start: 0.8624 (mpt180) cc_final: 0.8370 (tpp-160) REVERT: C 148 LYS cc_start: 0.8008 (mppt) cc_final: 0.7537 (ttmm) REVERT: C 165 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7329 (mt-10) REVERT: D 46 ASP cc_start: 0.9007 (m-30) cc_final: 0.8606 (m-30) REVERT: D 73 ASN cc_start: 0.8800 (p0) cc_final: 0.8347 (p0) REVERT: D 79 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7554 (tp30) REVERT: D 105 ARG cc_start: 0.8721 (mpt180) cc_final: 0.8486 (tpp-160) REVERT: D 124 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8406 (t80) REVERT: D 143 GLN cc_start: 0.7979 (mm110) cc_final: 0.7742 (mm-40) REVERT: D 147 GLN cc_start: 0.7879 (mm110) cc_final: 0.7447 (mm110) REVERT: D 148 LYS cc_start: 0.8015 (mmtm) cc_final: 0.7794 (tttt) REVERT: E 32 GLN cc_start: 0.6828 (tm-30) cc_final: 0.6462 (tp40) REVERT: E 46 ASP cc_start: 0.9063 (m-30) cc_final: 0.8846 (m-30) REVERT: E 71 ASN cc_start: 0.8804 (t0) cc_final: 0.8601 (t0) REVERT: E 79 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7522 (tp30) REVERT: E 105 ARG cc_start: 0.8619 (mpt180) cc_final: 0.8365 (tpp-160) REVERT: E 148 LYS cc_start: 0.8001 (mppt) cc_final: 0.7535 (ttmm) REVERT: E 165 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7341 (mt-10) REVERT: F 46 ASP cc_start: 0.9002 (m-30) cc_final: 0.8609 (m-30) REVERT: F 73 ASN cc_start: 0.8795 (p0) cc_final: 0.8323 (p0) REVERT: F 79 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7524 (tp30) REVERT: F 105 ARG cc_start: 0.8713 (mpt180) cc_final: 0.8478 (tpp-160) REVERT: F 124 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8403 (t80) REVERT: F 147 GLN cc_start: 0.7698 (mm110) cc_final: 0.7440 (mm110) REVERT: F 148 LYS cc_start: 0.8145 (mppt) cc_final: 0.7894 (tttt) REVERT: F 165 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7494 (mt-10) REVERT: F 167 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8104 (mp0) REVERT: F 220 HIS cc_start: 0.8316 (m-70) cc_final: 0.8115 (m170) REVERT: G 32 GLN cc_start: 0.6682 (tm-30) cc_final: 0.6302 (tp40) REVERT: G 46 ASP cc_start: 0.9051 (m-30) cc_final: 0.8838 (m-30) REVERT: G 79 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7523 (tp30) REVERT: G 105 ARG cc_start: 0.8680 (mpt180) cc_final: 0.8425 (tpp-160) REVERT: G 148 LYS cc_start: 0.8000 (mppt) cc_final: 0.7535 (ttmm) REVERT: G 165 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7328 (mt-10) REVERT: H 46 ASP cc_start: 0.8989 (m-30) cc_final: 0.8595 (m-30) REVERT: H 73 ASN cc_start: 0.8811 (p0) cc_final: 0.8359 (p0) REVERT: H 79 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7595 (tp30) REVERT: H 105 ARG cc_start: 0.8716 (mpt180) cc_final: 0.8482 (tpp-160) REVERT: H 124 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8401 (t80) REVERT: H 147 GLN cc_start: 0.7692 (mm110) cc_final: 0.7436 (mm110) REVERT: H 148 LYS cc_start: 0.8146 (mppt) cc_final: 0.7900 (tttt) outliers start: 26 outliers final: 17 residues processed: 346 average time/residue: 0.1297 time to fit residues: 63.9135 Evaluate side-chains 355 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 334 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 169 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 F residue 181 LEU Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 169 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 Chi-restraints excluded: chain H residue 181 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 58 optimal weight: 0.3980 chunk 144 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 178 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.163629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.106108 restraints weight = 18205.440| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.37 r_work: 0.2969 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3059 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= 0.118 Angle : 0.502 5.747 20408 Z= 0.261 Chirality : 0.037 