Starting phenix.real_space_refine on Sat Mar 7 14:26:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vai_21140/03_2026/6vai_21140.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vai_21140/03_2026/6vai_21140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vai_21140/03_2026/6vai_21140.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vai_21140/03_2026/6vai_21140.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vai_21140/03_2026/6vai_21140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vai_21140/03_2026/6vai_21140.map" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 1.017 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 154 5.16 5 C 29436 2.51 5 N 7964 2.21 5 O 8030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 256 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45584 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "D" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "F" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "G" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "H" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "I" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "J" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "K" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "L" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "M" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "N" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "O" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "P" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "Q" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "R" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "S" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "T" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "U" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "V" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2072 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Time building chain proxies: 9.51, per 1000 atoms: 0.21 Number of scatterers: 45584 At special positions: 0 Unit cell: (145.22, 146.28, 191.86, 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 154 16.00 O 8030 8.00 N 7964 7.00 C 29436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 130 " distance=2.02 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 130 " distance=2.02 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 130 " distance=2.02 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 130 " distance=2.02 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 162 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 130 " distance=2.02 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 130 " distance=2.02 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 162 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 130 " distance=2.03 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 162 " distance=2.03 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 130 " distance=2.02 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 162 " distance=2.03 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 130 " distance=2.03 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 162 " distance=2.03 Simple disulfide: pdb=" SG CYS J 46 " - pdb=" SG CYS J 130 " distance=2.03 Simple disulfide: pdb=" SG CYS J 48 " - pdb=" SG CYS J 162 " distance=2.03 Simple disulfide: pdb=" SG CYS K 46 " - pdb=" SG CYS K 130 " distance=2.02 Simple disulfide: pdb=" SG CYS K 48 " - pdb=" SG CYS K 162 " distance=2.03 Simple disulfide: pdb=" SG CYS L 46 " - pdb=" SG CYS L 130 " distance=2.02 Simple disulfide: pdb=" SG CYS L 48 " - pdb=" SG CYS L 162 " distance=2.03 Simple disulfide: pdb=" SG CYS M 46 " - pdb=" SG CYS M 130 " distance=2.02 Simple disulfide: pdb=" SG CYS M 48 " - pdb=" SG CYS M 162 " distance=2.03 Simple disulfide: pdb=" SG CYS N 46 " - pdb=" SG CYS N 130 " distance=2.03 Simple disulfide: pdb=" SG CYS N 48 " - pdb=" SG CYS N 162 " distance=2.03 Simple disulfide: pdb=" SG CYS O 46 " - pdb=" SG CYS O 130 " distance=2.03 Simple disulfide: pdb=" SG CYS O 48 " - pdb=" SG CYS O 162 " distance=2.03 Simple disulfide: pdb=" SG CYS P 46 " - pdb=" SG CYS P 130 " distance=2.02 Simple disulfide: pdb=" SG CYS P 48 " - pdb=" SG CYS P 162 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 46 " - pdb=" SG CYS Q 130 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 48 " - pdb=" SG CYS Q 162 " distance=2.03 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 130 " distance=2.02 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 162 " distance=2.03 Simple disulfide: pdb=" SG CYS S 46 " - pdb=" SG CYS S 130 " distance=2.02 Simple disulfide: pdb=" SG CYS S 48 " - pdb=" SG CYS S 162 " distance=2.03 Simple disulfide: pdb=" SG CYS T 46 " - pdb=" SG CYS T 130 " distance=2.02 Simple disulfide: pdb=" SG CYS T 48 " - pdb=" SG CYS T 162 " distance=2.03 Simple disulfide: pdb=" SG CYS U 46 " - pdb=" SG CYS U 130 " distance=2.03 Simple disulfide: pdb=" SG CYS U 48 " - pdb=" SG CYS U 162 " distance=2.03 Simple disulfide: pdb=" SG CYS V 46 " - pdb=" SG CYS V 130 " distance=2.02 Simple disulfide: pdb=" SG CYS V 48 " - pdb=" SG CYS V 162 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.31 Conformation dependent library (CDL) restraints added in 1.8 seconds 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11132 Finding SS restraints... Secondary structure from input PDB file: 242 helices and 0 sheets defined 71.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 25 through 40 removed outlier: 4.210A pdb=" N ALA A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 76 through 86 removed outlier: 4.255A pdb=" N TRP A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 removed outlier: 3.765A pdb=" N ILE A 120 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL A 176 " --> pdb=" O PHE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 252 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP B 80 " --> pdb=" O ASN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE B 120 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 252 Processing helix chain 'B' and resid 257 through 267 Processing helix chain 'B' and resid 274 through 282 removed outlier: 3.542A pdb=" N TRP B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Proline residue: C 64 - end of helix Processing helix chain 'C' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP C 80 " --> pdb=" O ASN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE C 120 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'C' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU C 175 " --> pdb=" O ASP C 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL C 176 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 252 Processing helix chain 'C' and resid 257 through 267 Processing helix chain 'C' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP C 278 " --> pdb=" O PRO C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 302 Processing helix chain 'D' and resid 26 through 40 Processing helix chain 'D' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 111 removed outlier: 3.709A pdb=" N SER D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 160 Processing helix chain 'D' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL D 176 " --> pdb=" O PHE D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 252 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP D 278 " --> pdb=" O PRO D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'E' and resid 26 through 40 Processing helix chain 'E' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Proline residue: E 64 - end of helix Processing helix chain 'E' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP E 80 " --> pdb=" O ASN E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 111 removed outlier: 3.709A pdb=" N SER E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE E 120 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY E 125 " --> pdb=" O SER E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 160 Processing helix chain 'E' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU E 175 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL E 176 " --> pdb=" O PHE E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 252 Processing helix chain 'E' and resid 257 through 267 Processing helix chain 'E' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 302 Processing helix chain 'F' and resid 26 through 40 Processing helix chain 'F' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Proline residue: F 64 - end of helix Processing helix chain 'F' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP F 80 " --> pdb=" O ASN F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE F 120 " --> pdb=" O THR F 116 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 160 Processing helix chain 'F' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU F 174 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU F 175 " --> pdb=" O ASP F 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL F 176 " --> pdb=" O PHE F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 252 Processing helix chain 'F' and resid 257 through 267 Processing helix chain 'F' and resid 274 through 282 removed outlier: 3.542A pdb=" N TRP F 278 " --> pdb=" O PRO F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 302 Processing helix chain 'G' and resid 26 through 40 Processing helix chain 'G' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) Proline residue: G 64 - end of helix Processing helix chain 'G' and resid 76 through 86 removed outlier: 4.255A pdb=" N TRP G 80 " --> pdb=" O ASN G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER G 105 " --> pdb=" O LEU G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE G 120 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY G 125 " --> pdb=" O SER G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 160 Processing helix chain 'G' and resid 166 through 209 removed outlier: 3.993A pdb=" N GLU G 174 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU G 175 " --> pdb=" O ASP G 171 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL G 176 " --> pdb=" O PHE G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 252 Processing helix chain 'G' and resid 257 through 267 Processing helix chain 'G' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP G 278 " --> pdb=" O PRO G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 302 Processing helix chain 'H' and resid 26 through 40 Processing helix chain 'H' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU H 55 " --> pdb=" O ALA H 51 " (cutoff:3.500A) Proline residue: H 64 - end of helix Processing helix chain 'H' and resid 76 through 86 removed outlier: 4.255A pdb=" N TRP H 80 " --> pdb=" O ASN H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 111 removed outlier: 3.711A pdb=" N SER H 105 " --> pdb=" O LEU H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 160 Processing helix chain 'H' and resid 166 through 209 removed outlier: 3.993A pdb=" N GLU H 174 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU H 175 " --> pdb=" O ASP H 171 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL H 176 " --> pdb=" O PHE H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 252 Processing helix chain 'H' and resid 257 through 267 Processing helix chain 'H' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP H 278 " --> pdb=" O PRO H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 302 Processing helix chain 'I' and resid 26 through 40 Processing helix chain 'I' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'I' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP I 80 " --> pdb=" O ASN I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 111 removed outlier: 3.709A pdb=" N SER I 105 " --> pdb=" O LEU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 125 removed outlier: 3.767A pdb=" N ILE I 120 " --> pdb=" O THR I 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY I 125 " --> pdb=" O SER I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 160 Processing helix chain 'I' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU I 174 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLU I 175 " --> pdb=" O ASP I 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL I 176 " --> pdb=" O PHE I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 252 Processing helix chain 'I' and resid 257 through 267 Processing helix chain 'I' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP I 278 " --> pdb=" O PRO I 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 302 Processing helix chain 'J' and resid 26 through 40 Processing helix chain 'J' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU J 55 " --> pdb=" O ALA J 51 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'J' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP J 80 " --> pdb=" O ASN J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER J 105 " --> pdb=" O LEU J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE J 120 " --> pdb=" O THR J 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY J 125 " --> pdb=" O SER J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 160 Processing helix chain 'J' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU J 174 " --> pdb=" O SER J 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU J 175 " --> pdb=" O ASP J 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL J 176 " --> pdb=" O PHE J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 214 through 252 Processing helix chain 'J' and resid 257 through 267 Processing helix chain 'J' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP J 278 " --> pdb=" O PRO J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 302 Processing helix chain 'K' and resid 26 through 40 Processing helix chain 'K' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU K 55 " --> pdb=" O ALA K 51 " (cutoff:3.500A) Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP K 80 " --> pdb=" O ASN K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER K 105 " --> pdb=" O LEU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE K 120 " --> pdb=" O THR K 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY K 125 " --> pdb=" O SER K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 160 Processing helix chain 'K' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU K 174 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU K 175 " --> pdb=" O ASP K 171 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL K 176 " --> pdb=" O PHE K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 252 Processing helix chain 'K' and resid 257 through 267 Processing helix chain 'K' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP K 278 " --> pdb=" O PRO K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 302 Processing helix chain 'L' and resid 26 through 40 Processing helix chain 'L' and resid 51 through 75 removed outlier: 4.368A pdb=" N LEU L 55 " --> pdb=" O ALA L 51 " (cutoff:3.500A) Proline residue: L 64 - end of helix Processing helix chain 'L' and resid 76 through 86 removed outlier: 4.255A pdb=" N TRP L 80 " --> pdb=" O ASN L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 111 removed outlier: 3.709A pdb=" N SER L 105 " --> pdb=" O LEU L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE L 120 " --> pdb=" O THR L 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 160 Processing helix chain 'L' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU L 174 " --> pdb=" O SER L 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU L 175 " --> pdb=" O ASP L 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL L 176 " --> pdb=" O PHE L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 252 Processing helix chain 'L' and resid 257 through 267 Processing helix chain 'L' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP L 278 " --> pdb=" O PRO L 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 302 Processing helix chain 'M' and resid 26 through 40 Processing helix chain 'M' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU M 55 " --> pdb=" O ALA M 51 " (cutoff:3.500A) Proline residue: M 64 - end of helix Processing helix chain 'M' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP M 80 " --> pdb=" O ASN M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER M 105 " --> pdb=" O LEU M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 125 removed outlier: 3.767A pdb=" N ILE M 120 " --> pdb=" O THR M 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY M 125 " --> pdb=" O SER M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 160 Processing helix chain 'M' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU M 174 " --> pdb=" O SER M 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU M 175 " --> pdb=" O ASP M 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL M 176 " --> pdb=" O PHE M 172 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 252 Processing helix chain 'M' and resid 257 through 267 Processing helix chain 'M' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP M 278 " --> pdb=" O PRO M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 297 through 302 Processing helix chain 'N' and resid 26 through 40 Processing helix chain 'N' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU N 55 " --> pdb=" O ALA N 51 " (cutoff:3.500A) Proline residue: N 64 - end of helix Processing helix chain 'N' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP N 80 " --> pdb=" O ASN N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 111 removed outlier: 3.709A pdb=" N SER N 105 " --> pdb=" O LEU N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 125 removed outlier: 3.767A pdb=" N ILE N 120 " --> pdb=" O THR N 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY N 125 " --> pdb=" O SER N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 156 through 160 Processing helix chain 'N' and resid 166 through 209 removed outlier: 3.993A pdb=" N GLU N 174 " --> pdb=" O SER N 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU N 175 " --> pdb=" O ASP N 171 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL N 176 " --> pdb=" O PHE N 172 " (cutoff:3.500A) Processing helix chain 'N' and resid 214 through 252 Processing helix chain 'N' and resid 257 through 267 Processing helix chain 'N' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP N 278 " --> pdb=" O PRO N 274 " (cutoff:3.500A) Processing helix chain 'N' and resid 297 through 302 Processing helix chain 'O' and resid 26 through 40 Processing helix chain 'O' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU O 55 " --> pdb=" O ALA O 51 " (cutoff:3.500A) Proline residue: O 64 - end of helix Processing helix chain 'O' and resid 76 through 86 removed outlier: 4.255A pdb=" N TRP O 80 " --> pdb=" O ASN O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER O 105 " --> pdb=" O LEU O 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE O 120 " --> pdb=" O THR O 116 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY O 125 " --> pdb=" O SER O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 156 through 160 Processing helix chain 'O' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU O 174 " --> pdb=" O SER O 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU O 175 " --> pdb=" O ASP O 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL O 176 " --> pdb=" O PHE O 172 " (cutoff:3.500A) Processing helix chain 'O' and resid 214 through 252 Processing helix chain 'O' and resid 257 through 267 Processing helix chain 'O' and resid 274 through 282 removed outlier: 3.542A pdb=" N TRP O 278 " --> pdb=" O PRO O 274 " (cutoff:3.500A) Processing helix chain 'O' and resid 297 through 302 Processing helix chain 'P' and resid 26 through 40 Processing helix chain 'P' and resid 51 through 75 removed outlier: 4.368A pdb=" N LEU P 55 " --> pdb=" O ALA P 51 " (cutoff:3.500A) Proline residue: P 64 - end of helix Processing helix chain 'P' and resid 76 through 86 removed outlier: 4.255A pdb=" N TRP P 80 " --> pdb=" O ASN P 76 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER P 105 " --> pdb=" O LEU P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 125 removed outlier: 3.767A pdb=" N ILE P 120 " --> pdb=" O THR P 116 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY P 125 " --> pdb=" O SER P 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 160 Processing helix chain 'P' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU P 174 " --> pdb=" O SER P 170 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLU P 175 " --> pdb=" O ASP P 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL P 176 " --> pdb=" O PHE P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 214 through 252 Processing helix chain 'P' and resid 257 through 267 Processing helix chain 'P' and resid 274 through 282 removed outlier: 3.542A pdb=" N TRP P 278 " --> pdb=" O PRO P 274 " (cutoff:3.500A) Processing helix chain 'P' and resid 297 through 302 Processing helix chain 'Q' and resid 26 through 40 Processing helix chain 'Q' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU Q 55 " --> pdb=" O ALA Q 51 " (cutoff:3.500A) Proline residue: Q 64 - end of helix Processing helix chain 'Q' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP Q 80 " --> pdb=" O ASN Q 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 111 removed outlier: 3.709A pdb=" N SER Q 105 " --> pdb=" O LEU Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 125 removed outlier: 3.765A pdb=" N ILE Q 120 " --> pdb=" O THR Q 116 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY Q 125 " --> pdb=" O SER Q 121 " (cutoff:3.500A) Processing helix chain 'Q' and resid 156 through 160 Processing helix chain 'Q' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU Q 174 " --> pdb=" O SER Q 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU Q 175 " --> pdb=" O ASP Q 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL Q 176 " --> pdb=" O PHE Q 172 " (cutoff:3.500A) Processing helix chain 'Q' and resid 214 through 252 Processing helix chain 'Q' and resid 257 through 267 Processing helix chain 'Q' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP Q 278 " --> pdb=" O PRO Q 274 " (cutoff:3.500A) Processing helix chain 'Q' and resid 297 through 302 Processing helix chain 'R' and resid 26 through 40 Processing helix chain 'R' and resid 51 through 75 removed outlier: 4.368A pdb=" N LEU R 55 " --> pdb=" O ALA R 51 " (cutoff:3.500A) Proline residue: R 64 - end of helix Processing helix chain 'R' and resid 76 through 86 removed outlier: 4.255A pdb=" N TRP R 80 " --> pdb=" O ASN R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE R 120 " --> pdb=" O THR R 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY R 125 " --> pdb=" O SER R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 160 Processing helix chain 'R' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU R 174 " --> pdb=" O SER R 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU R 175 " --> pdb=" O ASP R 171 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL R 176 " --> pdb=" O PHE R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 252 Processing helix chain 'R' and resid 257 through 267 Processing helix chain 'R' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP R 278 " --> pdb=" O PRO R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 297 through 302 Processing helix chain 'S' and resid 26 through 40 Processing helix chain 'S' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU S 55 " --> pdb=" O ALA S 51 " (cutoff:3.500A) Proline residue: S 64 - end of helix Processing helix chain 'S' and resid 76 through 86 removed outlier: 4.255A pdb=" N TRP S 80 " --> pdb=" O ASN S 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER S 105 " --> pdb=" O LEU S 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE S 120 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY S 125 " --> pdb=" O SER S 121 " (cutoff:3.500A) Processing helix chain 'S' and resid 156 through 160 Processing helix chain 'S' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU S 174 " --> pdb=" O SER S 170 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLU S 175 " --> pdb=" O ASP S 171 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL S 176 " --> pdb=" O PHE S 172 " (cutoff:3.500A) Processing helix chain 'S' and resid 214 through 252 Processing helix chain 'S' and resid 257 through 267 Processing helix chain 'S' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP S 278 " --> pdb=" O PRO S 274 " (cutoff:3.500A) Processing helix chain 'S' and resid 297 through 302 Processing helix chain 'T' and resid 26 through 40 Processing helix chain 'T' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU T 55 " --> pdb=" O ALA T 51 " (cutoff:3.500A) Proline residue: T 64 - end of helix Processing helix chain 'T' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP T 80 " --> pdb=" O ASN T 76 " (cutoff:3.500A) Processing helix chain 'T' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER T 105 " --> pdb=" O LEU T 101 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE T 120 " --> pdb=" O THR T 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY T 125 " --> pdb=" O SER T 121 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 160 Processing helix chain 'T' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU T 174 " --> pdb=" O SER T 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU T 175 " --> pdb=" O ASP T 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL T 176 " --> pdb=" O PHE T 172 " (cutoff:3.500A) Processing helix chain 'T' and resid 214 through 252 Processing helix chain 'T' and resid 257 through 267 Processing helix chain 'T' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP T 278 " --> pdb=" O PRO T 274 " (cutoff:3.500A) Processing helix chain 'T' and resid 297 through 302 Processing helix chain 'U' and resid 26 through 40 Processing helix chain 'U' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU U 55 " --> pdb=" O ALA U 51 " (cutoff:3.500A) Proline residue: U 64 - end of helix Processing helix chain 'U' and resid 76 through 86 removed outlier: 4.255A pdb=" N TRP U 80 " --> pdb=" O ASN U 76 " (cutoff:3.500A) Processing helix chain 'U' and resid 100 through 111 removed outlier: 3.710A pdb=" N SER U 105 " --> pdb=" O LEU U 101 " (cutoff:3.500A) Processing helix chain 'U' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE U 120 " --> pdb=" O THR U 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY U 125 " --> pdb=" O SER U 121 " (cutoff:3.500A) Processing helix chain 'U' and resid 156 through 160 Processing helix chain 'U' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU U 174 " --> pdb=" O SER U 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU U 175 " --> pdb=" O ASP U 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL U 176 " --> pdb=" O PHE U 172 " (cutoff:3.500A) Processing helix chain 'U' and resid 214 through 252 Processing helix chain 'U' and resid 257 through 267 Processing helix chain 'U' and resid 274 through 282 removed outlier: 3.542A pdb=" N TRP U 278 " --> pdb=" O PRO U 274 " (cutoff:3.500A) Processing helix chain 'U' and resid 297 through 302 Processing helix chain 'V' and resid 26 through 40 Processing helix chain 'V' and resid 51 through 75 removed outlier: 4.367A pdb=" N LEU V 55 " --> pdb=" O ALA V 51 " (cutoff:3.500A) Proline residue: V 64 - end of helix Processing helix chain 'V' and resid 76 through 86 removed outlier: 4.254A pdb=" N TRP V 80 " --> pdb=" O ASN V 76 " (cutoff:3.500A) Processing helix chain 'V' and resid 100 through 111 removed outlier: 3.709A pdb=" N SER V 105 " --> pdb=" O LEU V 101 " (cutoff:3.500A) Processing helix chain 'V' and resid 111 through 125 removed outlier: 3.766A pdb=" N ILE V 120 " --> pdb=" O THR V 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY V 125 " --> pdb=" O SER V 121 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 160 Processing helix chain 'V' and resid 166 through 209 removed outlier: 3.994A pdb=" N GLU V 174 " --> pdb=" O SER V 170 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU V 175 " --> pdb=" O ASP V 171 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL V 176 " --> pdb=" O PHE V 172 " (cutoff:3.500A) Processing helix chain 'V' and resid 214 through 252 Processing helix chain 'V' and resid 257 through 267 Processing helix chain 'V' and resid 274 through 282 removed outlier: 3.541A pdb=" N TRP V 278 " --> pdb=" O PRO V 274 " (cutoff:3.500A) Processing helix chain 'V' and resid 297 through 302 3014 hydrogen bonds defined for protein. 8910 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: 8.58 Time building geometry restraints manager: 5.66 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: 14938 1.34 - 1.46: 10399 1.46 - 1.58: 21303 1.58 - 1.69: 0 1.69 - 1.81: 154 Bond restraints: 46794 Sorted by residual: bond pdb=" CA VAL D 269 " pdb=" CB VAL D 269 " ideal model delta sigma weight residual 1.550 1.537 0.013 1.03e-02 9.43e+03 1.70e+00 bond pdb=" CA VAL K 269 " pdb=" CB VAL K 269 " ideal model delta sigma weight residual 1.550 1.537 0.013 1.03e-02 9.43e+03 1.69e+00 bond pdb=" CA VAL B 269 " pdb=" CB VAL B 269 " ideal model delta sigma weight residual 1.550 1.538 0.013 1.03e-02 9.43e+03 1.51e+00 bond pdb=" CA VAL A 269 " pdb=" CB VAL A 269 " ideal model delta sigma weight residual 1.550 1.538 0.012 1.03e-02 9.43e+03 1.47e+00 bond pdb=" CA VAL P 269 " pdb=" CB VAL P 269 " ideal model delta sigma weight residual 1.550 1.538 0.012 1.03e-02 9.43e+03 1.43e+00 ... (remaining 46789 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 58946 1.17 - 2.33: 4046 2.33 - 3.50: 566 3.50 - 4.66: 180 4.66 - 5.83: 150 Bond angle restraints: 63888 Sorted by residual: angle pdb=" N GLY N 252 " pdb=" CA GLY N 252 " pdb=" C GLY N 252 " ideal model delta sigma weight residual 114.85 110.72 4.13 1.35e+00 5.49e-01 9.37e+00 angle pdb=" N GLY M 252 " pdb=" CA GLY M 252 " pdb=" C GLY M 252 " ideal model delta sigma weight residual 114.85 110.73 4.12 1.35e+00 5.49e-01 9.29e+00 angle pdb=" N GLY R 252 " pdb=" CA GLY R 252 " pdb=" C GLY R 252 " ideal model delta sigma weight residual 114.85 110.75 4.10 1.35e+00 5.49e-01 9.21e+00 angle pdb=" N GLY D 252 " pdb=" CA GLY D 252 " pdb=" C GLY D 252 " ideal model delta sigma weight residual 114.85 110.76 4.09 1.35e+00 5.49e-01 9.20e+00 angle pdb=" N GLY L 252 " pdb=" CA GLY L 252 " pdb=" C GLY L 252 " ideal model delta sigma weight residual 114.85 110.76 4.09 1.35e+00 5.49e-01 9.18e+00 ... (remaining 63883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 24167 17.22 - 34.44: 2739 34.44 - 51.67: 352 51.67 - 68.89: 110 68.89 - 86.11: 88 Dihedral angle restraints: 27456 sinusoidal: 10252 harmonic: 17204 Sorted by residual: dihedral pdb=" CA ARG N 144 " pdb=" C ARG N 144 " pdb=" N GLU N 145 " pdb=" CA GLU N 145 " ideal model delta harmonic sigma weight residual -180.00 -153.77 -26.23 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA ARG I 144 " pdb=" C ARG I 144 " pdb=" N GLU I 145 " pdb=" CA GLU I 145 " ideal model delta harmonic sigma weight residual -180.00 -153.78 -26.22 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA ARG C 144 " pdb=" C ARG C 144 " pdb=" N GLU C 145 " pdb=" CA GLU C 145 " ideal model delta harmonic sigma weight residual -180.00 -153.79 -26.21 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 27453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3948 0.027 - 0.054: 2236 0.054 - 0.081: 628 0.081 - 0.108: 225 0.108 - 0.135: 113 Chirality restraints: 7150 Sorted by residual: chirality pdb=" CA LYS O 163 " pdb=" N LYS O 163 " pdb=" C LYS O 163 " pdb=" CB LYS O 163 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA LYS D 163 " pdb=" N LYS D 163 " pdb=" C LYS D 163 " pdb=" CB LYS D 163 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA LYS F 163 " pdb=" N LYS F 163 " pdb=" C LYS F 163 " pdb=" CB LYS F 163 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 7147 not shown) Planarity restraints: 8228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS P 162 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.81e+00 pdb=" C CYS P 162 " 0.023 2.00e-02 2.50e+03 pdb=" O CYS P 162 " -0.009 2.00e-02 2.50e+03 pdb=" N LYS P 163 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS S 162 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.81e+00 pdb=" C CYS S 162 " 0.023 2.00e-02 2.50e+03 pdb=" O CYS S 162 " -0.009 2.00e-02 2.50e+03 pdb=" N LYS S 163 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS K 162 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C CYS K 162 " -0.023 2.00e-02 2.50e+03 pdb=" O CYS K 162 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS K 163 " 0.008 2.00e-02 2.50e+03 ... (remaining 8225 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 11943 2.79 - 3.32: 46739 3.32 - 3.85: 73198 3.85 - 4.37: 77909 4.37 - 4.90: 134056 Nonbonded interactions: 343845 Sorted by model distance: nonbonded pdb=" NH1 ARG Q 240 " pdb=" OD2 ASP Q 260 " model vdw 2.266 3.120 nonbonded pdb=" NH1 ARG H 240 " pdb=" OD2 ASP H 260 " model vdw 2.267 3.120 nonbonded pdb=" NH1 ARG D 240 " pdb=" OD2 ASP D 260 " model vdw 2.267 3.120 nonbonded pdb=" NH1 ARG B 240 " pdb=" OD2 ASP B 260 " model vdw 2.267 3.120 nonbonded pdb=" NH1 ARG N 240 " pdb=" OD2 ASP N 260 " model vdw 2.267 3.120 ... (remaining 343840 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: 0.08 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' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } 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 group one per residue 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 0.670 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 38.600 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 0.005 0.026 46838 Z= 0.246 Angle : 0.692 5.827 63976 Z= 0.402 Chirality : 0.039 0.135 7150 Planarity : 0.004 0.028 8228 Dihedral : 14.950 86.112 16192 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.96 % Allowed : 8.15 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.10), residues: 5786 helix: -0.42 (0.07), residues: 4268 sheet: None (None), residues: 0 loop : -4.96 (0.09), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 144 TYR 0.016 0.002 TYR E 54 PHE 0.008 0.001 PHE S 187 TRP 0.007 0.001 TRP U 302 HIS 0.005 0.001 HIS Q 238 Details of bonding type rmsd covalent geometry : bond 0.00533 (46794) covalent geometry : angle 0.69182 (63888) SS BOND : bond 0.00443 ( 44) SS BOND : angle 0.99688 ( 88) hydrogen bonds : bond 0.14914 ( 3014) hydrogen bonds : angle 5.62407 ( 8910) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 4972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 833 time to evaluate : 1.743 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: symmetry clash REVERT: A 232 GLN cc_start: 0.8706 (tp40) cc_final: 0.8464 (tp40) REVERT: E 232 GLN cc_start: 0.8674 (tp40) cc_final: 0.8410 (tp40) REVERT: I 291 GLN cc_start: 0.7820 (pp30) cc_final: 0.7537 (pp30) REVERT: K 203 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8249 (tttm) REVERT: L 232 GLN cc_start: 0.8709 (tp40) cc_final: 0.8456 (tp40) REVERT: P 232 GLN cc_start: 0.8666 (tp40) cc_final: 0.8350 (mm-40) REVERT: S 291 GLN cc_start: 0.7795 (pp30) cc_final: 0.7568 (pp30) REVERT: V 203 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8263 (tttm) outliers start: 44 outliers final: 27 residues processed: 855 average time/residue: 0.2852 time to fit residues: 393.8432 Evaluate side-chains 565 residues out of total 4972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 538 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 132 LEU Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain U residue 201 LEU Chi-restraints excluded: chain V residue 201 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 394 optimal weight: 2.9990 chunk 430 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 265 optimal weight: 0.8980 chunk 523 optimal weight: 0.9990 chunk 497 optimal weight: 3.9990 chunk 414 optimal weight: 6.9990 chunk 310 optimal weight: 4.9990 chunk 488 optimal weight: 0.9980 chunk 366 optimal weight: 5.9990 chunk 223 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 238 HIS A 246 ASN B 53 ASN B 238 HIS B 246 ASN C 53 ASN C 238 HIS C 246 ASN D 53 ASN D 238 HIS D 246 ASN E 53 ASN E 238 HIS E 246 ASN F 53 ASN F 232 GLN F 238 HIS F 246 ASN G 53 ASN G 238 HIS G 246 ASN H 53 ASN H 232 GLN H 238 HIS H 246 ASN I 53 ASN I 232 GLN I 238 HIS I 246 ASN J 53 ASN J 238 HIS J 246 ASN K 53 ASN K 238 HIS K 246 ASN L 53 ASN L 238 HIS L 246 ASN M 53 ASN M 238 HIS M 246 ASN N 53 ASN N 238 HIS N 246 ASN O 53 ASN O 238 HIS O 246 ASN P 53 ASN P 238 HIS P 246 ASN Q 53 ASN Q 238 HIS Q 246 ASN R 53 ASN R 238 HIS R 246 ASN S 53 ASN S 232 GLN S 238 HIS S 246 ASN T 53 ASN T 238 HIS T 246 ASN U 53 ASN U 238 HIS U 246 ASN V 53 ASN V 238 HIS V 246 ASN Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.097300 restraints weight = 83034.