Starting phenix.real_space_refine on Tue Dec 31 03:02:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lyg_30016/12_2024/6lyg_30016.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lyg_30016/12_2024/6lyg_30016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lyg_30016/12_2024/6lyg_30016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lyg_30016/12_2024/6lyg_30016.map" model { file = "/net/cci-nas-00/data/ceres_data/6lyg_30016/12_2024/6lyg_30016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lyg_30016/12_2024/6lyg_30016.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, '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: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, '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: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, '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: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, '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: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, '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: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, '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: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, '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: {'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.71, per 1000 atoms: 0.59 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: 4.14 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.37 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: 4.07 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4495 1.34 - 1.46: 3261 1.46 - 1.58: 7092 1.58 - 1.69: 0 1.69 - 1.81: 176 Bond restraints: 15024 Sorted by residual: bond pdb=" N ALA G 93 " pdb=" CA ALA G 93 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.81e+00 bond pdb=" N ALA B 93 " pdb=" CA ALA B 93 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.27e-02 6.20e+03 4.65e+00 bond pdb=" N ALA E 93 " pdb=" CA ALA E 93 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.23e-02 6.61e+03 4.62e+00 bond pdb=" N ALA C 93 " pdb=" CA ALA C 93 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.23e-02 6.61e+03 4.62e+00 bond pdb=" N ALA H 93 " pdb=" CA ALA H 93 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.60e+00 ... (remaining 15019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 19842 1.52 - 3.04: 381 3.04 - 4.56: 77 4.56 - 6.08: 44 6.08 - 7.60: 8 Bond angle restraints: 20352 Sorted by residual: angle pdb=" N ALA H 93 " pdb=" CA ALA H 93 " pdb=" C ALA H 93 " ideal model delta sigma weight residual 111.36 118.96 -7.60 1.09e+00 8.42e-01 4.86e+01 angle pdb=" N ALA D 93 " pdb=" CA ALA D 93 " pdb=" C ALA D 93 " ideal model delta sigma weight residual 111.36 118.96 -7.60 1.09e+00 8.42e-01 4.86e+01 angle pdb=" N ALA E 93 " pdb=" CA ALA E 93 " pdb=" C ALA E 93 " ideal model delta sigma weight residual 111.36 118.95 -7.59 1.09e+00 8.42e-01 4.85e+01 angle pdb=" N ALA C 93 " pdb=" CA ALA C 93 " pdb=" C ALA C 93 " ideal model delta sigma weight residual 111.36 118.95 -7.59 1.09e+00 8.42e-01 4.85e+01 angle pdb=" N ALA F 93 " pdb=" CA ALA F 93 " pdb=" C ALA F 93 " ideal model delta sigma weight residual 111.36 118.95 -7.59 1.09e+00 8.42e-01 4.85e+01 ... (remaining 20347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 8231 17.00 - 34.00: 661 34.00 - 51.00: 140 51.00 - 67.99: 48 67.99 - 84.99: 24 Dihedral angle restraints: 9104 sinusoidal: 3600 harmonic: 5504 Sorted by residual: dihedral pdb=" CB CYS B 43 " pdb=" SG CYS B 43 " pdb=" SG CYS B 159 " pdb=" CB CYS B 159 " ideal model delta sinusoidal sigma weight residual 93.00 119.90 -26.90 1 1.00e+01 1.00e-02 1.04e+01 dihedral pdb=" CB CYS F 43 " pdb=" SG CYS F 43 " pdb=" SG CYS F 159 " pdb=" CB CYS F 159 " ideal model delta sinusoidal sigma weight residual 93.00 119.90 -26.90 1 1.00e+01 1.00e-02 1.04e+01 dihedral pdb=" CB CYS C 43 " pdb=" SG CYS C 43 " pdb=" SG CYS C 159 " pdb=" CB CYS C 159 " ideal model delta sinusoidal sigma weight residual 93.00 119.89 -26.89 1 1.00e+01 1.00e-02 1.04e+01 ... (remaining 9101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2068 0.059 - 0.118: 250 0.118 - 0.178: 3 0.178 - 0.237: 9 0.237 - 0.296: 6 Chirality restraints: 2336 Sorted by residual: chirality pdb=" CA ALA F 93 " pdb=" N ALA F 93 " pdb=" C ALA F 93 " pdb=" CB ALA F 93 " both_signs ideal model delta sigma weight residual False 2.48 2.19 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA ALA D 93 " pdb=" N ALA D 93 " pdb=" C ALA D 93 " pdb=" CB ALA D 93 " both_signs ideal model delta sigma weight residual False 2.48 2.19 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA ALA G 93 " pdb=" N ALA G 93 " pdb=" C ALA G 93 " pdb=" CB ALA G 93 " both_signs ideal model delta sigma weight residual False 2.48 2.19 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 2333 not shown) Planarity restraints: 2512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 59 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO D 60 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 60 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 60 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 59 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO B 60 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 60 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 60 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 59 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.32e+00 pdb=" N PRO A 60 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 60 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 60 " 0.026 5.00e-02 4.00e+02 ... (remaining 2509 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4363 2.82 - 3.34: 14844 3.34 - 3.86: 23737 3.86 - 4.38: 24593 4.38 - 4.90: 45157 Nonbonded interactions: 112694 Sorted by model distance: nonbonded pdb=" OH TYR H 68 " pdb=" OG1 THR H 103 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR F 68 " pdb=" OG1 THR F 103 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR B 68 " pdb=" OG1 THR B 103 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR A 68 " pdb=" OG1 THR A 103 " model vdw 2.300 3.040 nonbonded pdb=" OH TYR G 68 " pdb=" OG1 THR G 103 " model vdw 2.300 3.040 ... (remaining 112689 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 1.210 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.160 Process input model: 33.940 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15024 Z= 0.233 Angle : 0.580 7.601 20352 Z= 0.358 Chirality : 0.042 0.296 2336 Planarity : 0.004 0.046 2504 Dihedral : 14.338 84.992 5456 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.29 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP H 62 HIS 0.002 0.000 HIS H 220 PHE 0.007 0.001 PHE H 64 TYR 0.008 0.001 TYR H 177 ARG 0.002 0.000 ARG B 201 *********************** 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 : 1.788 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: 0.7704 (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: 0.5774 (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: 0.7886 (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: 0.7922 (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: 0.3549 time to fit residues: 244.6103 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 : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 144 optimal weight: 0.2980 chunk 55 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS B 236 HIS C 236 HIS E 236 HIS G 236 HIS H 236 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15024 Z= 0.196 Angle : 0.523 5.780 20352 Z= 0.275 Chirality : 0.037 0.123 2336 Planarity : 0.004 0.044 2504 Dihedral : 4.205 21.588 2144 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.92 % Allowed : 21.12 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.20), residues: 1792 helix: 2.15 (0.13), residues: 1408 sheet: None (None), residues: 0 loop : -2.26 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 62 HIS 0.005 0.002 HIS A 236 PHE 0.007 0.001 PHE D 124 TYR 0.008 0.001 TYR D 221 ARG 0.001 0.000 ARG D 171 *********************** 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 367 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 353 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.5724 (tm-30) cc_final: 0.5390 (tp40) REVERT: A 33 MET cc_start: 0.7499 (ttm) cc_final: 0.7179 (ttt) REVERT: A 46 ASP cc_start: 0.8791 (m-30) cc_final: 0.8440 (m-30) REVERT: A 71 ASN cc_start: 0.8600 (t0) cc_final: 0.8147 (t0) REVERT: A 105 ARG cc_start: 0.7899 (mpt180) cc_final: 0.7654 (tpp-160) REVERT: A 143 GLN cc_start: 0.7475 (mm110) cc_final: 0.7243 (mm110) REVERT: A 148 LYS cc_start: 0.8338 (mppt) cc_final: 0.7727 (ttmt) REVERT: A 165 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7023 (mp0) REVERT: B 38 GLU cc_start: 0.8143 (tp30) cc_final: 0.7781 (tp30) REVERT: B 46 ASP cc_start: 0.8770 (m-30) cc_final: 0.8171 (m-30) REVERT: B 71 ASN cc_start: 0.8754 (t0) cc_final: 0.8526 (t0) REVERT: B 73 ASN cc_start: 0.8681 (p0) cc_final: 0.8413 (p0) REVERT: B 105 ARG cc_start: 0.8009 (mpt180) cc_final: 0.7693 (tpp-160) REVERT: B 148 LYS cc_start: 0.8361 (mmtm) cc_final: 0.7878 (tttt) REVERT: B 165 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7121 (mp0) REVERT: B 220 HIS cc_start: 0.8010 (m-70) cc_final: 0.7759 (m170) REVERT: C 32 GLN cc_start: 0.5726 (tm-30) cc_final: 0.5392 (tp40) REVERT: C 33 MET cc_start: 0.7502 (ttm) cc_final: 0.7181 (ttt) REVERT: C 46 ASP cc_start: 0.8790 (m-30) cc_final: 0.8440 (m-30) REVERT: C 71 ASN cc_start: 0.8596 (t0) cc_final: 0.8144 (t0) REVERT: C 105 ARG cc_start: 0.7895 (mpt180) cc_final: 0.7650 (tpp-160) REVERT: C 143 GLN cc_start: 0.7476 (mm110) cc_final: 0.7243 (mm110) REVERT: C 148 LYS cc_start: 0.8341 (mppt) cc_final: 0.7731 (ttmt) REVERT: C 165 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7023 (mp0) REVERT: D 38 GLU cc_start: 0.8142 (tp30) cc_final: 0.7778 (tp30) REVERT: D 46 ASP cc_start: 0.8768 (m-30) cc_final: 0.8227 (m-30) REVERT: D 71 ASN cc_start: 0.8736 (t0) cc_final: 0.8504 (t0) REVERT: D 73 ASN cc_start: 0.8678 (p0) cc_final: 0.8417 (p0) REVERT: D 105 ARG cc_start: 0.8007 (mpt180) cc_final: 0.7690 (tpp-160) REVERT: D 148 LYS cc_start: 0.8352 (mmtm) cc_final: 0.7815 (tttt) REVERT: D 165 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7125 (mp0) REVERT: D 220 HIS cc_start: 0.8006 (m-70) cc_final: 0.7754 (m170) REVERT: E 32 GLN cc_start: 0.5723 (tm-30) cc_final: 0.5389 (tp40) REVERT: E 33 MET cc_start: 0.7501 (ttm) cc_final: 0.7180 (ttt) REVERT: E 46 ASP cc_start: 0.8789 (m-30) cc_final: 0.8439 (m-30) REVERT: E 71 ASN cc_start: 0.8594 (t0) cc_final: 0.8142 (t0) REVERT: E 105 ARG cc_start: 0.7898 (mpt180) cc_final: 0.7652 (tpp-160) REVERT: E 143 GLN cc_start: 0.7475 (mm110) cc_final: 0.7241 (mm110) REVERT: E 148 LYS cc_start: 0.8340 (mppt) cc_final: 0.7729 (ttmt) REVERT: E 165 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7026 (mp0) REVERT: F 32 GLN cc_start: 0.7891 (tp40) cc_final: 0.7645 (tp40) REVERT: F 38 GLU cc_start: 0.8140 (tp30) cc_final: 0.7776 (tp30) REVERT: F 46 ASP cc_start: 0.8766 (m-30) cc_final: 0.8283 (m-30) REVERT: F 71 ASN cc_start: 0.8752 (t0) cc_final: 0.8524 (t0) REVERT: F 73 ASN cc_start: 0.8678 (p0) cc_final: 0.8414 (p0) REVERT: F 105 ARG cc_start: 0.8008 (mpt180) cc_final: 0.7691 (tpp-160) REVERT: F 148 LYS cc_start: 0.8313 (mppt) cc_final: 0.7890 (tttt) REVERT: F 165 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7122 (mp0) REVERT: F 220 HIS cc_start: 0.7979 (m-70) cc_final: 0.7766 (m170) REVERT: G 32 GLN cc_start: 0.5722 (tm-30) cc_final: 0.5389 (tp40) REVERT: G 33 MET cc_start: 0.7501 (ttm) cc_final: 0.7180 (ttt) REVERT: G 46 ASP cc_start: 0.8790 (m-30) cc_final: 0.8439 (m-30) REVERT: G 71 ASN cc_start: 0.8595 (t0) cc_final: 0.8140 (t0) REVERT: G 105 ARG cc_start: 0.7896 (mpt180) cc_final: 0.7650 (tpp-160) REVERT: G 143 GLN cc_start: 0.7475 (mm110) cc_final: 0.7242 (mm110) REVERT: G 148 LYS cc_start: 0.8340 (mppt) cc_final: 0.7729 (ttmt) REVERT: G 165 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7025 (mp0) REVERT: H 32 GLN cc_start: 0.7891 (tp40) cc_final: 0.7648 (tp40) REVERT: H 38 GLU cc_start: 0.8141 (tp30) cc_final: 0.7777 (tp30) REVERT: H 46 ASP cc_start: 0.8765 (m-30) cc_final: 0.8279 (m-30) REVERT: H 71 ASN cc_start: 0.8754 (t0) cc_final: 0.8525 (t0) REVERT: H 73 ASN cc_start: 0.8680 (p0) cc_final: 0.8415 (p0) REVERT: H 105 ARG cc_start: 0.8008 (mpt180) cc_final: 0.7691 (tpp-160) REVERT: H 148 LYS cc_start: 0.8316 (mppt) cc_final: 0.7898 (tttt) REVERT: H 165 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7116 (mp0) REVERT: H 220 HIS cc_start: 0.7962 (m-70) cc_final: 0.7743 (m170) outliers start: 14 outliers final: 6 residues processed: 353 average time/residue: 0.3277 time to fit residues: 163.2426 Evaluate side-chains 339 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 333 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 181 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 139 optimal weight: 0.2980 chunk 113 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 167 optimal weight: 0.6980 chunk 180 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 57 optimal weight: 0.3980 chunk 134 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN C 71 ASN E 71 ASN G 71 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15024 Z= 0.169 Angle : 0.485 5.546 20352 Z= 0.254 Chirality : 0.036 0.122 2336 Planarity : 0.004 0.045 2504 Dihedral : 3.657 15.611 2144 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.32 % Allowed : 19.34 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.20), residues: 1792 helix: 2.66 (0.14), residues: 1408 sheet: None (None), residues: 0 loop : -2.03 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 62 HIS 0.003 0.001 HIS A 220 PHE 0.006 0.001 PHE A 64 TYR 0.018 0.001 TYR G 142 ARG 0.001 0.000 ARG H 176 *********************** 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 459 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 439 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.5918 (tm-30) cc_final: 0.5607 (tp40) REVERT: A 46 ASP cc_start: 0.8808 (m-30) cc_final: 0.8466 (m-30) REVERT: A 71 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.7954 (t0) REVERT: A 79 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7404 (tp30) REVERT: A 105 ARG cc_start: 0.7901 (mpt180) cc_final: 0.7651 (tpp-160) REVERT: A 143 GLN cc_start: 0.7825 (mm110) cc_final: 0.7288 (mm110) REVERT: A 147 GLN cc_start: 0.7545 (mm110) cc_final: 0.7199 (mm110) REVERT: A 148 LYS cc_start: 0.8264 (mppt) cc_final: 0.7712 (ttmm) REVERT: A 164 GLU cc_start: 0.7745 (pm20) cc_final: 0.7455 (pm20) REVERT: A 165 GLU cc_start: 0.7523 (mt-10) cc_final: 0.6782 (mt-10) REVERT: A 167 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7681 (mp0) REVERT: A 240 PHE cc_start: 0.7882 (m-80) cc_final: 0.7463 (m-80) REVERT: B 46 ASP cc_start: 0.8774 (m-30) cc_final: 0.8288 (m-30) REVERT: B 71 ASN cc_start: 0.8701 (t0) cc_final: 0.8403 (t0) REVERT: B 73 ASN cc_start: 0.8692 (p0) cc_final: 0.8359 (p0) REVERT: B 79 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7473 (tp30) REVERT: B 105 ARG cc_start: 0.7964 (mpt180) cc_final: 0.7652 (tpp-160) REVERT: B 148 LYS cc_start: 0.8272 (mmtm) cc_final: 0.7898 (tttt) REVERT: B 165 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7221 (mp0) REVERT: B 167 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7560 (mp0) REVERT: B 220 HIS cc_start: 0.8025 (m-70) cc_final: 0.7789 (m170) REVERT: C 32 GLN cc_start: 0.5917 (tm-30) cc_final: 0.5608 (tp40) REVERT: C 46 ASP cc_start: 0.8807 (m-30) cc_final: 0.8464 (m-30) REVERT: C 71 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.7956 (t0) REVERT: C 79 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7412 (tp30) REVERT: C 105 ARG cc_start: 0.7894 (mpt180) cc_final: 0.7647 (tpp-160) REVERT: C 143 GLN cc_start: 0.7823 (mm110) cc_final: 0.7286 (mm110) REVERT: C 147 GLN cc_start: 0.7544 (mm110) cc_final: 0.7198 (mm110) REVERT: C 148 LYS cc_start: 0.8267 (mppt) cc_final: 0.7714 (ttmm) REVERT: C 164 GLU cc_start: 0.7747 (pm20) cc_final: 0.7456 (pm20) REVERT: C 165 GLU cc_start: 0.7525 (mt-10) cc_final: 0.6782 (mt-10) REVERT: C 167 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7681 (mp0) REVERT: C 240 PHE cc_start: 0.7870 (m-80) cc_final: 0.7451 (m-80) REVERT: D 46 ASP cc_start: 0.8771 (m-30) cc_final: 0.8286 (m-30) REVERT: D 71 ASN cc_start: 0.8700 (t0) cc_final: 0.8403 (t0) REVERT: D 73 ASN cc_start: 0.8685 (p0) cc_final: 0.8361 (p0) REVERT: D 79 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7481 (tp30) REVERT: D 105 ARG cc_start: 0.7959 (mpt180) cc_final: 0.7647 (tpp-160) REVERT: D 148 LYS cc_start: 0.8270 (mmtm) cc_final: 0.7824 (tttt) REVERT: D 165 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7221 (mp0) REVERT: D 167 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7488 (mp0) REVERT: D 220 HIS cc_start: 0.8004 (m-70) cc_final: 0.7766 (m170) REVERT: E 32 GLN cc_start: 0.5918 (tm-30) cc_final: 0.5609 (tp40) REVERT: E 46 ASP cc_start: 0.8806 (m-30) cc_final: 0.8463 (m-30) REVERT: E 71 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.7954 (t0) REVERT: E 79 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7416 (tp30) REVERT: E 105 ARG cc_start: 0.7899 (mpt180) cc_final: 0.7649 (tpp-160) REVERT: E 143 GLN cc_start: 0.7826 (mm110) cc_final: 0.7288 (mm110) REVERT: E 147 GLN cc_start: 0.7543 (mm110) cc_final: 0.7197 (mm110) REVERT: E 148 LYS cc_start: 0.8265 (mppt) cc_final: 0.7712 (ttmm) REVERT: E 164 GLU cc_start: 0.7746 (pm20) cc_final: 0.7457 (pm20) REVERT: E 165 GLU cc_start: 0.7527 (mt-10) cc_final: 0.6784 (mt-10) REVERT: E 167 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7682 (mp0) REVERT: E 240 PHE cc_start: 0.7871 (m-80) cc_final: 0.7452 (m-80) REVERT: F 46 ASP cc_start: 0.8776 (m-30) cc_final: 0.8292 (m-30) REVERT: F 71 ASN cc_start: 0.8706 (t0) cc_final: 0.8405 (t0) REVERT: F 73 ASN cc_start: 0.8685 (p0) cc_final: 0.8359 (p0) REVERT: F 79 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7483 (tp30) REVERT: F 105 ARG cc_start: 0.7963 (mpt180) cc_final: 0.7650 (tpp-160) REVERT: F 147 GLN cc_start: 0.7565 (mm110) cc_final: 0.7244 (mm-40) REVERT: F 148 LYS cc_start: 0.8262 (mppt) cc_final: 0.7881 (tttt) REVERT: F 165 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7252 (mp0) REVERT: F 167 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7642 (mp0) REVERT: F 220 HIS cc_start: 0.7990 (m-70) cc_final: 0.7778 (m170) REVERT: G 32 GLN cc_start: 0.5921 (tm-30) cc_final: 0.5611 (tp40) REVERT: G 46 ASP cc_start: 0.8808 (m-30) cc_final: 0.8464 (m-30) REVERT: G 71 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.7955 (t0) REVERT: G 79 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7417 (tp30) REVERT: G 105 ARG cc_start: 0.7897 (mpt180) cc_final: 0.7649 (tpp-160) REVERT: G 143 GLN cc_start: 0.7825 (mm110) cc_final: 0.7289 (mm110) REVERT: G 147 GLN cc_start: 0.7545 (mm110) cc_final: 0.7199 (mm110) REVERT: G 148 LYS cc_start: 0.8265 (mppt) cc_final: 0.7712 (ttmm) REVERT: G 164 GLU cc_start: 0.7750 (pm20) cc_final: 0.7460 (pm20) REVERT: G 165 GLU cc_start: 0.7525 (mt-10) cc_final: 0.6783 (mt-10) REVERT: G 167 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7683 (mp0) REVERT: G 240 PHE cc_start: 0.7872 (m-80) cc_final: 0.7453 (m-80) REVERT: H 46 ASP cc_start: 0.8767 (m-30) cc_final: 0.8324 (m-30) REVERT: H 71 ASN cc_start: 0.8704 (t0) cc_final: 0.8403 (t0) REVERT: H 73 ASN cc_start: 0.8687 (p0) cc_final: 0.8359 (p0) REVERT: H 79 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7534 (tp30) REVERT: H 105 ARG cc_start: 0.7964 (mpt180) cc_final: 0.7652 (tpp-160) REVERT: H 147 GLN cc_start: 0.7596 (mm110) cc_final: 0.7282 (mm-40) REVERT: H 148 LYS cc_start: 0.8261 (mppt) cc_final: 0.7884 (tttt) REVERT: H 165 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7218 (mp0) REVERT: H 167 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7635 (mp0) REVERT: H 220 HIS cc_start: 0.7986 (m-70) cc_final: 0.7775 (m170) outliers start: 20 outliers final: 4 residues processed: 443 average time/residue: 0.3403 time to fit residues: 217.2977 Evaluate side-chains 400 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 392 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain G residue 71 ASN Chi-restraints excluded: chain G residue 161 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 112 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15024 Z= 0.214 Angle : 0.499 5.552 20352 Z= 0.261 Chirality : 0.037 0.125 2336 Planarity : 0.004 0.046 2504 Dihedral : 3.555 15.741 2144 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.58 % Allowed : 18.29 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.20), residues: 1792 helix: 2.74 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.86 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 62 HIS 0.002 0.001 HIS A 220 PHE 0.006 0.001 PHE B 124 TYR 0.018 0.001 TYR E 142 ARG 0.001 0.000 ARG G 204 *********************** 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 397 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 373 time to evaluate : 1.803 Fit side-chains revert: symmetry clash REVERT: A 32 GLN cc_start: 0.5765 (tm-30) cc_final: 0.5501 (tp40) REVERT: A 46 ASP cc_start: 0.8814 (m-30) cc_final: 0.8483 (m-30) REVERT: A 79 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7452 (tp30) REVERT: A 105 ARG cc_start: 0.7933 (mpt180) cc_final: 0.7699 (tpp-160) REVERT: A 143 GLN cc_start: 0.7823 (mm110) cc_final: 0.7454 (mm110) REVERT: A 147 GLN cc_start: 0.7570 (mm110) cc_final: 0.7255 (mm110) REVERT: A 148 LYS cc_start: 0.8166 (mppt) cc_final: 0.7630 (ttmm) REVERT: A 164 GLU cc_start: 0.7738 (pm20) cc_final: 0.7175 (pm20) REVERT: A 165 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7021 (mp0) REVERT: B 38 GLU cc_start: 0.8229 (tp30) cc_final: 0.7717 (tp30) REVERT: B 46 ASP cc_start: 0.8779 (m-30) cc_final: 0.8291 (m-30) REVERT: B 71 ASN cc_start: 0.8688 (t0) cc_final: 0.8353 (t0) REVERT: B 73 ASN cc_start: 0.8707 (p0) cc_final: 0.8367 (p0) REVERT: B 79 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7516 (tp30) REVERT: B 105 ARG cc_start: 0.7978 (mpt180) cc_final: 0.7676 (tpp-160) REVERT: B 147 GLN cc_start: 0.7685 (mm110) cc_final: 0.7307 (mm-40) REVERT: B 148 LYS cc_start: 0.8251 (mmtm) cc_final: 0.7923 (tttt) REVERT: B 164 GLU cc_start: 0.7801 (pm20) cc_final: 0.7141 (pm20) REVERT: B 165 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7054 (mp0) REVERT: B 220 HIS cc_start: 0.7996 (m-70) cc_final: 0.7757 (m170) REVERT: C 32 GLN cc_start: 0.5765 (tm-30) cc_final: 0.5500 (tp40) REVERT: C 46 ASP cc_start: 0.8816 (m-30) cc_final: 0.8482 (m-30) REVERT: C 79 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7461 (tp30) REVERT: C 105 ARG cc_start: 0.7927 (mpt180) cc_final: 0.7695 (tpp-160) REVERT: C 143 GLN cc_start: 0.7824 (mm110) cc_final: 0.7454 (mm110) REVERT: C 147 GLN cc_start: 0.7570 (mm110) cc_final: 0.7256 (mm110) REVERT: C 148 LYS cc_start: 0.8169 (mppt) cc_final: 0.7631 (ttmm) REVERT: C 164 GLU cc_start: 0.7738 (pm20) cc_final: 0.7174 (pm20) REVERT: C 165 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7022 (mp0) REVERT: D 38 GLU cc_start: 0.8228 (tp30) cc_final: 0.7715 (tp30) REVERT: D 46 ASP cc_start: 0.8777 (m-30) cc_final: 0.8290 (m-30) REVERT: D 71 ASN cc_start: 0.8687 (t0) cc_final: 0.8353 (t0) REVERT: D 73 ASN cc_start: 0.8699 (p0) cc_final: 0.8364 (p0) REVERT: D 79 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7525 (tp30) REVERT: D 105 ARG cc_start: 0.7976 (mpt180) cc_final: 0.7674 (tpp-160) REVERT: D 147 GLN cc_start: 0.7712 (mm110) cc_final: 0.7308 (mm-40) REVERT: D 148 LYS cc_start: 0.8193 (mmtm) cc_final: 0.7786 (tttt) REVERT: D 164 GLU cc_start: 0.7800 (pm20) cc_final: 0.7136 (pm20) REVERT: D 165 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7057 (mp0) REVERT: D 220 HIS cc_start: 0.7988 (m-70) cc_final: 0.7746 (m170) REVERT: E 32 GLN cc_start: 0.5765 (tm-30) cc_final: 0.5501 (tp40) REVERT: E 46 ASP cc_start: 0.8814 (m-30) cc_final: 0.8481 (m-30) REVERT: E 79 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7464 (tp30) REVERT: E 105 ARG cc_start: 0.7931 (mpt180) cc_final: 0.7698 (tpp-160) REVERT: E 143 GLN cc_start: 0.7826 (mm110) cc_final: 0.7456 (mm110) REVERT: E 147 GLN cc_start: 0.7569 (mm110) cc_final: 0.7254 (mm110) REVERT: E 148 LYS cc_start: 0.8166 (mppt) cc_final: 0.7629 (ttmm) REVERT: E 164 GLU cc_start: 0.7738 (pm20) cc_final: 0.7174 (pm20) REVERT: E 165 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7024 (mp0) REVERT: F 38 GLU cc_start: 0.8226 (tp30) cc_final: 0.7714 (tp30) REVERT: F 46 ASP cc_start: 0.8775 (m-30) cc_final: 0.8330 (m-30) REVERT: F 71 ASN cc_start: 0.8691 (t0) cc_final: 0.8354 (t0) REVERT: F 73 ASN cc_start: 0.8695 (p0) cc_final: 0.8361 (p0) REVERT: F 79 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7527 (tp30) REVERT: F 105 ARG cc_start: 0.7981 (mpt180) cc_final: 0.7676 (tpp-160) REVERT: F 147 GLN cc_start: 0.7625 (mm110) cc_final: 0.7313 (mm-40) REVERT: F 148 LYS cc_start: 0.8200 (mppt) cc_final: 0.7856 (tttt) REVERT: F 164 GLU cc_start: 0.7861 (pm20) cc_final: 0.7185 (pm20) REVERT: F 165 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7043 (mp0) REVERT: F 220 HIS cc_start: 0.7977 (m-70) cc_final: 0.7757 (m170) REVERT: G 32 GLN cc_start: 0.5768 (tm-30) cc_final: 0.5502 (tp40) REVERT: G 46 ASP cc_start: 0.8814 (m-30) cc_final: 0.8480 (m-30) REVERT: G 71 ASN cc_start: 0.8383 (t0) cc_final: 0.8102 (t0) REVERT: G 79 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7465 (tp30) REVERT: G 105 ARG cc_start: 0.7930 (mpt180) cc_final: 0.7698 (tpp-160) REVERT: G 143 GLN cc_start: 0.7824 (mm110) cc_final: 0.7455 (mm110) REVERT: G 147 