0.123 2336 Planarity : 0.004 0.046 2504 Dihedral : 3.529 16.795 1976 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.18 % Allowed : 20.00 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.14 (0.20), residues: 1792 helix: 2.95 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -1.70 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 204 TYR 0.018 0.001 TYR A 142 PHE 0.007 0.001 PHE C 124 TRP 0.005 0.001 TRP F 62 HIS 0.003 0.001 HIS D 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (15024) covalent geometry : angle 0.49557 / 0.26 (20352) SS BOND : bond 0.00295 / 0.22 ( 16) SS BOND : angle 0.88482 / 0.69 ( 32) hydrogen bonds : bond 0.03704 / 2.48 ( 1049) hydrogen bonds : angle 3.03581 / 2.22 ( 3147) link_NAG-ASN : bond 0.00196 / 0.16 ( 8) link_NAG-ASN : angle 2.29282 / 1.75 ( 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 351 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 333 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.6692 (tm-30) cc_final: 0.6310 (tp40) REVERT: A 46 ASP cc_start: 0.9056 (m-30) cc_final: 0.8845 (m-30) REVERT: A 79 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7516 (tp30) REVERT: A 105 ARG cc_start: 0.8682 (mpt180) cc_final: 0.8422 (tpp-160) REVERT: A 143 GLN cc_start: 0.7756 (mm110) cc_final: 0.7550 (mm110) REVERT: A 147 GLN cc_start: 0.7576 (mm110) cc_final: 0.7246 (mm110) REVERT: A 148 LYS cc_start: 0.7967 (mppt) cc_final: 0.7509 (ttmm) REVERT: A 165 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7616 (mp0) REVERT: B 46 ASP cc_start: 0.8991 (m-30) cc_final: 0.8593 (m-30) REVERT: B 73 ASN cc_start: 0.8737 (p0) cc_final: 0.8250 (p0) REVERT: B 79 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7542 (tp30) REVERT: B 105 ARG cc_start: 0.8715 (mpt180) cc_final: 0.8467 (tpp-160) REVERT: B 124 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8381 (t80) REVERT: B 143 GLN cc_start: 0.7975 (mm110) cc_final: 0.7741 (mm-40) REVERT: C 32 GLN cc_start: 0.6692 (tm-30) cc_final: 0.6308 (tp40) REVERT: C 46 ASP cc_start: 0.9067 (m-30) cc_final: 0.8856 (m-30) REVERT: C 79 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7527 (tp30) REVERT: C 105 ARG cc_start: 0.8616 (mpt180) cc_final: 0.8357 (tpp-160) REVERT: C 143 GLN cc_start: 0.7757 (mm110) cc_final: 0.7552 (mm110) REVERT: C 147 GLN cc_start: 0.7587 (mm110) cc_final: 0.7254 (mm110) REVERT: C 148 LYS cc_start: 0.7974 (mppt) cc_final: 0.7512 (ttmm) REVERT: C 165 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7304 (mt-10) REVERT: D 46 ASP cc_start: 0.9008 (m-30) cc_final: 0.8611 (m-30) REVERT: D 73 ASN cc_start: 0.8735 (p0) cc_final: 0.8250 (p0) REVERT: D 79 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7545 (tp30) REVERT: D 105 ARG cc_start: 0.8719 (mpt180) cc_final: 0.8477 (tpp-160) REVERT: D 124 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8382 (t80) REVERT: D 147 GLN cc_start: 0.7893 (mm110) cc_final: 0.7473 (mm110) REVERT: D 148 LYS cc_start: 0.8008 (mmtm) cc_final: 0.7799 (tttt) REVERT: E 32 GLN cc_start: 0.6702 (tm-30) cc_final: 0.6320 (tp40) REVERT: E 46 ASP cc_start: 0.9067 (m-30) cc_final: 0.8855 (m-30) REVERT: E 79 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7519 (tp30) REVERT: E 105 ARG cc_start: 0.8610 (mpt180) cc_final: 0.8348 (tpp-160) REVERT: E 143 GLN cc_start: 0.7766 (mm110) cc_final: 0.7562 (mm110) REVERT: E 147 GLN cc_start: 0.7578 (mm110) cc_final: 0.7250 (mm110) REVERT: E 148 LYS cc_start: 0.7966 (mppt) cc_final: 0.7510 (ttmm) REVERT: E 165 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7318 (mt-10) REVERT: F 46 ASP cc_start: 0.9004 (m-30) cc_final: 0.8644 (m-30) REVERT: F 73 ASN cc_start: 0.8731 (p0) cc_final: 0.8248 (p0) REVERT: F 79 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7498 (tp30) REVERT: F 105 ARG cc_start: 0.8712 (mpt180) cc_final: 0.8469 (tpp-160) REVERT: F 124 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8381 (t80) REVERT: F 147 GLN cc_start: 0.7697 (mm110) cc_final: 0.7458 (mm110) REVERT: F 148 LYS cc_start: 0.8116 (mppt) cc_final: 0.7872 (tttt) REVERT: F 164 GLU cc_start: 0.7892 (pm20) cc_final: 0.7450 (pm20) REVERT: G 32 GLN cc_start: 0.6692 (tm-30) cc_final: 0.6312 (tp40) REVERT: G 46 ASP cc_start: 0.9062 (m-30) cc_final: 0.8851 (m-30) REVERT: G 73 ASN cc_start: 0.8542 (p0) cc_final: 0.8201 (p0) REVERT: G 79 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7520 (tp30) REVERT: G 105 ARG cc_start: 0.8672 (mpt180) cc_final: 0.8413 (tpp-160) REVERT: G 147 GLN cc_start: 0.7587 (mm110) cc_final: 0.7258 (mm110) REVERT: G 148 LYS cc_start: 0.7965 (mppt) cc_final: 0.7508 (ttmm) REVERT: G 165 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7316 (mt-10) REVERT: H 46 ASP cc_start: 0.8988 (m-30) cc_final: 0.8629 (m-30) REVERT: H 73 ASN cc_start: 0.8754 (p0) cc_final: 0.8271 (p0) REVERT: H 79 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7559 (tp30) REVERT: H 105 ARG cc_start: 0.8716 (mpt180) cc_final: 0.8474 (tpp-160) REVERT: H 124 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8380 (t80) REVERT: H 147 GLN cc_start: 0.7710 (mm110) cc_final: 0.7460 (mm110) REVERT: H 148 LYS cc_start: 0.8137 (mppt) cc_final: 0.7886 (tttt) REVERT: H 164 GLU cc_start: 0.7817 (pm20) cc_final: 0.7301 (pm20) REVERT: H 165 GLU cc_start: 0.7635 (mp0) cc_final: 0.7089 (mp0) REVERT: H 167 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8067 (mp0) outliers start: 18 outliers final: 12 residues processed: 337 average time/residue: 0.1275 time to fit residues: 61.3512 Evaluate side-chains 343 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 327 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 98 MET 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 124 PHE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 124 PHE Chi-restraints excluded: chain H residue 181 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 0.4980 chunk 71 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 GLN D 104 GLN F 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.163788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.106410 restraints weight = 18295.678| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.35 r_work: 0.2972 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15048 Z= 0.120 Angle : 0.511 6.786 20408 Z= 0.266 Chirality : 0.037 0.123 2336 Planarity : 0.004 0.046 2504 Dihedral : 3.545 17.259 1976 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.45 % Allowed : 19.93 % 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: 3.19 (0.20), residues: 1792 helix: 2.97 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -1.64 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG G 176 TYR 0.018 0.001 TYR B 142 PHE 0.007 0.001 PHE G 124 TRP 0.005 0.001 TRP D 62 HIS 0.003 0.001 HIS G 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (15024) covalent geometry : angle 0.50520 / 0.26 (20352) SS BOND : bond 0.00302 / 0.22 ( 16) SS BOND : angle 0.88567 / 0.69 ( 32) hydrogen bonds : bond 0.03674 / 2.46 ( 1049) hydrogen bonds : angle 3.02548 / 2.21 ( 3147) link_NAG-ASN : bond 0.00049 / 0.04 ( 8) link_NAG-ASN : angle 2.16867 / 1.68 ( 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 356 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 334 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.6687 (tm-30) cc_final: 0.6310 (tp40) REVERT: A 46 ASP cc_start: 0.9056 (m-30) cc_final: 0.8845 (m-30) REVERT: A 79 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7520 (tp30) REVERT: A 105 ARG cc_start: 0.8675 (mpt180) cc_final: 0.8411 (tpp-160) REVERT: A 147 GLN cc_start: 0.7621 (mm110) cc_final: 0.7299 (mm110) REVERT: A 148 LYS cc_start: 0.8009 (mppt) cc_final: 0.7542 (ttmm) REVERT: A 165 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7636 (mp0) REVERT: B 46 ASP cc_start: 0.8986 (m-30) cc_final: 0.8592 (m-30) REVERT: B 73 ASN