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100432 restraints weight = 45758.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.102674 restraints weight = 31181.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.104035 restraints weight = 24268.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105210 restraints weight = 20655.390| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 46838 Z= 0.143 Angle : 0.598 6.849 63976 Z= 0.307 Chirality : 0.038 0.134 7150 Planarity : 0.004 0.034 8228 Dihedral : 6.030 52.298 6500 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.37 % Allowed : 15.25 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.11), residues: 5786 helix: 1.08 (0.08), residues: 4334 sheet: None (None), residues: 0 loop : -4.18 (0.11), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 181 TYR 0.019 0.002 TYR M 285 PHE 0.007 0.001 PHE R 100 TRP 0.010 0.001 TRP G 80 HIS 0.005 0.001 HIS Q 238 Details of bonding type rmsd covalent geometry : bond 0.00314 (46794) covalent geometry : angle 0.59850 (63888) SS BOND : bond 0.00209 ( 44) SS BOND : angle 0.52319 ( 88) hydrogen bonds : bond 0.04884 ( 3014) hydrogen bonds : angle 3.89168 ( 8910) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 4972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 671 time to evaluate : 1.671 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 GLN cc_start: 0.9436 (tp40) cc_final: 0.9061 (tp40) REVERT: B 144 ARG cc_start: 0.8062 (ttt180) cc_final: 0.7835 (ptm160) REVERT: C 236 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8422 (tm-30) REVERT: D 232 GLN cc_start: 0.9317 (tp40) cc_final: 0.9114 (tp40) REVERT: E 232 GLN cc_start: 0.9389 (tp40) cc_final: 0.9056 (tp40) REVERT: G 163 LYS cc_start: 0.8759 (pptt) cc_final: 0.8452 (tppt) REVERT: H 201 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8775 (mm) REVERT: J 236 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8189 (tm-30) REVERT: J 285 TYR cc_start: 0.7905 (t80) cc_final: 0.7629 (t80) REVERT: L 232 GLN cc_start: 0.9418 (tp40) cc_final: 0.9056 (tp40) REVERT: M 144 ARG cc_start: 0.8071 (ttt180) cc_final: 0.7851 (ptm160) REVERT: N 163 LYS cc_start: 0.8724 (pptt) cc_final: 0.8475 (tppt) REVERT: N 236 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8352 (tm-30) REVERT: O 236 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8418 (tm-30) REVERT: Q 236 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8354 (tm-30) REVERT: S 259 ASP cc_start: 0.8662 (m-30) cc_final: 0.8269 (p0) REVERT: S 291 GLN cc_start: 0.8651 (pp30) cc_final: 0.8056 (pp30) REVERT: T 116 THR cc_start: 0.8999 (t) cc_final: 0.8747 (t) REVERT: T 183 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7537 (mt-10) REVERT: U 236 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8203 (tm-30) outliers start: 200 outliers final: 138 residues processed: 766 average time/residue: 0.2509 time to fit residues: 325.5933 Evaluate side-chains 723 residues out of total 4972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 584 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 134 GLU Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 202 THR Chi-restraints excluded: chain N residue 228 ASP Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 202 THR Chi-restraints excluded: chain P residue 54 TYR Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 134 GLU Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 102 LEU Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain Q residue 194 VAL Chi-restraints excluded: chain Q residue 199 VAL Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 134 GLU Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 202 THR Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 106 ILE Chi-restraints excluded: chain S residue 134 GLU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 202 THR Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain T residue 106 ILE Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 190 LEU Chi-restraints excluded: chain U residue 199 VAL Chi-restraints excluded: chain U residue 202 THR Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 106 ILE Chi-restraints excluded: chain V residue 134 GLU Chi-restraints excluded: chain V residue 190 LEU Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 201 LEU Chi-restraints excluded: chain V residue 202 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 460 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 153 optimal weight: 0.0010 chunk 359 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 chunk 346 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 565 optimal weight: 1.9990 chunk 214 optimal weight: 0.0770 chunk 72 optimal weight: 5.9990 chunk 488 optimal weight: 0.9980 overall best weight: 0.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.125375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.100240 restraints weight = 81464.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103488 restraints weight = 43311.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.105859 restraints weight = 28936.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.107476 restraints weight = 22103.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.108585 restraints weight = 18440.852| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 46838 Z= 0.115 Angle : 0.543 6.754 63976 Z= 0.280 Chirality : 0.036 0.135 7150 Planarity : 0.004 0.038 8228 Dihedral : 5.211 42.798 6476 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 4.81 % Allowed : 18.36 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.11), residues: 5786 helix: 1.76 (0.08), residues: 4334 sheet: None (None), residues: 0 loop : -3.81 (0.12), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 181 TYR 0.016 0.001 TYR O 285 PHE 0.010 0.001 PHE L 100 TRP 0.013 0.001 TRP R 278 HIS 0.002 0.000 HIS P 238 Details of bonding type rmsd covalent geometry : bond 0.00240 (46794) covalent geometry : angle 0.54321 (63888) SS BOND : bond 0.00142 ( 44) SS BOND : angle 0.40345 ( 88) hydrogen bonds : bond 0.04021 ( 3014) hydrogen bonds : angle 3.57675 ( 8910) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 4972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 679 time to evaluate : 1.831 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 GLN cc_start: 0.9405 (tp40) cc_final: 0.9080 (tp40) REVERT: B 144 ARG cc_start: 0.8106 (ttt180) cc_final: 0.7868 (ptm160) REVERT: C 144 ARG cc_start: 0.7960 (ttt180) cc_final: 0.7641 (ptm160) REVERT: C 223 TYR cc_start: 0.9211 (t80) cc_final: 0.8867 (t80) REVERT: D 232 GLN cc_start: 0.9320 (tp40) cc_final: 0.9103 (tp40) REVERT: E 144 ARG cc_start: 0.7963 (ttt180) cc_final: 0.7573 (ttp-170) REVERT: E 223 TYR cc_start: 0.9254 (t80) cc_final: 0.8432 (t80) REVERT: E 232 GLN cc_start: 0.9390 (tp40) cc_final: 0.9096 (tp40) REVERT: F 144 ARG cc_start: 0.8082 (ttt180) cc_final: 0.7702 (ttp-170) REVERT: G 163 LYS cc_start: 0.8646 (pptt) cc_final: 0.8302 (tmtt) REVERT: J 236 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8210 (tm-30) REVERT: K 236 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8471 (tm-30) REVERT: L 232 GLN cc_start: 0.9399 (tp40) cc_final: 0.9073 (tp40) REVERT: N 236 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8348 (tm-30) REVERT: O 163 LYS cc_start: 0.8684 (pptt) cc_final: 0.8308 (tmtt) REVERT: O 236 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8477 (tm-30) REVERT: P 232 GLN cc_start: 0.9379 (tp40) cc_final: 0.8890 (mm-40) REVERT: Q 236 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8342 (tm-30) REVERT: S 259 ASP cc_start: 0.8542 (m-30) cc_final: 0.8186 (p0) REVERT: T 102 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8495 (mm) REVERT: T 183 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7558 (mt-10) REVERT: U 236 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8184 (tm-30) REVERT: U 285 TYR cc_start: 0.7618 (t80) cc_final: 0.7210 (t80) outliers start: 220 outliers final: 121 residues processed: 826 average time/residue: 0.2519 time to fit residues: 354.5085 Evaluate side-chains 705 residues out of total 4972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 583 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain L residue 154 THR Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain M residue 48 CYS Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 86 CYS Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain N residue 48 CYS Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 134 GLU Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 228 ASP Chi-restraints excluded: chain O residue 48 CYS Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain P residue 54 TYR Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 134 GLU Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain Q residue 48 CYS Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain Q residue 102 LEU Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain Q residue 192 ILE Chi-restraints excluded: chain Q residue 199 VAL Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 134 GLU Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain S residue 48 CYS Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 134 GLU Chi-restraints excluded: chain S residue 192 ILE Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 48 CYS Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain T residue 102 LEU Chi-restraints excluded: chain T residue 132 LEU Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain U residue 48 CYS Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain U residue 201 LEU Chi-restraints excluded: chain V residue 48 CYS Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 134 GLU Chi-restraints excluded: chain V residue 192 ILE Chi-restraints excluded: chain V residue 199 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 80 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 259 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 509 optimal weight: 4.9990 chunk 210 optimal weight: 0.0170 chunk 176 optimal weight: 10.0000 chunk 284 optimal weight: 10.0000 chunk 213 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 458 optimal weight: 4.9990 overall best weight: 2.