GLN cc_start: 0.7571 (mm110) cc_final: 0.7256 (mm110) REVERT: G 148 LYS cc_start: 0.8166 (mppt) cc_final: 0.7630 (ttmm) REVERT: G 164 GLU cc_start: 0.7740 (pm20) cc_final: 0.7175 (pm20) REVERT: G 165 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7023 (mp0) REVERT: H 38 GLU cc_start: 0.8229 (tp30) cc_final: 0.7716 (tp30) REVERT: H 46 ASP cc_start: 0.8772 (m-30) cc_final: 0.8328 (m-30) REVERT: H 71 ASN cc_start: 0.8690 (t0) cc_final: 0.8352 (t0) REVERT: H 73 ASN cc_start: 0.8696 (p0) cc_final: 0.8361 (p0) REVERT: H 79 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7533 (tp30) REVERT: H 105 ARG cc_start: 0.7978 (mpt180) cc_final: 0.7676 (tpp-160) REVERT: H 147 GLN cc_start: 0.7628 (mm110) cc_final: 0.7321 (mm-40) REVERT: H 148 LYS cc_start: 0.8192 (mppt) cc_final: 0.7875 (tttt) REVERT: H 164 GLU cc_start: 0.7858 (pm20) cc_final: 0.7181 (pm20) REVERT: H 165 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7032 (mp0) REVERT: H 220 HIS cc_start: 0.7973 (m-70) cc_final: 0.7754 (m170) outliers start: 24 outliers final: 12 residues processed: 381 average time/residue: 0.3025 time to fit residues: 163.1868 Evaluate side-chains 407 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 395 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 181 LEU 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 148 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 0 optimal weight: 60.0000 chunk 90 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 ASN G 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15024 Z= 0.199 Angle : 0.477 5.543 20352 Z= 0.250 Chirality : 0.037 0.124 2336 Planarity : 0.004 0.046 2504 Dihedral : 3.472 15.999 2144 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.79 % Allowed : 18.62 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.20), residues: 1792 helix: 2.87 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.78 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 62 HIS 0.003 0.001 HIS B 236 PHE 0.006 0.001 PHE B 124 TYR 0.015 0.001 TYR E 142 ARG 0.001 0.000 ARG E 204 *********************** 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 424 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 412 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.5805 (tm-30) cc_final: 0.5566 (tp40) REVERT: A 46 ASP cc_start: 0.8827 (m-30) cc_final: 0.8499 (m-30) REVERT: A 79 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7447 (tp30) REVERT: A 105 ARG cc_start: 0.8035 (mpt180) cc_final: 0.7774 (tpp-160) REVERT: A 143 GLN cc_start: 0.7979 (mm110) cc_final: 0.7526 (mm110) REVERT: A 148 LYS cc_start: 0.8146 (mppt) cc_final: 0.7613 (ttmm) REVERT: A 164 GLU cc_start: 0.7709 (pm20) cc_final: 0.7056 (pm20) REVERT: A 165 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7040 (mp0) REVERT: A 167 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7704 (mp0) REVERT: B 38 GLU cc_start: 0.8240 (tp30) cc_final: 0.7908 (tp30) REVERT: B 46 ASP cc_start: 0.8780 (m-30) cc_final: 0.8290 (m-30) REVERT: B 79 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7542 (tp30) REVERT: B 105 ARG cc_start: 0.8044 (mpt180) cc_final: 0.7748 (tpp-160) REVERT: B 147 GLN cc_start: 0.7730 (mm110) cc_final: 0.7348 (mm-40) REVERT: B 148 LYS cc_start: 0.8221 (mmtm) cc_final: 0.7889 (tttt) REVERT: B 164 GLU cc_start: 0.7754 (pm20) cc_final: 0.7391 (pm20) REVERT: B 165 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7123 (mp0) REVERT: B 220 HIS cc_start: 0.7945 (m-70) cc_final: 0.7702 (m170) REVERT: C 32 GLN cc_start: 0.5805 (tm-30) cc_final: 0.5565 (tp40) REVERT: C 46 ASP cc_start: 0.8826 (m-30) cc_final: 0.8497 (m-30) REVERT: C 71 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.7793 (t0) REVERT: C 79 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7454 (tp30) REVERT: C 105 ARG cc_start: 0.8030 (mpt180) cc_final: 0.7771 (tpp-160) REVERT: C 143 GLN cc_start: 0.7977 (mm110) cc_final: 0.7524 (mm110) REVERT: C 148 LYS cc_start: 0.8148 (mppt) cc_final: 0.7614 (ttmm) REVERT: C 164 GLU cc_start: 0.7708 (pm20) cc_final: 0.7057 (pm20) REVERT: C 165 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7039 (mp0) REVERT: C 167 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7705 (mp0) REVERT: D 38 GLU cc_start: 0.8239 (tp30) cc_final: 0.7905 (tp30) REVERT: D 46 ASP cc_start: 0.8779 (m-30) cc_final: 0.8290 (m-30) REVERT: D 79 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7550 (tp30) REVERT: D 105 ARG cc_start: 0.8042 (mpt180) cc_final: 0.7747 (tpp-160) REVERT: D 147 GLN cc_start: 0.7793 (mm110) cc_final: 0.7371 (mm-40) REVERT: D 148 LYS cc_start: 0.8197 (mmtm) cc_final: 0.7768 (tttt) REVERT: D 164 GLU cc_start: 0.7753 (pm20) cc_final: 0.7387 (pm20) REVERT: D 165 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7182 (mp0) REVERT: D 220 HIS cc_start: 0.7942 (m-70) cc_final: 0.7696 (m170) REVERT: E 32 GLN cc_start: 0.5808 (tm-30) cc_final: 0.5569 (tp40) REVERT: E 46 ASP cc_start: 0.8825 (m-30) cc_final: 0.8498 (m-30) REVERT: E 79 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7458 (tp30) REVERT: E 105 ARG cc_start: 0.8033 (mpt180) cc_final: 0.7772 (tpp-160) REVERT: E 143 GLN cc_start: 0.7980 (mm110) cc_final: 0.7526 (mm110) REVERT: E 148 LYS cc_start: 0.8146 (mppt) cc_final: 0.7612 (ttmm) REVERT: E 164 GLU cc_start: 0.7710 (pm20) cc_final: 0.7057 (pm20) REVERT: E 165 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7042 (mp0) REVERT: E 167 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7706 (mp0) REVERT: F 38 GLU cc_start: 0.8240 (tp30) cc_final: 0.7906 (tp30) REVERT: F 46 ASP cc_start: 0.8774 (m-30) cc_final: 0.8328 (m-30) REVERT: F 79 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7542 (tp30) REVERT: F 105 ARG cc_start: 0.8041 (mpt180) cc_final: 0.7746 (tpp-160) REVERT: F 142 TYR cc_start: 0.7933 (m-80) cc_final: 0.7504 (m-80) REVERT: F 147 GLN cc_start: 0.7652 (mm110) cc_final: 0.7372 (mm-40) REVERT: F 148 LYS cc_start: 0.8238 (mppt) cc_final: 0.7872 (tttt) REVERT: F 164 GLU cc_start: 0.7751 (pm20) cc_final: 0.7387 (pm20) REVERT: F 165 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7179 (mp0) REVERT: F 220 HIS cc_start: 0.7932 (m-70) cc_final: 0.7704 (m170) REVERT: G 32 GLN cc_start: 0.5809 (tm-30) cc_final: 0.5568 (tp40) REVERT: G 46 ASP cc_start: 0.8827 (m-30) cc_final: 0.8498 (m-30) REVERT: G 71 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.7741 (t0) REVERT: G 79 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7477 (tp30) REVERT: G 105 ARG cc_start: 0.7898 (mpt180) cc_final: 0.7644 (tpp-160) REVERT: G 143 GLN cc_start: 0.7980 (mm110) cc_final: 0.7527 (mm110) REVERT: G 148 LYS cc_start: 0.8146 (mppt) cc_final: 0.7613 (ttmm) REVERT: G 164 GLU cc_start: 0.7712 (pm20) cc_final: 0.7061 (pm20) REVERT: G 165 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7042 (mp0) REVERT: G 167 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7705 (mp0) REVERT: H 38 GLU cc_start: 0.8240 (tp30) cc_final: 0.7905 (tp30) REVERT: H 46 ASP cc_start: 0.8773 (m-30) cc_final: 0.8328 (m-30) REVERT: H 79 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7548 (tp30) REVERT: H 105 ARG cc_start: 0.8044 (mpt180) cc_final: 0.7748 (tpp-160) REVERT: H 147 GLN cc_start: 0.7657 (mm110) cc_final: 0.7377 (mm-40) REVERT: H 148 LYS cc_start: 0.8238 (mppt) cc_final: 0.7897 (tttt) REVERT: H 164 GLU cc_start: 0.7735 (pm20) cc_final: 0.7368 (pm20) REVERT: H 165 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7175 (mp0) REVERT: H 220 HIS cc_start: 0.7925 (m-70) cc_final: 0.7699 (m170) outliers start: 12 outliers final: 6 residues processed: 414 average time/residue: 0.3012 time to fit residues: 175.3003 Evaluate side-chains 375 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 367 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 71 ASN Chi-restraints excluded: chain G residue 161 ASP 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 59 optimal weight: 0.9990 chunk 160 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15024 Z= 0.197 Angle : 0.479 5.513 20352 Z= 0.251 Chirality : 0.037 0.124 2336 Planarity : 0.004 0.046 2504 Dihedral : 3.412 16.142 2144 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.46 % Allowed : 18.62 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.20), residues: 1792 helix: 2.91 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.63 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 62 HIS 0.003 0.001 HIS H 236 PHE 0.006 0.001 PHE B 124 TYR 0.016 0.001 TYR E 142 ARG 0.001 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 366 time to evaluate : 1.893 Fit side-chains revert: symmetry clash REVERT: A 32 GLN cc_start: 0.5803 (tm-30) cc_final: 0.5571 (tp40) REVERT: A 46 ASP cc_start: 0.8828 (m-30) cc_final: 0.8503 (m-30) REVERT: A 79 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7460 (tp30) REVERT: A 105 ARG cc_start: 0.8056 (mpt180) cc_final: 0.7791 (tpp-160) REVERT: A 143 GLN cc_start: 0.7922 (mm110) cc_final: 0.7501 (mm-40) REVERT: A 148 LYS cc_start: 0.8101 (mppt) cc_final: 0.7588 (ttmm) REVERT: A 164 GLU cc_start: 0.7686 (pm20) cc_final: 0.7084 (pm20) REVERT: A 165 GLU cc_start: 0.7522 (mt-10) cc_final: 0.6996 (mp0) REVERT: B 38 GLU cc_start: 0.8234 (tp30) cc_final: 0.7890 (tp30) REVERT: B 46 ASP cc_start: 0.8781 (m-30) cc_final: 0.8291 (m-30) REVERT: B 73 ASN cc_start: 0.8533 (p0) cc_final: 0.8077 (p0) REVERT: B 79 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7573 (tp30) REVERT: B 105 ARG cc_start: 0.8046 (mpt180) cc_final: 0.7746 (tpp-160) REVERT: B 147 GLN cc_start: 0.7754 (mm110) cc_final: 0.7360 (mm-40) REVERT: B 148 LYS cc_start: 0.8187 (mmtm) cc_final: 0.7881 (tttt) REVERT: B 164 GLU cc_start: 0.7738 (pm20) cc_final: 0.7356 (pm20) REVERT: B 165 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7166 (mp0) REVERT: B 220 HIS cc_start: 0.7966 (m-70) cc_final: 0.7729 (m170) REVERT: C 32 GLN cc_start: 0.5800 (tm-30) cc_final: 0.5569 (tp40) REVERT: C 46 ASP cc_start: 0.8827 (m-30) cc_final: 0.8502 (m-30) REVERT: C 79 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7469 (tp30) REVERT: C 105 ARG cc_start: 0.7957 (mpt180) cc_final: 0.7699 (tpp-160) REVERT: C 143 GLN cc_start: 0.7921 (mm110) cc_final: 0.7499 (mm-40) REVERT: C 148 LYS cc_start: 0.8104 (mppt) cc_final: 0.7587 (ttmm) REVERT: C 164 GLU cc_start: 0.7686 (pm20) cc_final: 0.7083 (pm20) REVERT: C 165 GLU cc_start: 0.7519 (mt-10) cc_final: 0.6995 (mp0) REVERT: D 38 GLU cc_start: 0.8233 (tp30) cc_final: 0.7890 (tp30) REVERT: D 46 ASP cc_start: 0.8779 (m-30) cc_final: 0.8290 (m-30) REVERT: D 73 ASN cc_start: 0.8530 (p0) cc_final: 0.8075 (p0) REVERT: D 79 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7582 (tp30) REVERT: D 105 ARG cc_start: 0.8039 (mpt180) cc_final: 0.7742 (tpp-160) REVERT: D 143 GLN cc_start: 0.8008 (mm110) cc_final: 0.7690 (mm-40) REVERT: D 147 GLN cc_start: 0.7793 (mm110) cc_final: 0.7380 (mm-40) REVERT: D 148 LYS cc_start: 0.8147 (mmtm) cc_final: 0.7789 (tttt) REVERT: D 164 GLU cc_start: 0.7723 (pm20) cc_final: 0.7336 (pm20) REVERT: D 165 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7171 (mp0) REVERT: D 220 HIS cc_start: 0.7963 (m-70) cc_final: 0.7724 (m170) REVERT: E 32 GLN cc_start: 0.5804 (tm-30) cc_final: 0.5573 (tp40) REVERT: E 46 ASP cc_start: 0.8828 (m-30) cc_final: 0.8503 (m-30) REVERT: E 79 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7471 (tp30) REVERT: E 105 ARG cc_start: 0.8054 (mpt180) cc_final: 0.7789 (tpp-160) REVERT: E 143 GLN cc_start: 0.7923 (mm110) cc_final: 0.7500 (mm-40) REVERT: E 148 LYS cc_start: 0.8101 (mppt) cc_final: 0.7586 (ttmm) REVERT: E 164 GLU cc_start: 0.7690 (pm20) cc_final: 0.7087 (pm20) REVERT: E 165 GLU cc_start: 0.7523 (mt-10) cc_final: 0.6997 (mp0) REVERT: F 38 GLU cc_start: 0.8233 (tp30) cc_final: 0.7889 (tp30) REVERT: F 46 ASP cc_start: 0.8781 (m-30) cc_final: 0.8290 (m-30) REVERT: F 73 ASN cc_start: 0.8531 (p0) cc_final: 0.8078 (p0) REVERT: F 79 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7578 (tp30) REVERT: F 105 ARG cc_start: 0.8039 (mpt180) cc_final: 0.7743 (tpp-160) REVERT: F 147 GLN cc_start: 0.7688 (mm110) cc_final: 0.7422 (mm-40) REVERT: F 148 LYS cc_start: 0.8222 (mppt) cc_final: 0.7905 (tttt) REVERT: F 164 GLU cc_start: 0.7722 (pm20) cc_final: 0.7337 (pm20) REVERT: F 165 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7159 (mp0) REVERT: F 220 HIS cc_start: 0.7931 (m-70) cc_final: 0.7702 (m170) REVERT: G 32 GLN cc_start: 0.5806 (tm-30) cc_final: 0.5573 (tp40) REVERT: G 46 ASP cc_start: 0.8828 (m-30) cc_final: 0.8501 (m-30) REVERT: G 79 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7473 (tp30) REVERT: G 105 ARG cc_start: 0.7931 (mpt180) cc_final: 0.7674 (tpp-160) REVERT: G 143 GLN cc_start: 0.7923 (mm110) cc_final: 0.7500 (mm-40) REVERT: G 148 LYS cc_start: 0.8102 (mppt) cc_final: 0.7587 (ttmm) REVERT: G 164 GLU cc_start: 0.7690 (pm20) cc_final: 0.7086 (pm20) REVERT: G 165 GLU cc_start: 0.7524 (mt-10) cc_final: 0.6999 (mp0) REVERT: H 38 GLU cc_start: 0.8226 (tp30) cc_final: 0.7876 (tp30) REVERT: H 46 ASP cc_start: 0.8780 (m-30) cc_final: 0.8289 (m-30) REVERT: H 73 ASN cc_start: 0.8530 (p0) cc_final: 0.8075 (p0) REVERT: H 79 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7550 (tp30) REVERT: H 105 ARG cc_start: 0.8038 (mpt180) cc_final: 0.7742 (tpp-160) REVERT: H 147 GLN cc_start: 0.7690 (mm110) cc_final: 0.7425 (mm-40) REVERT: H 148 LYS cc_start: 0.8224 (mppt) cc_final: 0.7909 (tttt) REVERT: H 164 GLU cc_start: 0.7723 (pm20) cc_final: 0.7334 (pm20) REVERT: H 165 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7152 (mp0) REVERT: H 220 HIS cc_start: 0.7925 (m-70) cc_final: 0.7696 (m170) outliers start: 7 outliers final: 7 residues processed: 367 average time/residue: 0.3125 time to fit residues: 160.9556 Evaluate side-chains 373 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 366 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 161 ASP 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 171 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 101 optimal weight: 0.4980 chunk 130 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 177 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 ASN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN F 71 ASN H 71 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15024 Z= 0.182 Angle : 0.466 5.492 20352 Z= 0.244 Chirality : 0.037 0.152 2336 Planarity : 0.004 0.046 2504 Dihedral : 3.385 16.175 2144 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.86 % Allowed : 17.96 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.18 (0.20), residues: 1792 helix: 2.96 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.52 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 62 HIS 0.003 0.001 HIS H 236 PHE 0.006 0.001 PHE B 124 TYR 0.016 0.001 TYR E 142 ARG 0.000 0.000 ARG G 201 *********************** 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 365 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 352 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.5821 (tm-30) cc_final: 0.5574 (tp40) REVERT: A 46 ASP cc_start: 0.8830 (m-30) cc_final: 0.8507 (m-30) REVERT: A 79 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7456 (tp30) REVERT: A 105 ARG cc_start: 0.8059 (mpt180) cc_final: 0.7791 (tpp-160) REVERT: A 133 ASP cc_start: 0.8919 (t70) cc_final: 0.8620 (t0) REVERT: A 143 GLN cc_start: 0.7917 (mm110) cc_final: 0.7570 (mm-40) REVERT: A 148 LYS cc_start: 0.8093 (mppt) cc_final: 0.7584 (ttmm) REVERT: A 164 GLU cc_start: 0.7652 (pm20) cc_final: 0.7196 (pm20) REVERT: A 165 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6980 (mp0) REVERT: B 38 GLU cc_start: 0.8227 (tp30) cc_final: 0.7884 (tp30) REVERT: B 46 ASP cc_start: 0.8774 (m-30) cc_final: 0.8295 (m-30) REVERT: B 71 ASN cc_start: 0.8652 (t0) cc_final: 0.8261 (t0) REVERT: B 73 ASN cc_start: 0.8461 (p0) cc_final: 0.7802 (p0) REVERT: B 79 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7513 (tp30) REVERT: B 105 ARG cc_start: 0.8056 (mpt180) cc_final: 0.7756 (tpp-160) REVERT: B 124 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7525 (t80) REVERT: B 147 GLN cc_start: 0.7788 (mm110) cc_final: 0.7395 (mm-40) REVERT: B 148 LYS cc_start: 0.8131 (mmtm) cc_final: 0.7862 (tttt) REVERT: B 164 GLU cc_start: 0.7686 (pm20) cc_final: 0.7332 (pm20) REVERT: B 165 GLU cc_start: 0.7604 (mt-10) cc_final: 0.6965 (mp0) REVERT: B 220 HIS cc_start: 0.7963 (m-70) cc_final: 0.7727 (m170) REVERT: C 32 GLN cc_start: 0.5825 (tm-30) cc_final: 0.5575 (tp40) REVERT: C 46 ASP cc_start: 0.8828 (m-30) cc_final: 0.8509 (m-30) REVERT: C 79 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7464 (tp30) REVERT: C 105 ARG cc_start: 0.8023 (mpt180) cc_final: 0.7760 (tpp-160) REVERT: C 133 ASP cc_start: 0.8920 (t70) cc_final: 0.8621 (t0) REVERT: C 143 GLN cc_start: 0.7917 (mm110) cc_final: 0.7569 (mm-40) REVERT: C 148 LYS cc_start: 0.8095 (mppt) cc_final: 0.7585 (ttmm) REVERT: C 164 GLU cc_start: 0.7653 (pm20) cc_final: 0.7196 (pm20) REVERT: C 165 GLU cc_start: 0.7502 (mt-10) cc_final: 0.6980 (mp0) REVERT: D 38 GLU cc_start: 0.8226 (tp30) cc_final: 0.7881 (tp30) REVERT: D 46 ASP cc_start: 0.8771 (m-30) cc_final: 0.8294 (m-30) REVERT: D 71 ASN cc_start: 0.8650 (t0) cc_final: 0.8262 (t0) REVERT: D 73 ASN cc_start: 0.8458 (p0) cc_final: 0.7802 (p0) REVERT: D 79 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7520 (tp30) REVERT: D 105 ARG cc_start: 0.8070 (mpt180) cc_final: 0.7770 (tpp-160) REVERT: D 124 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7526 (t80) REVERT: D 147 GLN cc_start: 0.7822 (mm110) cc_final: 0.7415 (mm-40) REVERT: D 148 LYS cc_start: 0.8089 (mmtm) cc_final: 0.7751 (tttt) REVERT: D 164 GLU cc_start: 0.7683 (pm20) cc_final: 0.7302 (pm20) REVERT: D 165 GLU cc_start: 0.7606 (mt-10) cc_final: 0.6960 (mp0) REVERT: D 220 HIS cc_start: 0.7960 (m-70) cc_final: 0.7719 (m170) REVERT: E 32 GLN cc_start: 0.5860 (tm-30) cc_final: 0.5616 (tp40) REVERT: E 46 ASP cc_start: 0.8829 (m-30) cc_final: 0.8508 (m-30) REVERT: E 79 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7466 (tp30) REVERT: E 105 ARG cc_start: 0.8027 (mpt180) cc_final: 0.7765 (tpp-160) REVERT: E 133 ASP cc_start: 0.8920 (t70) cc_final: 0.8620 (t0) REVERT: E 143 GLN cc_start: 0.7916 (mm110) cc_final: 0.7570 (mm-40) REVERT: E 148 LYS cc_start: 0.8093 (mppt) cc_final: 0.7584 (ttmm) REVERT: E 164 GLU cc_start: 0.7654 (pm20) cc_final: 0.7196 (pm20) REVERT: E 165 GLU cc_start: 0.7502 (mt-10) cc_final: 0.6982 (mp0) REVERT: F 38 GLU cc_start: 0.8227 (tp30) cc_final: 0.7883 (tp30) REVERT: F 46 ASP cc_start: 0.8773 (m-30) cc_final: 0.8296 (m-30) REVERT: F 71 ASN cc_start: 0.8653 (t0) cc_final: 0.8264 (t0) REVERT: F 73 ASN cc_start: 0.8460 (p0) cc_final: 0.7807 (p0) REVERT: F 79 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7517 (tp30) REVERT: F 105 ARG cc_start: 0.8069 (mpt180) cc_final: 0.7769 (tpp-160) REVERT: F 124 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7525 (t80) REVERT: F 147 GLN cc_start: 0.7719 (mm110) cc_final: 0.7352 (mm110) REVERT: F 148 LYS cc_start: 0.8222 (mppt) cc_final: 0.7861 (tttt) REVERT: F 164 GLU cc_start: 0.7685 (pm20) cc_final: 0.7211 (pm20) REVERT: F 165 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7157 (mp0) REVERT: F 220 HIS cc_start: 0.7932 (m-70) cc_final: 0.7700 (m170) REVERT: G 32 GLN cc_start: 0.5862 (tm-30) cc_final: 0.5616 (tp40) REVERT: G 46 ASP cc_start: 0.8829 (m-30) cc_final: 0.8507 (m-30) REVERT: G 79 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7502 (tp30) REVERT: G 105 ARG cc_start: 0.8024 (mpt180) cc_final: 0.7759 (tpp-160) REVERT: G 133 ASP cc_start: 0.8921 (t70) cc_final: 0.8624 (t0) REVERT: G 143 GLN cc_start: 0.7916 (mm110) cc_final: 0.7570 (mm-40) REVERT: G 148 LYS cc_start: 0.8094 (mppt) cc_final: 0.7584 (ttmm) REVERT: G 164 GLU cc_start: 0.7652 (pm20) cc_final: 0.7195 (pm20) REVERT: G 165 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6982 (mp0) REVERT: H 38 GLU cc_start: 0.8227 (tp30) cc_final: 0.7882 (tp30) REVERT: H 46 ASP cc_start: 0.8773 (m-30) cc_final: 0.8294 (m-30) REVERT: H 71 ASN cc_start: 0.8653 (t0) cc_final: 0.8264 (t0) REVERT: H 73 ASN cc_start: 0.8459 (p0) cc_final: 0.7806 (p0) REVERT: H 79 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7552 (tp30) REVERT: H 105 ARG cc_start: 0.8069 (mpt180) cc_final: 0.7769 (tpp-160) REVERT: H 124 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7525 (t80) REVERT: H 147 GLN cc_start: 0.7705 (mm110) cc_final: 0.7335 (mm110) REVERT: H 148 LYS cc_start: 0.8234 (mppt) cc_final: 0.7883 (tttt) REVERT: H 164 GLU cc_start: 0.7679 (pm20) cc_final: 0.7201 (pm20) REVERT: H 165 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7120 (mp0) REVERT: H 220 HIS cc_start: 0.7926 (m-70) cc_final: 0.7696 (m170) outliers start: 13 outliers final: 5 residues processed: 357 average time/residue: 0.3161 time to fit residues: 157.4549 Evaluate side-chains 361 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 352 time to evaluate : 1.872 ------------------------------------------------------------------------------- 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 124 PHE Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 124 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 1.9990 chunk 70 optimal weight: 0.0470 chunk 105 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 139 optimal weight: 0.4980 chunk 161 optimal weight: 70.0000 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 HIS D 236 HIS F 143 GLN F 236 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15024 Z= 0.163 Angle : 0.460 5.693 20352 Z= 0.239 Chirality : 0.036 0.123 2336 Planarity : 0.004 0.046 2504 Dihedral : 3.308 15.935 2144 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.66 % Allowed : 18.68 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.20), residues: 1792 helix: 3.02 (0.13), residues: 1432 sheet: None (None), residues: 0 loop : -1.37 (0.36), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 62 HIS 0.003 0.001 HIS A 220 PHE 0.005 0.001 PHE B 124 TYR 0.016 0.001 TYR G 142 ARG 0.000 0.000 ARG G 176 *********************** 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 370 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 360 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.5876 (tm-30) cc_final: 0.5635 (tp40) REVERT: A 46 ASP cc_start: 0.8823 (m-30) cc_final: 0.8500 (m-30) REVERT: A 79 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7482 (tp30) REVERT: A 105 ARG cc_start: 0.8028 (mpt180) cc_final: 0.7757 (tpp-160) REVERT: A 133 ASP cc_start: 0.8892 (t70) cc_final: 0.8595 (t0) REVERT: A 143 GLN cc_start: 0.8125 (mm110) cc_final: 0.7909 (mm-40) REVERT: A 147 GLN cc_start: 0.7619 (mm110) cc_final: 0.7242 (mm110) REVERT: A 148 LYS cc_start: 0.8077 (mppt) cc_final: 0.7539 (ttmm) REVERT: A 164 GLU cc_start: 0.7646 (pm20) cc_final: 0.7201 (pm20) REVERT: A 165 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6938 (mp0) REVERT: B 38 GLU cc_start: 0.8217 (tp30) cc_final: 0.7862 (tp30) REVERT: B 46 ASP cc_start: 0.8772 (m-30) cc_final: 0.8298 (m-30) REVERT: B 71 ASN cc_start: 0.8637 (t0) cc_final: 0.8302 (t0) REVERT: B 73 ASN cc_start: 0.8358 (p0) cc_final: 0.7712 (p0) REVERT: B 79 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7474 (tp30) REVERT: B 105 ARG cc_start: 0.8084 (mpt180) cc_final: 0.7766 (tpp-160) REVERT: B 143 GLN cc_start: 0.8026 (mm110) cc_final: 0.7670 (mm110) REVERT: B 147 GLN cc_start: 0.7804 (mm110) cc_final: 0.7428 (mm-40) REVERT: B 148 LYS cc_start: 0.8082 (mmtm) cc_final: 0.7854 (tttt) REVERT: B 165 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7317 (mp0) REVERT: B 220 HIS cc_start: 0.7966 (m-70) cc_final: 0.7735 (m170) REVERT: C 32 GLN cc_start: 0.5877 (tm-30) cc_final: 0.5634 (tp40) REVERT: C 46 ASP cc_start: 0.8825 (m-30) cc_final: 0.8500 (m-30) REVERT: C 73 ASN cc_start: 0.8182 (p0) cc_final: 0.7827 (p0) REVERT: C 79 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7490 (tp30) REVERT: C 105 ARG cc_start: 0.8017 (mpt180) cc_final: 0.7746 (tpp-160) REVERT: C 133 ASP cc_start: 0.8893 (t70) cc_final: 0.8595 (t0) REVERT: C 143 GLN cc_start: 0.8125 (mm110) cc_final: 0.7909 (mm-40) REVERT: C 147 GLN cc_start: 0.7618 (mm110) cc_final: 0.7240 (mm110) REVERT: C 148 LYS cc_start: 0.8078 (mppt) cc_final: 0.7539 (ttmm) REVERT: C 164 GLU cc_start: 0.7649 (pm20) cc_final: 0.7204 (pm20) REVERT: C 165 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6939 (mp0) REVERT: D 38 GLU cc_start: 0.8215 (tp30) cc_final: 0.7861 (tp30) REVERT: D 46 ASP cc_start: 0.8770 (m-30) cc_final: 0.8295 (m-30) REVERT: D 71 ASN cc_start: 0.8634 (t0) cc_final: 0.8298 (t0) REVERT: D 73 ASN cc_start: 0.8350 (p0) cc_final: 0.7692 (p0) REVERT: D 79 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7484 (tp30) REVERT: D 105 ARG cc_start: 0.8081 (mpt180) cc_final: 0.7763 (tpp-160) REVERT: D 147 GLN cc_start: 0.7823 (mm110) cc_final: 0.7441 (mm-40) REVERT: D 148 LYS cc_start: 0.8096 (mmtm) cc_final: 0.7823 (tttt) REVERT: D 165 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7330 (mp0) REVERT: D 220 HIS cc_start: 0.7964 (m-70) cc_final: 0.7726 (m170) REVERT: E 32 GLN cc_start: 0.5878 (tm-30) cc_final: 0.5634 (tp40) REVERT: E 46 ASP cc_start: 0.8827 (m-30) cc_final: 0.8501 (m-30) REVERT: E 79 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7492 (tp30) REVERT: E 105 ARG cc_start: 0.8048 (mpt180) cc_final: 0.7756 (tpp-160) REVERT: E 133 ASP cc_start: 0.8891 (t70) cc_final: 0.8595 (t0) REVERT: E 143 GLN cc_start: 0.8126 (mm110) cc_final: 0.7909 (mm-40) REVERT: E 147 GLN cc_start: 0.7617 (mm110) cc_final: 0.7239 (mm110) REVERT: E 148 LYS cc_start: 0.8077 (mppt) cc_final: 0.7538 (ttmm) REVERT: E 164 GLU cc_start: 0.7649 (pm20) cc_final: 0.7203 (pm20) REVERT: E 165 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6940 (mp0) REVERT: F 46 ASP cc_start: 0.8772 (m-30) cc_final: 0.8298 (m-30) REVERT: F 71 ASN cc_start: 0.8636 (t0) cc_final: 0.8301 (t0) REVERT: F 73 ASN cc_start: 0.8354 (p0) cc_final: 0.7710 (p0) REVERT: F 79 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7487 (tp30) REVERT: F 105 ARG cc_start: 0.8082 (mpt180) cc_final: 0.7763 (tpp-160) REVERT: F 147 GLN cc_start: 0.7737 (mm110) cc_final: 0.7388 (mm110) REVERT: F 148 LYS cc_start: 0.8204 (mppt) cc_final: 0.7841 (tttt) REVERT: F 165 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7353 (mp0) REVERT: F 167 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7807 (mp0) REVERT: F 220 HIS cc_start: 0.7962 (m-70) cc_final: 0.7735 (m170) REVERT: G 32 GLN cc_start: 0.5878 (tm-30) cc_final: 0.5634 (tp40) REVERT: G 46 ASP cc_start: 0.8826 (m-30) cc_final: 0.8502 (m-30) REVERT: G 79 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7530 (tp30) REVERT: G 105 ARG cc_start: 0.8029 (mpt180) cc_final: 0.7754 (tpp-160) REVERT: G 133 ASP cc_start: 0.8893 (t70) cc_final: 0.8599 (t0) REVERT: G 143 GLN cc_start: 0.8125 (mm110) cc_final: 0.7908 (mm-40) REVERT: G 147 GLN cc_start: 0.7619 (mm110) cc_final: 0.7241 (mm110) REVERT: G 148 LYS cc_start: 0.8077 (mppt) cc_final: 0.7538 (ttmm) REVERT: G 164 GLU cc_start: 0.7651 (pm20) cc_final: 0.7202 (pm20) REVERT: G 165 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6942 (mp0) REVERT: H 46 ASP cc_start: 0.8771 (m-30) cc_final: 0.8296 (m-30) REVERT: H 71 ASN cc_start: 0.8636 (t0) cc_final: 0.8302 (t0) REVERT: H 73 ASN cc_start: 0.8353 (p0) cc_final: 0.7693 (p0) REVERT: H 79 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7510 (tp30) REVERT: H 105 ARG cc_start: 0.8083 (mpt180) cc_final: 0.7765 (tpp-160) REVERT: H 147 GLN cc_start: 0.7739 (mm110) cc_final: 0.7398 (mm110) REVERT: H 148 LYS cc_start: 0.8201 (mppt) cc_final: 0.7844 (tttt) REVERT: H 167 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7734 (mp0) REVERT: H 220 HIS cc_start: 0.7956 (m-70) cc_final: 0.7730 (m170) outliers start: 10 outliers final: 9 residues processed: 363 average time/residue: 0.3143 time to fit residues: 159.1110 Evaluate side-chains 364 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 355 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 131 THR 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 169 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 129 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 149 optimal weight: 0.2980 chunk 156 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 HIS ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15024 Z= 0.167 Angle : 0.475 5.798 20352 Z= 0.247 Chirality : 0.036 0.123 2336 Planarity : 0.004 0.046 2504 Dihedral : 3.262 15.787 2144 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.25 % Allowed : 17.30 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.20), residues: 1792 helix: 3.06 (0.13), residues: 1432 sheet: None (None), residues: 0 loop : -1.31 (0.36), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 62 HIS 0.003 0.001 HIS E 220 PHE 0.006 0.001 PHE D 124 TYR 0.016 0.001 TYR E 142 ARG 0.001 0.000 ARG F 171 *********************** 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 368 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 349 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.5884 (tm-30) cc_final: 0.5637 (tp40) REVERT: A 46 ASP cc_start: 0.8825 (m-30) cc_final: 0.8503 (m-30) REVERT: A 73 ASN cc_start: 0.8148 (p0) cc_final: 0.7783 (p0) REVERT: A 79 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7479 (tp30) REVERT: A 105 ARG cc_start: 0.8067 (mpt180) cc_final: 0.7768 (tpp-160) REVERT: A 133 ASP cc_start: 0.8879 (t70) cc_final: 0.8585 (t0) REVERT: A 147 GLN cc_start: 0.7661 (mm110) cc_final: 0.7309 (mm110) REVERT: A 148 LYS cc_start: 0.8069 (mppt) cc_final: 0.7538 (ttmm) REVERT: A 164 GLU cc_start: 0.7641 (pm20) cc_final: 0.7219 (pm20) REVERT: A 165 GLU cc_start: 0.7467 (mt-10) cc_final: 0.6937 (mp0) REVERT: B 46 ASP cc_start: 0.8775 (m-30) cc_final: 0.8299 (m-30) REVERT: B 71 ASN cc_start: 0.8622 (t0) cc_final: 0.8289 (t0) REVERT: B 73 ASN cc_start: 0.8277 (p0) cc_final: 0.7641 (p0) REVERT: B 79 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7469 (tp30) REVERT: B 105 ARG cc_start: 0.8087 (mpt180) cc_final: 0.7761 (tpp-160) REVERT: B 124 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7470 (t80) REVERT: B 143 GLN cc_start: 0.8072 (mm110) cc_final: 0.7742 (mm110) REVERT: B 147 GLN cc_start: 0.7793 (mm110) cc_final: 0.7340 (mm110) REVERT: B 148 LYS cc_start: 0.8055 (mmtm) cc_final: 0.7835 (tttt) REVERT: B 165 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7315 (mt-10) REVERT: B 167 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7650 (mp0) REVERT: B 220 HIS cc_start: 0.7969 (m-70) cc_final: 0.7736 (m170) REVERT: C 32 GLN cc_start: 0.5884 (tm-30) cc_final: 0.5638 (tp40) REVERT: C 46 ASP cc_start: 0.8826 (m-30) cc_final: 0.8503 (m-30) REVERT: C 73 ASN cc_start: 0.8064 (p0) cc_final: 0.7766 (p0) REVERT: C 79 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7487 (tp30) REVERT: C 105 ARG cc_start: 0.8057 (mpt180) cc_final: 0.7758 (tpp-160) REVERT: C 133 ASP cc_start: 0.8880 (t70) cc_final: 0.8587 (t0) REVERT: C 147 GLN cc_start: 0.7658 (mm110) cc_final: 0.7306 (mm110) REVERT: C 148 LYS cc_start: 0.8070 (mppt) cc_final: 0.7539 (ttmm) REVERT: C 164 GLU cc_start: 0.7642 (pm20) cc_final: 0.7219 (pm20) REVERT: C 165 GLU cc_start: 0.7470 (mt-10) cc_final: 0.6940 (mp0) REVERT: D 46 ASP cc_start: 0.8772 (m-30) cc_final: 0.8296 (m-30) REVERT: D 71 ASN cc_start: 0.8620 (t0) cc_final: 0.8288 (t0) REVERT: D 73 ASN cc_start: 0.8292 (p0) cc_final: 0.7662 (p0) REVERT: D 79 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7478 (tp30) REVERT: D 105 ARG cc_start: 0.8084 (mpt180) cc_final: 0.7762 (tpp-160) REVERT: D 124 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7467 (t80) REVERT: D 147 GLN cc_start: 0.7809 (mm110) cc_final: 0.7337 (mm110) REVERT: D 148 LYS cc_start: 0.8067 (mmtm) cc_final: 0.7802 (tttt) REVERT: D 165 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7345 (mt-10) REVERT: D 167 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7686 (mp0) REVERT: D 220 HIS cc_start: 0.7964 (m-70) cc_final: 0.7727 (m170) REVERT: E 32 GLN cc_start: 0.5882 (tm-30) cc_final: 0.5638 (tp40) REVERT: E 46 ASP cc_start: 0.8829 (m-30) cc_final: 0.8506 (m-30) REVERT: E 73 ASN cc_start: 0.8121 (p0) cc_final: 0.7777 (p0) REVERT: E 79 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7489 (tp30) REVERT: E 105 ARG cc_start: 0.8057 (mpt180) cc_final: 0.7760 (tpp-160) REVERT: E 133 ASP cc_start: 0.8880 (t70) cc_final: 0.8586 (t0) REVERT: E 147 GLN cc_start: 0.7659 (mm110) cc_final: 0.7307 (mm110) REVERT: E 148 LYS cc_start: 0.8068 (mppt) cc_final: 0.7537 (ttmm) REVERT: E 164 GLU cc_start: 0.7642 (pm20) cc_final: 0.7219 (pm20) REVERT: E 165 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6942 (mp0) REVERT: F 38 GLU cc_start: 0.8215 (tp30) cc_final: 0.7853 (tp30) REVERT: F 46 ASP cc_start: 0.8774 (m-30) cc_final: 0.8300 (m-30) REVERT: F 71 ASN cc_start: 0.8616 (t0) cc_final: 0.8285 (t0) REVERT: F 73 ASN cc_start: 0.8288 (p0) cc_final: 0.7643 (p0) REVERT: F 79 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7504 (tp30) REVERT: F 105 ARG cc_start: 0.8086 (mpt180) cc_final: 0.7757 (tpp-160) REVERT: F 124 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7468 (t80) REVERT: F 147 GLN cc_start: 0.7746 (mm110) cc_final: 0.7417 (mm110) REVERT: F 148 LYS cc_start: 0.8187 (mppt) cc_final: 0.7833 (tttt) REVERT: F 165 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7264 (mt-10) REVERT: F 220 HIS cc_start: 0.7964 (m-70) cc_final: 0.7739 (m170) REVERT: G 32 GLN cc_start: 0.5882 (tm-30) cc_final: 0.5638 (tp40) REVERT: G 46 ASP cc_start: 0.8828 (m-30) cc_final: 0.8506 (m-30) REVERT: G 73 ASN cc_start: 0.8058 (p0) cc_final: 0.7739 (p0) REVERT: G 79 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7528 (tp30) REVERT: G 105 ARG cc_start: 0.8037 (mpt180) cc_final: 0.7751 (tpp-160) REVERT: G 133 ASP cc_start: 0.8880 (t70) cc_final: 0.8588 (t0) REVERT: G 147 GLN cc_start: 0.7660 (mm110) cc_final: 0.7308 (mm110) REVERT: G 148 LYS cc_start: 0.8068 (mppt) cc_final: 0.7537 (ttmm) REVERT: G 164 GLU cc_start: 0.7643 (pm20) cc_final: 0.7220 (pm20) REVERT: G 165 GLU cc_start: 0.7469 (mt-10) cc_final: 0.6941 (mp0) REVERT: H 38 GLU cc_start: 0.8216 (tp30) cc_final: 0.7856 (tp30) REVERT: H 46 ASP cc_start: 0.8767 (m-30) cc_final: 0.8335 (m-30) REVERT: H 71 ASN cc_start: 0.8620 (t0) cc_final: 0.8287 (t0) REVERT: H 73 ASN cc_start: 0.8291 (p0) cc_final: 0.7644 (p0) REVERT: H 79 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7507 (tp30) REVERT: H 105 ARG cc_start: 0.8086 (mpt180) cc_final: 0.7763 (tpp-160) REVERT: H 124 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7470 (t80) REVERT: H 147 GLN cc_start: 0.7749 (mm110) cc_final: 0.7420 (mm110) REVERT: H 148 LYS cc_start: 0.8183 (mppt) cc_final: 0.7828 (tttt) REVERT: H 220 HIS cc_start: 0.7956 (m-70) cc_final: 0.7730 (m170) outliers start: 19 outliers final: 12 residues processed: 356 average time/residue: 0.3132 time to fit residues: 155.2741 Evaluate side-chains 341 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 325 time to evaluate : 1.817 ------------------------------------------------------------------------------- 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 124 PHE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 161 ASP 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 131 THR 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 174 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 115 optimal weight: 50.