cc_start: 0.8738 (p0) cc_final: 0.8201 (p0) REVERT: B 79 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7539 (tp30) REVERT: B 105 ARG cc_start: 0.8713 (mpt180) cc_final: 0.8465 (tpp-160) REVERT: B 124 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8384 (t80) REVERT: B 143 GLN cc_start: 0.7950 (mm110) cc_final: 0.7696 (mm-40) REVERT: C 32 GLN cc_start: 0.6697 (tm-30) cc_final: 0.6317 (tp40) REVERT: C 46 ASP cc_start: 0.9058 (m-30) cc_final: 0.8846 (m-30) REVERT: C 79 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7523 (tp30) REVERT: C 105 ARG cc_start: 0.8612 (mpt180) cc_final: 0.8348 (tpp-160) REVERT: C 147 GLN cc_start: 0.7621 (mm110) cc_final: 0.7298 (mm110) REVERT: C 148 LYS cc_start: 0.8013 (mppt) cc_final: 0.7541 (ttmm) REVERT: C 165 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7639 (mp0) REVERT: D 46 ASP cc_start: 0.9006 (m-30) cc_final: 0.8606 (m-30) REVERT: D 73 ASN cc_start: 0.8736 (p0) cc_final: 0.8200 (p0) REVERT: D 79 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7539 (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: 0.8388 (t80) REVERT: D 147 GLN cc_start: 0.7914 (mm110) cc_final: 0.7504 (mm110) REVERT: E 32 GLN cc_start: 0.6693 (tm-30) cc_final: 0.6317 (tp40) REVERT: E 46 ASP cc_start: 0.9063 (m-30) cc_final: 0.8853 (m-30) REVERT: E 79 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7519 (tp30) REVERT: E 105 ARG cc_start: 0.8606 (mpt180) cc_final: 0.8341 (tpp-160) REVERT: E 147 GLN cc_start: 0.7620 (mm110) cc_final: 0.7300 (mm110) REVERT: E 148 LYS cc_start: 0.8009 (mppt) cc_final: 0.7542 (ttmm) REVERT: E 165 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7641 (mp0) REVERT: F 46 ASP cc_start: 0.8996 (m-30) cc_final: 0.8638 (m-30) REVERT: F 73 ASN cc_start: 0.8737 (p0) cc_final: 0.8182 (p0) REVERT: F 79 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7527 (tp30) REVERT: F 105 ARG cc_start: 0.8712 (mpt180) cc_final: 0.8470 (tpp-160) REVERT: F 124 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8384 (t80) REVERT: F 147 GLN cc_start: 0.7748 (mm110) cc_final: 0.7528 (mm110) REVERT: F 148 LYS cc_start: 0.8130 (mppt) cc_final: 0.7867 (tttt) REVERT: G 32 GLN cc_start: 0.6694 (tm-30) cc_final: 0.6318 (tp40) REVERT: G 46 ASP cc_start: 0.9061 (m-30) cc_final: 0.8851 (m-30) REVERT: G 79 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7521 (tp30) REVERT: G 105 ARG cc_start: 0.8663 (mpt180) cc_final: 0.8403 (tpp-160) REVERT: G 147 GLN cc_start: 0.7622 (mm110) cc_final: 0.7304 (mm110) REVERT: G 148 LYS cc_start: 0.8003 (mppt) cc_final: 0.7538 (ttmm) REVERT: G 165 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7634 (mp0) REVERT: H 46 ASP cc_start: 0.8989 (m-30) cc_final: 0.8630 (m-30) REVERT: H 73 ASN cc_start: 0.8737 (p0) cc_final: 0.8201 (p0) REVERT: H 79 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7559 (tp30) REVERT: H 105 ARG cc_start: 0.8713 (mpt180) cc_final: 0.8469 (tpp-160) REVERT: H 124 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8384 (t80) REVERT: H 147 GLN cc_start: 0.7712 (mm110) cc_final: 0.7475 (mm110) REVERT: H 148 LYS cc_start: 0.8128 (mppt) cc_final: 0.7865 (tttt) REVERT: H 164 GLU cc_start: 0.7877 (pm20) cc_final: 0.7582 (pm20) REVERT: H 165 GLU cc_start: 0.7678 (mp0) cc_final: 0.7115 (mp0) REVERT: H 167 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8019 (mp0) outliers start: 22 outliers final: 18 residues processed: 342 average time/residue: 0.1242 time to fit residues: 60.5968 Evaluate side-chains 362 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 340 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 169 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 E residue 169 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 F residue 181 LEU Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 169 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 Chi-restraints excluded: chain H residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 161 optimal weight: 60.0000 chunk 101 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN C 71 ASN ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN H 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.163350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.105733 restraints weight = 18173.330| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.36 r_work: 0.2962 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15048 Z= 0.126 Angle : 0.510 5.499 20408 Z= 0.265 Chirality : 0.037 0.134 2336 Planarity : 0.004 0.047 2504 Dihedral : 3.562 19.541 1976 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.51 % Allowed : 19.67 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.20), residues: 1792 helix: 2.97 (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 0.000 0.000 ARG C 176 TYR 0.018 0.001 TYR B 142 PHE 0.007 0.001 PHE G 124 TRP 0.004 0.001 TRP H 62 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (15024) covalent geometry : angle 0.50324 / 0.26 (20352) SS BOND : bond 0.00334 / 0.25 ( 16) SS BOND : angle 0.96398 / 0.75 ( 32) hydrogen bonds : bond 0.03765 / 2.52 ( 1049) hydrogen bonds : angle 3.04275 / 2.22 ( 3147) link_NAG-ASN : bond 0.00172 / 0.12 ( 8) link_NAG-ASN : angle 2.20604 / 1.71 ( 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 370 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 347 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.6692 (tm-30) cc_final: 0.6311 (tp40) REVERT: A 46 ASP cc_start: 0.9050 (m-30) cc_final: 0.8836 (m-30) REVERT: A 79 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7514 (tp30) REVERT: A 105 ARG cc_start: 0.8693 (mpt180) cc_final: 0.8429 (tpp-160) REVERT: A 147 GLN cc_start: 0.7652 (mm110) cc_final: 0.7341 (mm110) REVERT: A 148 LYS cc_start: 0.7990 (mppt) cc_final: 0.7550 (ttmm) REVERT: A 165 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7649 (mp0) REVERT: B 46 ASP cc_start: 0.8990 (m-30) cc_final: 0.8590 (m-30) REVERT: B 73 ASN cc_start: 0.8703 (p0) cc_final: 0.8153 (p0) REVERT: B 79 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7550 (tp30) REVERT: B 105 ARG cc_start: 0.8740 (mpt180) cc_final: 0.8479 (tpp-160) REVERT: B 124 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8408 (t80) REVERT: B 164 GLU cc_start: 0.7748 (pm20) cc_final: 0.7251 (pm20) REVERT: B 165 GLU cc_start: 0.7589 (mp0) cc_final: 0.7059 (mp0) REVERT: B 167 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8028 (mp0) REVERT: C 32 GLN cc_start: 0.6699 (tm-30) cc_final: 0.6319 (tp40) REVERT: C 46 ASP cc_start: 0.9050 (m-30) cc_final: 0.8838 (m-30) REVERT: C 79 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7522 (tp30) REVERT: C 105 ARG cc_start: 0.8682 (mpt180) cc_final: 0.8418 (tpp-160) REVERT: C 147 GLN cc_start: 0.7655 (mm110) cc_final: 0.7343 (mm110) REVERT: C 148 LYS cc_start: 0.7999 (mppt) cc_final: 0.7551 (ttmm) REVERT: C 165 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7649 (mp0) REVERT: D 46 ASP cc_start: 0.9006 (m-30) cc_final: 0.8606 (m-30) REVERT: D 73 ASN cc_start: 0.8677 (p0) cc_final: 0.8160 (p0) REVERT: D 79 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7545 (tp30) REVERT: D 105 ARG cc_start: 0.8730 (mpt180) cc_final: 0.8467 (tpp-160) REVERT: D 124 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8414 (t80) REVERT: D 164 GLU cc_start: 0.7742 (pm20) cc_final: 0.7528 (pm20) REVERT: E 32 GLN cc_start: 0.6697 (tm-30) cc_final: 0.6317 (tp40) REVERT: E 46 ASP cc_start: 0.9061 (m-30) cc_final: 0.8848 (m-30) REVERT: E 79 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7516 (tp30) REVERT: E 105 ARG cc_start: 0.8678 (mpt180) cc_final: 0.8413 (tpp-160) REVERT: E 147 GLN cc_start: 0.7654 (mm110) cc_final: 0.7343 (mm110) REVERT: E 148 LYS cc_start: 0.7996 (mppt) cc_final: 0.7549 (ttmm) REVERT: E 165 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7652 (mp0) REVERT: F 46 ASP