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 246 ASN L 300 HIS M 300 HIS V 246 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.097281 restraints weight = 82477.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.100349 restraints weight = 45172.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.102593 restraints weight = 30627.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.104150 restraints weight = 23635.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.105062 restraints weight = 19806.773| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 46838 Z= 0.160 Angle : 0.560 5.524 63976 Z= 0.289 Chirality : 0.037 0.131 7150 Planarity : 0.004 0.038 8228 Dihedral : 4.752 26.507 6446 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 3.58 % Allowed : 22.18 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.11), residues: 5786 helix: 1.80 (0.08), residues: 4356 sheet: None (None), residues: 0 loop : -3.68 (0.12), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 181 TYR 0.018 0.002 TYR D 223 PHE 0.008 0.001 PHE U 250 TRP 0.008 0.001 TRP G 278 HIS 0.003 0.001 HIS P 238 Details of bonding type rmsd covalent geometry : bond 0.00365 (46794) covalent geometry : angle 0.56052 (63888) SS BOND : bond 0.00260 ( 44) SS BOND : angle 0.50051 ( 88) hydrogen bonds : bond 0.04407 ( 3014) hydrogen bonds : angle 3.62296 ( 8910) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 4972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 577 time to evaluate : 1.617 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 GLN cc_start: 0.9419 (tp40) cc_final: 0.9111 (tp40) REVERT: B 144 ARG cc_start: 0.8063 (ttt180) cc_final: 0.7836 (ptm160) REVERT: C 144 ARG cc_start: 0.7941 (ttt180) cc_final: 0.7670 (ptm160) REVERT: E 144 ARG cc_start: 0.7983 (ttt180) cc_final: 0.7576 (ttp-170) REVERT: E 232 GLN cc_start: 0.9408 (tp40) cc_final: 0.9108 (tp40) REVERT: F 144 ARG cc_start: 0.7987 (ttt180) cc_final: 0.7642 (ttp-170) REVERT: G 144 ARG cc_start: 0.8096 (ttt180) cc_final: 0.7702 (tmt170) REVERT: J 236 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8120 (tm-30) REVERT: K 273 GLN cc_start: 0.8698 (mp10) cc_final: 0.8332 (mp10) REVERT: L 232 GLN cc_start: 0.9411 (tp40) cc_final: 0.9100 (tp40) REVERT: N 236 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8363 (tm-30) REVERT: O 163 LYS cc_start: 0.8595 (pptt) cc_final: 0.8283 (tmtt) REVERT: O 236 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8559 (tm-30) REVERT: P 144 ARG cc_start: 0.7945 (ttt180) cc_final: 0.7479 (ttp-170) REVERT: P 232 GLN cc_start: 0.9394 (tp40) cc_final: 0.9129 (tp40) REVERT: Q 236 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8349 (tm-30) REVERT: R 163 LYS cc_start: 0.8909 (tppt) cc_final: 0.8703 (tppp) REVERT: S 259 ASP cc_start: 0.8561 (m-30) cc_final: 0.8224 (p0) REVERT: U 236 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8078 (tm-30) REVERT: U 273 GLN cc_start: 0.8847 (mp10) cc_final: 0.8615 (mp10) REVERT: U 277 GLN cc_start: 0.9107 (tt0) cc_final: 0.8894 (tt0) REVERT: U 285 TYR cc_start: 0.7858 (t80) cc_final: 0.7449 (t80) REVERT: V 203 LYS cc_start: 0.8430 (mmtt) cc_final: 0.8155 (tttm) outliers start: 164 outliers final: 140 residues processed: 687 average time/residue: 0.2529 time to fit residues: 291.9932 Evaluate side-chains 689 residues out of total 4972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 549 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain M residue 48 CYS Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 190 LEU Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain N residue 48 CYS Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 134 GLU Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 228 ASP Chi-restraints excluded: chain O residue 48 CYS Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 194 VAL Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 284 VAL Chi-restraints excluded: chain P residue 48 CYS Chi-restraints excluded: chain P residue 54 TYR Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain P residue 134 GLU Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain Q residue 48 CYS Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 102 LEU Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain Q residue 192 ILE Chi-restraints excluded: chain Q residue 199 VAL Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 134 GLU Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain S residue 48 CYS Chi-restraints excluded: chain S residue 134 GLU Chi-restraints excluded: chain S residue 192 ILE Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 48 CYS Chi-restraints excluded: chain T residue 132 LEU Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain U residue 48 CYS Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 190 LEU Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain U residue 194 VAL Chi-restraints excluded: chain U residue 199 VAL Chi-restraints excluded: chain U residue 201 LEU Chi-restraints excluded: chain U residue 202 THR Chi-restraints excluded: chain V residue 48 CYS Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 134 GLU Chi-restraints excluded: chain V residue 199 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 273 optimal weight: 2.9990 chunk 238 optimal weight: 0.9990 chunk 473 optimal weight: 10.0000 chunk 491 optimal weight: 7.9990 chunk 452 optimal weight: 0.2980 chunk 414 optimal weight: 2.9990 chunk 479 optimal weight: 0.0870 chunk 241 optimal weight: 5.9990 chunk 218 optimal weight: 10.0000 chunk 285 optimal weight: 0.3980 chunk 203 optimal weight: 7.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN A 300 HIS B 246 ASN B 300 HIS C 300 HIS K 246 ASN M 246 ASN N 300 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.126135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.100554 restraints weight = 81783.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103838 restraints weight = 44258.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.106237 restraints weight = 29704.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107916 restraints weight = 22726.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109048 restraints weight = 18887.455| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 46838 Z= 0.109 Angle : 0.515 5.766 63976 Z= 0.264 Chirality : 0.036 0.145 7150 Planarity : 0.004 0.038 8228 Dihedral : 4.514 25.456 6446 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.63 % Allowed : 22.88 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.11), residues: 5786 helix: 2.03 (0.08), residues: 4356 sheet: None (None), residues: 0 loop : -3.56 (0.12), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 181 TYR 0.017 0.001 TYR A 285 PHE 0.007 0.001 PHE R 100 TRP 0.009 0.001 TRP N 278 HIS 0.003 0.000 HIS P 238 Details of bonding type rmsd covalent geometry : bond 0.00232 (46794) covalent geometry : angle 0.51559 (63888) SS BOND : bond 0.00107 ( 44) SS BOND : angle 0.29105 ( 88) hydrogen bonds : bond 0.03791 ( 3014) hydrogen bonds : angle 3.41998 ( 8910) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 4972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 603 time to evaluate : 2.017 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 ARG cc_start: 0.7991 (ttt180) cc_final: 0.7787 (ptm160) REVERT: C 144 ARG cc_start: 0.7995 (ttt180) cc_final: 0.7787 (ptm160) REVERT: C 223 TYR cc_start: 0.9205 (t80) cc_final: 0.8806 (t80) REVERT: C 277 GLN cc_start: 0.9101 (mt0) cc_final: 0.8849 (tt0) REVERT: D 163 LYS cc_start: 0.8506 (pptt) cc_final: 0.8224 (tmtt) REVERT: E 144 ARG cc_start: 0.7992 (ttt180) cc_final: 0.7595 (ttp-170) REVERT: E 223 TYR cc_start: 0.9233 (t80) cc_final: 0.8615 (t80) REVERT: E 232 GLN cc_start: 0.9384 (tp40) cc_final: 0.9101 (tp40) REVERT: F 144 ARG cc_start: 0.7962 (ttt180) cc_final: 0.7603 (ttp-170) REVERT: G 144 ARG cc_start: 0.8049 (ttt180) cc_final: 0.7770 (ttp-170) REVERT: G 183 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7517 (mt-10) REVERT: J 163 LYS cc_start: 0.8662 (pptt) cc_final: 0.8303 (tmtt) REVERT: J 236 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8199 (tm-30) REVERT: K 154 THR cc_start: 0.8417 (t) cc_final: 0.8118 (t) REVERT: K 236 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8451 (tm-30) REVERT: L 144 ARG cc_start: 0.8130 (ttt180) cc_final: 0.7918 (ptm160) REVERT: M 236 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8452 (tm-30) REVERT: N 223 TYR cc_start: 0.9202 (t80) cc_final: 0.8785 (t80) REVERT: N 236 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8343 (tm-30) REVERT: O 163 LYS cc_start: 0.8592 (pptt) cc_final: 0.8294 (tmtt) REVERT: O 236 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8522 (tm-30) REVERT: P 144 ARG cc_start: 0.7883 (ttt180) cc_final: 0.7451 (ttp-170) REVERT: P 223 TYR cc_start: 0.9171 (t80) cc_final: 0.8526 (t80) REVERT: Q 144 ARG cc_start: 0.7869 (ttt180) cc_final: 0.7396 (ttp-170) REVERT: Q 154 THR cc_start: 0.8107 (t) cc_final: 0.7707 (t) REVERT: Q 236 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8371 (tm-30) REVERT: R 163 LYS cc_start: 0.8891 (tppt) cc_final: 0.8652 (tppp) REVERT: S 259 ASP cc_start: 0.8535 (m-30) cc_final: 0.8123 (p0) REVERT: T 154 THR cc_start: 0.8200 (t) cc_final: 0.7837 (t) REVERT: T 236 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8508 (tm-30) REVERT: U 154 THR cc_start: 0.8233 (t) cc_final: 0.7845 (t) REVERT: U 236 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8221 (tm-30) REVERT: U 285 TYR cc_start: 0.7746 (t80) cc_final: 0.7351 (t80) REVERT: V 154 THR cc_start: 0.8387 (t) cc_final: 0.8185 (t) REVERT: V 203 LYS cc_start: 0.8384 (mmtt) cc_final: 0.8125 (tttm) outliers start: 166 outliers final: 136 residues processed: 712 average time/residue: 0.2513 time to fit residues: 299.8718 Evaluate side-chains 697 residues out of total 4972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 561 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 86 CYS Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 86 CYS Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain M residue 48 CYS Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 86 CYS Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 228 ASP Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain N residue 48 CYS Chi-restraints excluded: chain N residue 86 CYS Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 228 ASP Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain O residue 48 CYS Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain P residue 48 CYS Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain Q residue 48 CYS Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain Q residue 102 LEU Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain Q residue 192 ILE Chi-restraints excluded: chain Q residue 199 VAL Chi-restraints excluded: chain Q residue 228 ASP Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 134 GLU Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain S residue 48 CYS Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 86 CYS Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 134 GLU Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 192 ILE Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 48 CYS Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain T residue 86 CYS Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain U residue 48 CYS Chi-restraints excluded: chain U residue 86 CYS Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain V residue 48 CYS Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain V residue 86 CYS Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 134 GLU Chi-restraints excluded: chain V residue 190 LEU Chi-restraints excluded: chain V residue 199 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 35 optimal weight: 0.7980 chunk 540 optimal weight: 10.0000 chunk 286 optimal weight: 60.0000 chunk 487 optimal weight: 8.9990 chunk 279 optimal weight: 7.9990 chunk 63 optimal weight: 0.0070 chunk 256 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 420 optimal weight: 1.9990 chunk 377 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 overall best weight: 1.