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 32 GLN B 236 HIS D 32 GLN D 236 HIS ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 HIS H 236 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 15024 Z= 0.481 Angle : 0.634 6.907 20352 Z= 0.329 Chirality : 0.043 0.154 2336 Planarity : 0.005 0.049 2504 Dihedral : 3.707 16.984 2144 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.05 % Allowed : 18.22 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.20), residues: 1792 helix: 2.73 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -1.66 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 187 HIS 0.003 0.001 HIS B 236 PHE 0.011 0.002 PHE B 124 TYR 0.020 0.002 TYR E 142 ARG 0.002 0.000 ARG G 179 ********************** 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 361 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 345 time to evaluate : 1.866 Fit side-chains REVERT: A 32 GLN cc_start: 0.5914 (tm-30) cc_final: 0.5617 (tp40) REVERT: A 46 ASP cc_start: 0.8774 (m-30) cc_final: 0.8438 (m-30) REVERT: A 71 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.7810 (t0) REVERT: A 79 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7503 (tp30) REVERT: A 105 ARG cc_start: 0.8155 (mpt180) cc_final: 0.7843 (tpp-160) REVERT: A 133 ASP cc_start: 0.8890 (t70) cc_final: 0.8587 (t0) REVERT: A 147 GLN cc_start: 0.7762 (mm110) cc_final: 0.7429 (mm110) REVERT: A 148 LYS cc_start: 0.8173 (mppt) cc_final: 0.7658 (ttmm) REVERT: A 164 GLU cc_start: 0.7637 (pm20) cc_final: 0.7129 (pm20) REVERT: A 165 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7059 (mp0) REVERT: B 38 GLU cc_start: 0.8280 (tp30) cc_final: 0.7898 (tp30) REVERT: B 46 ASP cc_start: 0.8796 (m-30) cc_final: 0.8242 (m-30) REVERT: B 71 ASN cc_start: 0.8731 (t0) cc_final: 0.8393 (t0) REVERT: B 73 ASN cc_start: 0.8440 (p0) cc_final: 0.7693 (p0) REVERT: B 79 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7604 (tp30) REVERT: B 124 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.7702 (t80) REVERT: B 147 GLN cc_start: 0.7959 (mm110) cc_final: 0.7494 (mm110) REVERT: B 148 LYS cc_start: 0.8152 (mmtm) cc_final: 0.7889 (tttt) REVERT: B 164 GLU cc_start: 0.7762 (pm20) cc_final: 0.7337 (pm20) REVERT: B 165 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7180 (mp0) REVERT: C 32 GLN cc_start: 0.5909 (tm-30) cc_final: 0.5613 (tp40) REVERT: C 46 ASP cc_start: 0.8776 (m-30) cc_final: 0.8439 (m-30) REVERT: C 79 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7518 (tp30) REVERT: C 105 ARG cc_start: 0.8155 (mpt180) cc_final: 0.7843 (tpp-160) REVERT: C 133 ASP cc_start: 0.8891 (t70) cc_final: 0.8588 (t0) REVERT: C 147 GLN cc_start: 0.7761 (mm110) cc_final: 0.7428 (mm110) REVERT: C 148 LYS cc_start: 0.8173 (mppt) cc_final: 0.7657 (ttmm) REVERT: C 164 GLU cc_start: 0.7635 (pm20) cc_final: 0.7128 (pm20) REVERT: C 165 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7064 (mp0) REVERT: D 38 GLU cc_start: 0.8280 (tp30) cc_final: 0.7899 (tp30) REVERT: D 46 ASP cc_start: 0.8796 (m-30) cc_final: 0.8241 (m-30) REVERT: D 71 ASN cc_start: 0.8730 (t0) cc_final: 0.8397 (t0) REVERT: D 73 ASN cc_start: 0.8457 (p0) cc_final: 0.7663 (p0) REVERT: D 79 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7610 (tp30) REVERT: D 124 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.7701 (t80) REVERT: D 147 GLN cc_start: 0.7900 (mm110) cc_final: 0.7361 (mm110) REVERT: D 148 LYS cc_start: 0.8083 (mmtm) cc_final: 0.7780 (tttt) REVERT: D 164 GLU cc_start: 0.7763 (pm20) cc_final: 0.7333 (pm20) REVERT: D 165 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7187 (mp0) REVERT: E 32 GLN cc_start: 0.5908 (tm-30) cc_final: 0.5618 (tp40) REVERT: E 46 ASP cc_start: 0.8777 (m-30) cc_final: 0.8438 (m-30) REVERT: E 79 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7521 (tp30) REVERT: E 105 ARG cc_start: 0.8156 (mpt180) cc_final: 0.7845 (tpp-160) REVERT: E 133 ASP cc_start: 0.8891 (t70) cc_final: 0.8588 (t0) REVERT: E 147 GLN cc_start: 0.7761 (mm110) cc_final: 0.7427 (mm110) REVERT: E 148 LYS cc_start: 0.8170 (mppt) cc_final: 0.7655 (ttmm) REVERT: E 164 GLU cc_start: 0.7636 (pm20) cc_final: 0.7125 (pm20) REVERT: E 165 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7065 (mp0) REVERT: F 46 ASP cc_start: 0.8798 (m-30) cc_final: 0.8241 (m-30) REVERT: F 71 ASN cc_start: 0.8729 (t0) cc_final: 0.8389 (t0) REVERT: F 73 ASN cc_start: 0.8439 (p0) cc_final: 0.7698 (p0) REVERT: F 79 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7662 (tp30) REVERT: F 124 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.7700 (t80) REVERT: F 147 GLN cc_start: 0.7828 (mm110) cc_final: 0.7508 (mm110) REVERT: F 148 LYS cc_start: 0.8226 (mppt) cc_final: 0.7860 (tttt) REVERT: F 164 GLU cc_start: 0.7770 (pm20) cc_final: 0.7163 (pm20) REVERT: F 165 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7208 (mp0) REVERT: F 167 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7790 (mp0) REVERT: G 32 GLN cc_start: 0.5912 (tm-30) cc_final: 0.5618 (tp40) REVERT: G 46 ASP cc_start: 0.8777 (m-30) cc_final: 0.8440 (m-30) REVERT: G 79 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7514 (tp30) REVERT: G 105 ARG cc_start: 0.8164 (mpt180) cc_final: 0.7843 (tpp-160) REVERT: G 133 ASP cc_start: 0.8888 (t70) cc_final: 0.8585 (t0) REVERT: G 147 GLN cc_start: 0.7763 (mm110) cc_final: 0.7428 (mm110) REVERT: G 148 LYS cc_start: 0.8156 (mppt) cc_final: 0.7651 (ttmm) REVERT: G 164 GLU cc_start: 0.7635 (pm20) cc_final: 0.7124 (pm20) REVERT: G 165 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7065 (mp0) REVERT: H 38 GLU cc_start: 0.8283 (tp30) cc_final: 0.7902 (tp30) REVERT: H 46 ASP cc_start: 0.8797 (m-30) cc_final: 0.8242 (m-30) REVERT: H 71 ASN cc_start: 0.8732 (t0) cc_final: 0.8398 (t0) REVERT: H 73 ASN cc_start: 0.8457 (p0) cc_final: 0.7649 (p0) REVERT: H 79 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7670 (tp30) REVERT: H 124 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7698 (t80) REVERT: H 143 GLN cc_start: 0.8297 (mt0) cc_final: 0.8019 (mm110) REVERT: H 147 GLN cc_start: 0.7835 (mm110) cc_final: 0.7519 (mm110) REVERT: H 148 LYS cc_start: 0.8220 (mppt) cc_final: 0.7855 (tttt) outliers start: 16 outliers final: 3 residues processed: 351 average time/residue: 0.3180 time to fit residues: 155.6863 Evaluate side-chains 337 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 329 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 181 LEU 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 155 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 236 HIS D 32 GLN D 236 HIS E 71 ASN F 236 HIS H 236 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.161160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.103269 restraints weight = 18075.396| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.35 r_work: 0.2923 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15024 Z= 0.255 Angle : 0.560 6.768 20352 Z= 0.294 Chirality : 0.038 0.127 2336 Planarity : 0.004 0.048 2504 Dihedral : 3.684 17.329 2144 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.72 % Allowed : 19.61 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.20), residues: 1792 helix: 2.90 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.65 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 81 HIS 0.003 0.001 HIS B 220 PHE 0.008 0.001 PHE B 124 TYR 0.024 0.002 TYR G 142 ARG 0.001 0.000 ARG B 204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3665.52 seconds wall clock time: 67 minutes 49.91 seconds (4069.91 seconds total)