cc_start: 0.9005 (m-30) cc_final: 0.8643 (m-30) REVERT: F 73 ASN cc_start: 0.8673 (p0) cc_final: 0.8157 (p0) REVERT: F 79 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7528 (tp30) REVERT: F 105 ARG cc_start: 0.8718 (mpt180) cc_final: 0.8453 (tpp-160) REVERT: F 124 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8412 (t80) REVERT: F 147 GLN cc_start: 0.7754 (mm110) cc_final: 0.7551 (mm110) REVERT: F 148 LYS cc_start: 0.8119 (mppt) cc_final: 0.7865 (tttt) REVERT: F 165 GLU cc_start: 0.7517 (mp0) cc_final: 0.7223 (mp0) REVERT: F 167 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8184 (mp0) REVERT: G 32 GLN cc_start: 0.6697 (tm-30) cc_final: 0.6321 (tp40) REVERT: G 46 ASP cc_start: 0.9061 (m-30) cc_final: 0.8850 (m-30) REVERT: G 73 ASN cc_start: 0.8473 (p0) cc_final: 0.8110 (p0) REVERT: G 79 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7522 (tp30) REVERT: G 105 ARG cc_start: 0.8688 (mpt180) cc_final: 0.8418 (tpp-160) REVERT: G 147 GLN cc_start: 0.7653 (mm110) cc_final: 0.7345 (mm110) REVERT: G 148 LYS cc_start: 0.8003 (mppt) cc_final: 0.7552 (ttmm) REVERT: G 165 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7646 (mp0) REVERT: H 46 ASP cc_start: 0.8992 (m-30) cc_final: 0.8632 (m-30) REVERT: H 73 ASN cc_start: 0.8706 (p0) cc_final: 0.8155 (p0) REVERT: H 79 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7584 (tp30) REVERT: H 105 ARG cc_start: 0.8726 (mpt180) cc_final: 0.8469 (tpp-160) REVERT: H 124 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8408 (t80) REVERT: H 140 GLU cc_start: 0.7582 (pp20) cc_final: 0.7248 (pp20) REVERT: H 143 GLN cc_start: 0.7997 (mp-120) cc_final: 0.7785 (mm-40) REVERT: H 147 GLN cc_start: 0.7790 (mm110) cc_final: 0.7582 (mm110) REVERT: H 148 LYS cc_start: 0.8116 (mppt) cc_final: 0.7876 (tttt) REVERT: H 164 GLU cc_start: 0.7790 (pm20) cc_final: 0.7484 (pm20) outliers start: 23 outliers final: 18 residues processed: 355 average time/residue: 0.1295 time to fit residues: 65.6148 Evaluate side-chains 359 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 337 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 169 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 E residue 169 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 F residue 181 LEU Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 169 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 Chi-restraints excluded: chain H residue 181 LEU 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: 0.6980 chunk 173 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 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 = 0.3873 r_free = 0.3873 target = 0.164057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.106019 restraints weight = 18180.300| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.35 r_work: 0.2958 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3215 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= 0.136 Angle : 0.521 5.593 20408 Z= 0.271 Chirality : 0.038 0.125 2336 Planarity : 0.004 0.047 2504 Dihedral : 3.596 19.382 1976 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.64 % Allowed : 19.47 % Favored : 78.88 % 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: 2.96 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -1.63 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 201 TYR 0.024 0.002 TYR H 142 PHE 0.007 0.001 PHE A 124 TRP 0.004 0.001 TRP F 62 HIS 0.003 0.001 HIS E 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (15024) covalent geometry : angle 0.51410 / 0.27 (20352) SS BOND : bond 0.00371 / 0.27 ( 16) SS BOND : angle 1.01562 / 0.79 ( 32) hydrogen bonds : bond 0.03855 / 2.58 ( 1049) hydrogen bonds : angle 3.06891 / 2.24 ( 3147) link_NAG-ASN : bond 0.00088 / 0.06 ( 8) link_NAG-ASN : angle 2.29223 / 1.77 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3700.76 seconds wall clock time: 64 minutes 4.70 seconds (3844.70 seconds total)