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 246 ASN ** J 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 HIS Q 246 ASN R 246 ASN R 300 HIS S 300 HIS T 246 ASN U 300 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.126470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.101233 restraints weight = 81912.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.104440 restraints weight = 45072.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106763 restraints weight = 30538.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.108397 restraints weight = 23531.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.109498 restraints weight = 19648.092| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 46838 Z= 0.107 Angle : 0.503 5.640 63976 Z= 0.257 Chirality : 0.036 0.132 7150 Planarity : 0.004 0.034 8228 Dihedral : 4.405 25.148 6446 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.41 % Allowed : 23.34 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.11), residues: 5786 helix: 2.19 (0.08), residues: 4356 sheet: None (None), residues: 0 loop : -3.40 (0.12), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 181 TYR 0.018 0.001 TYR V 223 PHE 0.006 0.001 PHE R 100 TRP 0.009 0.001 TRP B 278 HIS 0.002 0.000 HIS G 238 Details of bonding type rmsd covalent geometry : bond 0.00227 (46794) covalent geometry : angle 0.50340 (63888) SS BOND : bond 0.00090 ( 44) SS BOND : angle 0.29534 ( 88) hydrogen bonds : bond 0.03681 ( 3014) hydrogen bonds : angle 3.35834 ( 8910) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 4972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 609 time to evaluate : 1.822 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ARG cc_start: 0.8138 (ttt180) cc_final: 0.7796 (ptm160) REVERT: A 232 GLN cc_start: 0.9441 (tp40) cc_final: 0.9143 (tp40) REVERT: A 236 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8400 (tm-30) REVERT: B 144 ARG cc_start: 0.7956 (ttt180) cc_final: 0.7666 (ptm160) REVERT: B 236 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8444 (tm-30) REVERT: C 144 ARG cc_start: 0.7970 (ttt180) cc_final: 0.7633 (ptm160) REVERT: C 277 GLN cc_start: 0.9090 (mt0) cc_final: 0.8764 (tt0) REVERT: D 154 THR cc_start: 0.8259 (t) cc_final: 0.7880 (t) REVERT: D 163 LYS cc_start: 0.8482 (pptt) cc_final: 0.8229 (tmtt) REVERT: D 183 GLU cc_start: 0.8133 (tt0) cc_final: 0.7933 (tt0) REVERT: E 144 ARG cc_start: 0.7934 (ttt180) cc_final: 0.7552 (ttp-170) REVERT: E 154 THR cc_start: 0.8262 (t) cc_final: 0.8009 (t) REVERT: E 223 TYR cc_start: 0.9243 (t80) cc_final: 0.8569 (t80) REVERT: E 232 GLN cc_start: 0.9388 (tp40) cc_final: 0.9099 (tp40) REVERT: F 144 ARG cc_start: 0.7875 (ttt180) cc_final: 0.7562 (ttp-170) REVERT: F 154 THR cc_start: 0.8254 (t) cc_final: 0.7870 (t) REVERT: F 236 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8491 (tm-30) REVERT: G 144 ARG cc_start: 0.8018 (ttt180) cc_final: 0.7699 (ttp-170) REVERT: I 154 THR cc_start: 0.8165 (t) cc_final: 0.7786 (t) REVERT: J 154 THR cc_start: 0.8142 (t) cc_final: 0.7752 (t) REVERT: J 163 LYS cc_start: 0.8641 (pptt) cc_final: 0.8357 (tmtt) REVERT: J 236 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8199 (tm-30) REVERT: K 154 THR cc_start: 0.8293 (t) cc_final: 0.8092 (t) REVERT: K 236 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8427 (tm-30) REVERT: L 232 GLN cc_start: 0.9434 (tp40) cc_final: 0.9132 (tp40) REVERT: L 236 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8409 (tm-30) REVERT: M 144 ARG cc_start: 0.8004 (ttt180) cc_final: 0.7434 (ttp80) REVERT: M 236 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8440 (tm-30) REVERT: N 236 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8391 (tm-30) REVERT: O 154 THR cc_start: 0.8162 (t) cc_final: 0.7755 (t) REVERT: O 236 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8514 (tm-30) REVERT: P 144 ARG cc_start: 0.7869 (ttt180) cc_final: 0.7464 (ttp-170) REVERT: P 154 THR cc_start: 0.8260 (t) cc_final: 0.8044 (t) REVERT: P 223 TYR cc_start: 0.9201 (t80) cc_final: 0.8571 (t80) REVERT: Q 144 ARG cc_start: 0.7813 (ttt180) cc_final: 0.7376 (ttp-170) REVERT: Q 154 THR cc_start: 0.8042 (t) cc_final: 0.7664 (t) REVERT: Q 163 LYS cc_start: 0.8682 (tppt) cc_final: 0.8448 (tppp) REVERT: Q 236 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8342 (tm-30) REVERT: R 163 LYS cc_start: 0.8855 (tppt) cc_final: 0.8626 (tppp) REVERT: S 259 ASP cc_start: 0.8554 (m-30) cc_final: 0.8135 (p0) REVERT: T 154 THR cc_start: 0.8221 (t) cc_final: 0.7823 (t) REVERT: T 236 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8465 (tm-30) REVERT: U 154 THR cc_start: 0.8218 (t) cc_final: 0.7835 (t) REVERT: U 163 LYS cc_start: 0.8654 (pptt) cc_final: 0.8421 (tmtt) REVERT: U 236 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8213 (tm-30) REVERT: U 285 TYR cc_start: 0.7838 (t80) cc_final: 0.7449 (t80) REVERT: V 144 ARG cc_start: 0.7859 (ttt180) cc_final: 0.7633 (ttt-90) REVERT: V 203 LYS cc_start: 0.8429 (mmtt) cc_final: 0.8187 (tttm) outliers start: 156 outliers final: 121 residues processed: 723 average time/residue: 0.2613 time to fit residues: 317.2452 Evaluate side-chains 692 residues out of total 4972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 571 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain H residue 86 CYS Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 86 CYS Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 277 GLN Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 86 CYS Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 126 GLU Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain M residue 48 CYS Chi-restraints excluded: chain M residue 86 CYS Chi-restraints excluded: chain M residue 126 GLU Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain N residue 48 CYS Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 134 GLU Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 228 ASP Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain O residue 48 CYS Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain P residue 48 CYS Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain Q residue 48 CYS Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain Q residue 192 ILE Chi-restraints excluded: chain Q residue 199 VAL Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain S residue 48 CYS Chi-restraints excluded: chain S residue 86 CYS Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 48 CYS Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain T residue 86 CYS Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain U residue 48 CYS Chi-restraints excluded: chain U residue 86 CYS Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain U residue 201 LEU Chi-restraints excluded: chain V residue 48 CYS Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 199 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 9 optimal weight: 5.9990 chunk 355 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 290 optimal weight: 2.9990 chunk 126 optimal weight: 0.4980 chunk 220 optimal weight: 0.9990 chunk 323 optimal weight: 7.9990 chunk 350 optimal weight: 0.9990 chunk 313 optimal weight: 30.0000 chunk 180 optimal weight: 5.9990 chunk 382 optimal weight: 10.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 277 GLN O 246 ASN ** P 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 300 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.124439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.099216 restraints weight = 82348.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.102321 restraints weight = 45641.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.104585 restraints weight = 31135.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.106190 restraints weight = 24091.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107120 restraints weight = 20221.372| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 46838 Z= 0.132 Angle : 0.521 6.116 63976 Z= 0.266 Chirality : 0.036 0.133 7150 Planarity : 0.004 0.037 8228 Dihedral : 4.424 25.030 6446 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.04 % Allowed : 22.64 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.11), residues: 5786 helix: 2.17 (0.08), residues: 4356 sheet: None (None), residues: 0 loop : -3.33 (0.12), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 181 TYR 0.016 0.001 TYR V 208 PHE 0.005 0.001 PHE L 44 TRP 0.025 0.001 TRP J 302 HIS 0.003 0.000 HIS C 238 Details of bonding type rmsd covalent geometry : bond 0.00295 (46794) covalent geometry : angle 0.52103 (63888) SS BOND : bond 0.00206 ( 44) SS BOND : angle 0.34281 ( 88) hydrogen bonds : bond 0.03968 ( 3014) hydrogen bonds : angle 3.41319 ( 8910) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 4972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 558 time to evaluate : 1.646 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ARG cc_start: 0.8111 (ttt180) cc_final: 0.7740 (ptm160) REVERT: A 232 GLN cc_start: 0.9448 (tp40) cc_final: 0.9142 (tp40) REVERT: B 144 ARG cc_start: 0.7927 (ttt180) cc_final: 0.7637 (ptm160) REVERT: E 144 ARG cc_start: 0.7923 (ttt180) cc_final: 0.7559 (ttp-170) REVERT: E 232 GLN cc_start: 0.9391 (tp40) cc_final: 0.9095 (tp40) REVERT: F 144 ARG cc_start: 0.7838 (ttt180) cc_final: 0.7530 (ttp-170) REVERT: F 236 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8488 (tm-30) REVERT: G 144 ARG cc_start: 0.7990 (ttt180) cc_final: 0.7676 (ttp-170) REVERT: J 236 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8158 (tm-30) REVERT: K 154 THR cc_start: 0.8397 (t) cc_final: 0.8141 (t) REVERT: L 232 GLN cc_start: 0.9438 (tp40) cc_final: 0.9132 (tp40) REVERT: M 144 ARG cc_start: 0.7954 (ttt180) cc_final: 0.7389 (ttp80) REVERT: N 236 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8386 (tm-30) REVERT: O 236 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8463 (tm-30) REVERT: O 273 GLN cc_start: 0.8476 (mp10) cc_final: 0.8210 (mp10) REVERT: P 144 ARG cc_start: 0.7907 (ttt180) cc_final: 0.7482 (ttp-170) REVERT: P 232 GLN cc_start: 0.9399 (tp40) cc_final: 0.9139 (tp40) REVERT: Q 144 ARG cc_start: 0.7780 (ttt180) cc_final: 0.7343 (ttp-170) REVERT: Q 154 THR cc_start: 0.8175 (t) cc_final: 0.7782 (t) REVERT: Q 163 LYS cc_start: 0.8667 (tppt) cc_final: 0.8454 (tppp) REVERT: Q 236 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8368 (tm-30) REVERT: S 259 ASP cc_start: 0.8601 (m-30) cc_final: 0.8242 (p0) REVERT: T 154 THR cc_start: 0.8293 (t) cc_final: 0.7936 (t) REVERT: T 236 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8488 (tm-30) REVERT: U 163 LYS cc_start: 0.8631 (pptt) cc_final: 0.8362 (tmtt) REVERT: U 236 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8140 (tm-30) REVERT: U 285 TYR cc_start: 0.7979 (t80) cc_final: 0.7579 (t80) REVERT: V 144 ARG cc_start: 0.7832 (ttt180) cc_final: 0.7607 (ttt-90) REVERT: V 203 LYS cc_start: 0.8439 (mmtt) cc_final: 0.8207 (tttm) outliers start: 185 outliers final: 154 residues processed: 666 average time/residue: 0.2650 time to fit residues: 295.8092 Evaluate side-chains 694 residues out of total 4972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 540 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 86 CYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 54 TYR Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 86 CYS Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 126 GLU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain M residue 48 CYS Chi-restraints excluded: chain M residue 86 CYS Chi-restraints excluded: chain M residue 126 GLU Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 228 ASP Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain N residue 48 CYS Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 86 CYS Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 126 GLU Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 134 GLU Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 228 ASP Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain O residue 48 CYS Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 86 CYS Chi-restraints excluded: chain O residue 126 GLU Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain P residue 48 CYS Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain Q residue 48 CYS Chi-restraints excluded: chain Q residue 86 CYS Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain Q residue 192 ILE Chi-restraints excluded: chain Q residue 199 VAL Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 126 GLU Chi-restraints excluded: chain R residue 134 GLU Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain S residue 48 CYS Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 86 CYS Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 134 GLU Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 228 ASP Chi-restraints excluded: chain T residue 48 CYS Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain T residue 126 GLU Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain U residue 48 CYS Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain U residue 201 LEU Chi-restraints excluded: chain V residue 48 CYS Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 126 GLU Chi-restraints excluded: chain V residue 190 LEU Chi-restraints excluded: chain V residue 199 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 67 optimal weight: 8.9990 chunk 443 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 130 optimal weight: 60.0000 chunk 92 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 378 optimal weight: 10.0000 chunk 368 optimal weight: 3.9990 chunk 547 optimal weight: 20.0000 chunk 384 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 277 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 ASN K 300 HIS M 273 GLN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 ASN V 300 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.120386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.095750 restraints weight = 83236.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098675 restraints weight = 45733.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100892 restraints weight = 31179.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102383 restraints weight = 24082.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.103273 restraints weight = 20222.401| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 46838 Z= 0.199 Angle : 0.575 5.926 63976 Z= 0.296 Chirality : 0.038 0.133 7150 Planarity : 0.004 0.093 8228 Dihedral : 4.688 25.522 6446 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 4.04 % Allowed : 23.06 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.11), residues: 5786 helix: 2.00 (0.08), residues: 4356 sheet: None (None), residues: 0 loop : -3.39 (0.12), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 181 TYR 0.029 0.002 TYR K 223 PHE 0.010 0.001 PHE V 135 TRP 0.014 0.001 TRP F 80 HIS 0.005 0.001 HIS R 147 Details of bonding type rmsd covalent geometry : bond 0.00457 (46794) covalent geometry : angle 0.57465 (63888) SS BOND : bond 0.00383 ( 44) SS BOND : angle 0.45491 ( 88) hydrogen bonds : bond 0.04697 ( 3014) hydrogen bonds : angle 3.64334 ( 8910) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 4972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 501 time to evaluate : 1.742 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: symmetry clash revert: symmetry clash REVERT: A 144 ARG cc_start: 0.8143 (ttt180) cc_final: 0.7717 (ptm160) REVERT: A 232 GLN cc_start: 0.9455 (tp40) cc_final: 0.9125 (tp40) REVERT: A 273 GLN cc_start: 0.8723 (mp10) cc_final: 0.8405 (mp10) REVERT: B 144 ARG cc_start: 0.7957 (ttt180) cc_final: 0.7694 (ptm160) REVERT: D 273 GLN cc_start: 0.8529 (mp10) cc_final: 0.8287 (mp10) REVERT: E 144 ARG cc_start: 0.7925 (ttt180) cc_final: 0.7555 (ttp-170) REVERT: E 232 GLN cc_start: 0.9387 (tp40) cc_final: 0.9074 (tp40) REVERT: F 144 ARG cc_start: 0.7840 (ttt180) cc_final: 0.7525 (ttp-170) REVERT: G 144 ARG cc_start: 0.7978 (ttt180) cc_final: 0.7667 (ttp-170) REVERT: J 163 LYS cc_start: 0.8660 (pptt) cc_final: 0.8337 (tmtt) REVERT: J 232 GLN cc_start: 0.9441 (tp40) cc_final: 0.9229 (mm110) REVERT: J 236 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8018 (tm-30) REVERT: K 291 GLN cc_start: 0.8388 (pp30) cc_final: 0.8136 (pt0) REVERT: L 144 ARG cc_start: 0.8134 (ttt180) cc_final: 0.7749 (ptm160) REVERT: L 232 GLN cc_start: 0.9448 (tp40) cc_final: 0.9118 (tp40) REVERT: L 273 GLN cc_start: 0.8732 (mp10) cc_final: 0.8408 (mp10) REVERT: M 144 ARG cc_start: 0.7910 (ttt180) cc_final: 0.7423 (ttp-170) REVERT: O 236 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8446 (tm-30) REVERT: P 144 ARG cc_start: 0.7885 (ttt180) cc_final: 0.7464 (ttp-170) REVERT: P 232 GLN cc_start: 0.9414 (tp40) cc_final: 0.9133 (tp40) REVERT: Q 144 ARG cc_start: 0.7794 (ttt180) cc_final: 0.7370 (ttp-170) REVERT: Q 163 LYS cc_start: 0.8653 (tppt) cc_final: 0.8447 (tppp) REVERT: S 259 ASP cc_start: 0.8665 (m-30) cc_final: 0.8370 (p0) REVERT: U 163 LYS cc_start: 0.8610 (pptt) cc_final: 0.8367 (tmtt) REVERT: U 232 GLN cc_start: 0.9440 (tp40) cc_final: 0.9213 (mm110) REVERT: U 236 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8441 (tm-30) REVERT: U 285 TYR cc_start: 0.8208 (t80) cc_final: 0.7758 (t80) REVERT: V 144 ARG cc_start: 0.7871 (ttt180) cc_final: 0.7596 (ttt-90) outliers start: 185 outliers final: 166 residues processed: 614 average time/residue: 0.2625 time to fit residues: 268.9617 Evaluate side-chains 648 residues out of total 4972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 482 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 86 CYS Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 126 GLU Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 54 TYR Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 86 CYS Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 86 CYS Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 126 GLU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain M residue 48 CYS Chi-restraints excluded: chain M residue 86 CYS Chi-restraints excluded: chain M residue 126 GLU Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain N residue 48 CYS Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 86 CYS Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 126 GLU Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 134 GLU Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 228 ASP Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain O residue 48 CYS Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 86 CYS Chi-restraints excluded: chain O residue 126 GLU Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain P residue 48 CYS Chi-restraints excluded: chain P residue 134 GLU Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain Q residue 48 CYS Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain Q residue 192 ILE Chi-restraints excluded: chain Q residue 199 VAL Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 126 GLU Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 134 GLU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain S residue 48 CYS Chi-restraints excluded: chain S residue 86 CYS Chi-restraints excluded: chain S residue 126 GLU Chi-restraints excluded: chain S residue 134 GLU Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 48 CYS Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain T residue 86 CYS Chi-restraints excluded: chain T residue 126 GLU Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain U residue 48 CYS Chi-restraints excluded: chain U residue 86 CYS Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 190 LEU Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain U residue 201 LEU Chi-restraints excluded: chain V residue 48 CYS Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain V residue 86 CYS Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 126 GLU Chi-restraints excluded: chain V residue 199 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 263 optimal weight: 5.9990 chunk 414 optimal weight: 0.6980 chunk 307 optimal weight: 0.9980 chunk 400 optimal weight: 1.9990 chunk 496 optimal weight: 4.9990 chunk 272 optimal weight: 0.8980 chunk 283 optimal weight: 10.0000 chunk 525 optimal weight: 7.9990 chunk 34 optimal weight: 0.0770 chunk 434 optimal weight: 7.9990 chunk 365 optimal weight: 0.9980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 273 GLN ** P 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.126115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.101230 restraints weight = 80992.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.104421 restraints weight = 44113.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106704 restraints weight = 29698.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.108307 restraints weight = 22825.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.109205 restraints weight = 19001.989| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 46838 Z= 0.110 Angle : 0.508 5.743 63976 Z= 0.260 Chirality : 0.036 0.125 7150 Planarity : 0.004 0.035 8228 Dihedral : 4.366 25.006 6446 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.19 % Allowed : 24.21 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.11), residues: 5786 helix: 2.24 (0.08), residues: 4356 sheet: None (None), residues: 0 loop : -3.22 (0.12), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 181 TYR 0.014 0.001 TYR V 208 PHE 0.008 0.001 PHE R 100 TRP 0.017 0.001 TRP J 302 HIS 0.004 0.001 HIS R 147 Details of bonding type rmsd covalent geometry : bond 0.00225 (46794) covalent geometry : angle 0.50870 (63888) SS BOND : bond 0.00034 ( 44) SS BOND : angle 0.21700 ( 88) hydrogen bonds : bond 0.03663 ( 3014) hydrogen bonds : angle 3.35923 ( 8910) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 4972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 580 time to evaluate : 1.273 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ARG cc_start: 0.8121 (ttt180) cc_final: 0.7714 (ptm160) REVERT: A 232 GLN cc_start: 0.9435 (tp40) cc_final: 0.9137 (tp40) REVERT: A 236 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8372 (tm-30) REVERT: B 144 ARG cc_start: 0.7900 (ttt180) cc_final: 0.7620 (ptm160) REVERT: C 223 TYR cc_start: 0.9209 (t80) cc_final: 0.8767 (t80) REVERT: D 154 THR cc_start: 0.8401 (t) cc_final: 0.8028 (t) REVERT: D 236 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8566 (tm-30) REVERT: E 144 ARG cc_start: 0.7921 (ttt180) cc_final: 0.7668 (ptm160) REVERT: E 223 TYR cc_start: 0.9199 (t80) cc_final: 0.8579 (t80) REVERT: E 232 GLN cc_start: 0.9384 (tp40) cc_final: 0.9098 (tp40) REVERT: E 236 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8528 (tm-30) REVERT: F 144 ARG cc_start: 0.7865 (ttt180) cc_final: 0.7538 (ttp-170) REVERT: F 236 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8413 (tm-30) REVERT: G 144 ARG cc_start: 0.7992 (ttt180) cc_final: 0.7665 (ttp-170) REVERT: H 223 TYR cc_start: 0.9213 (t80) cc_final: 0.8771 (t80) REVERT: H 236 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8527 (tm-30) REVERT: J 163 LYS cc_start: 0.8598 (pptt) cc_final: 0.8326 (tmtt) REVERT: J 232 GLN cc_start: 0.9430 (tp40) cc_final: 0.9220 (mm110) REVERT: J 236 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8184 (tm-30) REVERT: K 223 TYR cc_start: 0.9224 (t80) cc_final: 0.9000 (t80) REVERT: K 236 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8348 (tm-30) REVERT: L 232 GLN cc_start: 0.9426 (tp40) cc_final: 0.9127 (tp40) REVERT: L 236 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8386 (tm-30) REVERT: M 144 ARG cc_start: 0.7928 (ttt180) cc_final: 0.7434 (ttp-170) REVERT: N 223 TYR cc_start: 0.9218 (t80) cc_final: 0.8771 (t80) REVERT: N 236 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8403 (tm-30) REVERT: O 154 THR cc_start: 0.8289 (t) cc_final: 0.7908 (t) REVERT: O 236 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8491 (tm-30) REVERT: P 144 ARG cc_start: 0.7959 (ttt180) cc_final: 0.7563 (ttp-170) REVERT: P 223 TYR cc_start: 0.9189 (t80) cc_final: 0.8544 (t80) REVERT: P 232 GLN cc_start: 0.9400 (tp40) cc_final: 0.9103 (tp40) REVERT: Q 144 ARG cc_start: 0.7799 (ttt180) cc_final: 0.7357 (ttp-170) REVERT: Q 154 THR cc_start: 0.8214 (t) cc_final: 0.7839 (t) REVERT: Q 163 LYS cc_start: 0.8599 (tppt) cc_final: 0.8398 (tppp) REVERT: Q 236 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8342 (tm-30) REVERT: R 163 LYS cc_start: 0.8769 (tppt) cc_final: 0.8566 (tppp) REVERT: S 259 ASP cc_start: 0.8542 (m-30) cc_final: 0.8114 (p0) REVERT: T 116 THR cc_start: 0.9068 (t) cc_final: 0.8850 (t) REVERT: T 154 THR cc_start: 0.8360 (t) cc_final: 0.7976 (t) REVERT: T 236 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8461 (tm-30) REVERT: U 163 LYS cc_start: 0.8556 (pptt) cc_final: 0.8290 (tmtt) REVERT: U 236 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8160 (tm-30) REVERT: V 144 ARG cc_start: 0.7870 (ttt180) cc_final: 0.7585 (ttt-90) REVERT: V 223 TYR cc_start: 0.9225 (t80) cc_final: 0.8997 (t80) REVERT: V 236 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8398 (tm-30) outliers start: 146 outliers final: 134 residues processed: 669 average time/residue: 0.2578 time to fit residues: 286.7583 Evaluate side-chains 690 residues out of total 4972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 556 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 86 CYS Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 86 CYS Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 86 CYS Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 86 CYS Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 126 GLU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain M residue 48 CYS Chi-restraints excluded: chain M residue 86 CYS Chi-restraints excluded: chain M residue 126 GLU Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 228 ASP Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain N residue 48 CYS Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 86 CYS Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 126 GLU Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 228 ASP Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain O residue 48 CYS Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 86 CYS Chi-restraints excluded: chain O residue 126 GLU Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain P residue 48 CYS Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain Q residue 48 CYS Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain Q residue 192 ILE Chi-restraints excluded: chain Q residue 199 VAL Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain S residue 48 CYS Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 86 CYS Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 48 CYS Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain T residue 86 CYS Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain U residue 86 CYS Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain U residue 201 LEU Chi-restraints excluded: chain V residue 48 CYS Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain V residue 86 CYS Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 126 GLU Chi-restraints excluded: chain V residue 190 LEU Chi-restraints excluded: chain V residue 199 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 422 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 349 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 40 optimal weight: 0.4980 chunk 205 optimal weight: 9.9990 chunk 324 optimal weight: 4.9990 chunk 447 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 300 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN B 273 GLN F 216 GLN ** I 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 273 GLN ** P 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.122507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.097725 restraints weight = 83034.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100799 restraints weight = 45436.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.103025 restraints weight = 30748.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.104555 restraints weight = 23687.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105597 restraints weight = 19847.012| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 46838 Z= 0.155 Angle : 0.542 5.940 63976 Z= 0.276 Chirality : 0.037 0.181 7150 Planarity : 0.004 0.034 8228 Dihedral : 4.518 25.841 6446 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.08 % Allowed : 24.50 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.11), residues: 5786 helix: 2.14 (0.08), residues: 4378 sheet: None (None), residues: 0 loop : -3.23 (0.13), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 181 TYR 0.022 0.002 TYR Q 223 PHE 0.009 0.001 PHE T 100 TRP 0.014 0.001 TRP J 302 HIS 0.003 0.001 HIS Q 45 Details of bonding type rmsd covalent geometry : bond 0.00352 (46794) covalent geometry : angle 0.54170 (63888) SS BOND : bond 0.00279 ( 44) SS BOND : angle 0.38373 ( 88) hydrogen bonds : bond 0.04215 ( 3014) hydrogen bonds : angle 3.46561 ( 8910) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 4972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 512 time to evaluate : 1.684 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ARG cc_start: 0.8135 (ttt180) cc_final: 0.7735 (ptm160) REVERT: A 232 GLN cc_start: 0.9450 (tp40) cc_final: 0.9144 (tp40) REVERT: B 144 ARG cc_start: 0.7855 (ttt180) cc_final: 0.7585 (ptm160) REVERT: E 144 ARG cc_start: 0.7905 (ttt180) cc_final: 0.7515 (ttp-170) REVERT: E 232 GLN cc_start: 0.9387 (tp40) cc_final: 0.9081 (tp40) REVERT: F 144 ARG cc_start: 0.7864 (ttt180) cc_final: 0.7546 (ttp-170) REVERT: F 236 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8446 (tm-30) REVERT: G 144 ARG cc_start: 0.7983 (ttt180) cc_final: 0.7668 (ttp-170) REVERT: J 232 GLN cc_start: 0.9434 (tp40) cc_final: 0.9221 (mm110) REVERT: J 236 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8062 (tm-30) REVERT: L 232 GLN cc_start: 0.9445 (tp40) cc_final: 0.9135 (tp40) REVERT: M 144 ARG cc_start: 0.7920 (ttt180) cc_final: 0.7416 (ttp-170) REVERT: O 236 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8493 (tm-30) REVERT: O 259 ASP cc_start: 0.8617 (m-30) cc_final: 0.8386 (p0) REVERT: P 144 ARG cc_start: 0.7936 (ttt180) cc_final: 0.7531 (ttp-170) REVERT: P 232 GLN cc_start: 0.9415 (tp40) cc_final: 0.9148 (tp40) REVERT: Q 144 ARG cc_start: 0.7791 (ttt180) cc_final: 0.7359 (ttp-170) REVERT: Q 236 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8405 (tm-30) REVERT: S 259 ASP cc_start: 0.8619 (m-30) cc_final: 0.8259 (p0) REVERT: U 163 LYS cc_start: 0.8556 (pptt) cc_final: 0.8342 (tmtt) REVERT: U 236 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8055 (tm-30) REVERT: U 285 TYR cc_start: 0.8120 (t80) cc_final: 0.7670 (t80) REVERT: V 144 ARG cc_start: 0.7876 (ttt180) cc_final: 0.7593 (ttt-90) outliers start: 141 outliers final: 132 residues processed: 602 average time/residue: 0.2520 time to fit residues: 252.3766 Evaluate side-chains 639 residues out of total 4972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 507 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 86 CYS Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 86 CYS Chi-restraints excluded: chain J residue 126 GLU Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 86 CYS Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 126 GLU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 284 VAL Chi-restraints excluded: chain M residue 48 CYS Chi-restraints excluded: chain M residue 86 CYS Chi-restraints excluded: chain M residue 126 GLU Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain N residue 48 CYS Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 126 GLU Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 228 ASP Chi-restraints excluded: chain N residue 284 VAL Chi-restraints excluded: chain O residue 48 CYS Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 126 GLU Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain P residue 48 CYS Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain Q residue 48 CYS Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain Q residue 192 ILE Chi-restraints excluded: chain Q residue 199 VAL Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 126 GLU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain S residue 48 CYS Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 86 CYS Chi-restraints excluded: chain S residue 126 GLU Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 48 CYS Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain T residue 86 CYS Chi-restraints excluded: chain T residue 126 GLU Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain U residue 86 CYS Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain U residue 201 LEU Chi-restraints excluded: chain V residue 48 CYS Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain V residue 86 CYS Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 126 GLU Chi-restraints excluded: chain V residue 190 LEU Chi-restraints excluded: chain V residue 199 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 0 optimal weight: 50.0000 chunk 562 optimal weight: 7.9990 chunk 522 optimal weight: 9.9990 chunk 434 optimal weight: 0.9990 chunk 539 optimal weight: 8.9990 chunk 300 optimal weight: 5.9990 chunk 459 optimal weight: 6.9990 chunk 470 optimal weight: 0.0010 chunk 203 optimal weight: 0.7980 chunk 451 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.125077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.100194 restraints weight = 81733.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.103293 restraints weight = 44429.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105582 restraints weight = 30069.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106990 restraints weight = 23126.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.108163 restraints weight = 19492.116| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 46838 Z= 0.112 Angle : 0.511 5.537 63976 Z= 0.260 Chirality : 0.036 0.127 7150 Planarity : 0.004 0.034 8228 Dihedral : 4.380 25.427 6446 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.99 % Allowed : 24.76 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.11), residues: 5786 helix: 2.23 (0.08), residues: 4378 sheet: None (None), residues: 0 loop : -3.12 (0.13), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 181 TYR 0.018 0.001 TYR Q 223 PHE 0.009 0.001 PHE R 100 TRP 0.015 0.001 TRP J 302 HIS 0.002 0.000 HIS P 238 Details of bonding type rmsd covalent geometry : bond 0.00239 (46794) covalent geometry : angle 0.51117 (63888) SS BOND : bond 0.00118 ( 44) SS BOND : angle 0.29572 ( 88) hydrogen bonds : bond 0.03840 ( 3014) hydrogen bonds : angle 3.34520 ( 8910) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7668.76 seconds wall clock time: 133 minutes 29.12 seconds (8009.12 seconds total)