Starting phenix.real_space_refine on Mon Aug 25 23:03:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v66_31736/08_2025/7v66_31736.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v66_31736/08_2025/7v66_31736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v66_31736/08_2025/7v66_31736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v66_31736/08_2025/7v66_31736.map" model { file = "/net/cci-nas-00/data/ceres_data/7v66_31736/08_2025/7v66_31736.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v66_31736/08_2025/7v66_31736.cif" } resolution = 1.89 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 168 5.16 5 C 20904 2.51 5 N 5808 2.21 5 O 6336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33216 Number of models: 1 Model: "" Number of chains: 24 Chain: "U" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "G" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "I" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "J" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "K" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "L" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "M" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "N" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "O" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "Q" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "S" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "T" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "V" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "W" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "X" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 6.50, per 1000 atoms: 0.20 Number of scatterers: 33216 At special positions: 0 Unit cell: (130.295, 130.295, 130.295, 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 168 16.00 O 6336 8.00 N 5808 7.00 C 20904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.39 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.4 microseconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'U' and resid 9 through 38 Processing helix chain 'U' and resid 44 through 72 Processing helix chain 'U' and resid 91 through 120 Processing helix chain 'U' and resid 122 through 133 Processing helix chain 'U' and resid 133 through 154 Processing helix chain 'U' and resid 159 through 170 removed outlier: 3.809A pdb=" N GLU U 163 " --> pdb=" O SER U 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 38 Processing helix chain 'A' and resid 44 through 72 Processing helix chain 'A' and resid 91 through 120 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 133 through 154 Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 38 Processing helix chain 'B' and resid 44 through 72 Processing helix chain 'B' and resid 91 through 120 Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 133 through 154 Processing helix chain 'B' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 37 Processing helix chain 'C' and resid 44 through 72 Processing helix chain 'C' and resid 91 through 120 Processing helix chain 'C' and resid 122 through 133 Processing helix chain 'C' and resid 133 through 154 Processing helix chain 'C' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU C 163 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 37 Processing helix chain 'D' and resid 44 through 72 Processing helix chain 'D' and resid 91 through 120 Processing helix chain 'D' and resid 122 through 133 Processing helix chain 'D' and resid 133 through 154 Processing helix chain 'D' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU D 163 " --> pdb=" O SER D 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 38 Processing helix chain 'E' and resid 44 through 72 Processing helix chain 'E' and resid 91 through 120 Processing helix chain 'E' and resid 122 through 133 Processing helix chain 'E' and resid 133 through 154 Processing helix chain 'E' and resid 159 through 170 removed outlier: 3.809A pdb=" N GLU E 163 " --> pdb=" O SER E 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 38 Processing helix chain 'F' and resid 44 through 72 Processing helix chain 'F' and resid 91 through 120 Processing helix chain 'F' and resid 122 through 133 Processing helix chain 'F' and resid 133 through 154 Processing helix chain 'F' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 38 Processing helix chain 'G' and resid 44 through 72 Processing helix chain 'G' and resid 91 through 120 Processing helix chain 'G' and resid 122 through 133 Processing helix chain 'G' and resid 133 through 154 Processing helix chain 'G' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU G 163 " --> pdb=" O SER G 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 38 Processing helix chain 'H' and resid 44 through 72 Processing helix chain 'H' and resid 91 through 120 Processing helix chain 'H' and resid 122 through 133 Processing helix chain 'H' and resid 133 through 154 Processing helix chain 'H' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU H 163 " --> pdb=" O SER H 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 38 Processing helix chain 'I' and resid 44 through 72 Processing helix chain 'I' and resid 91 through 120 Processing helix chain 'I' and resid 122 through 133 Processing helix chain 'I' and resid 133 through 154 Processing helix chain 'I' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU I 163 " --> pdb=" O SER I 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 38 Processing helix chain 'J' and resid 44 through 72 Processing helix chain 'J' and resid 91 through 120 Processing helix chain 'J' and resid 122 through 133 Processing helix chain 'J' and resid 133 through 154 Processing helix chain 'J' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 38 Processing helix chain 'K' and resid 44 through 72 Processing helix chain 'K' and resid 91 through 120 Processing helix chain 'K' and resid 122 through 133 Processing helix chain 'K' and resid 133 through 154 Processing helix chain 'K' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU K 163 " --> pdb=" O SER K 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 38 Processing helix chain 'L' and resid 44 through 72 Processing helix chain 'L' and resid 91 through 120 Processing helix chain 'L' and resid 122 through 133 Processing helix chain 'L' and resid 133 through 154 Processing helix chain 'L' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU L 163 " --> pdb=" O SER L 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 38 Processing helix chain 'M' and resid 44 through 72 Processing helix chain 'M' and resid 91 through 120 Processing helix chain 'M' and resid 122 through 133 Processing helix chain 'M' and resid 133 through 154 Processing helix chain 'M' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU M 163 " --> pdb=" O SER M 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 37 Processing helix chain 'N' and resid 44 through 72 Processing helix chain 'N' and resid 91 through 120 Processing helix chain 'N' and resid 122 through 133 Processing helix chain 'N' and resid 133 through 154 Processing helix chain 'N' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU N 163 " --> pdb=" O SER N 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 38 Processing helix chain 'O' and resid 44 through 72 Processing helix chain 'O' and resid 91 through 120 Processing helix chain 'O' and resid 122 through 133 Processing helix chain 'O' and resid 133 through 154 Processing helix chain 'O' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU O 163 " --> pdb=" O SER O 159 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 38 Processing helix chain 'P' and resid 44 through 72 Processing helix chain 'P' and resid 91 through 120 Processing helix chain 'P' and resid 122 through 133 Processing helix chain 'P' and resid 133 through 154 Processing helix chain 'P' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU P 163 " --> pdb=" O SER P 159 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 38 Processing helix chain 'Q' and resid 44 through 72 Processing helix chain 'Q' and resid 91 through 120 Processing helix chain 'Q' and resid 122 through 133 Processing helix chain 'Q' and resid 133 through 154 Processing helix chain 'Q' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU Q 163 " --> pdb=" O SER Q 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 38 Processing helix chain 'R' and resid 44 through 72 Processing helix chain 'R' and resid 91 through 120 Processing helix chain 'R' and resid 122 through 133 Processing helix chain 'R' and resid 133 through 154 Processing helix chain 'R' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU R 163 " --> pdb=" O SER R 159 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 38 Processing helix chain 'S' and resid 44 through 72 Processing helix chain 'S' and resid 91 through 120 Processing helix chain 'S' and resid 122 through 133 Processing helix chain 'S' and resid 133 through 154 Processing helix chain 'S' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU S 163 " --> pdb=" O SER S 159 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 38 Processing helix chain 'T' and resid 44 through 72 Processing helix chain 'T' and resid 91 through 120 Processing helix chain 'T' and resid 122 through 133 Processing helix chain 'T' and resid 133 through 154 Processing helix chain 'T' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU T 163 " --> pdb=" O SER T 159 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 38 Processing helix chain 'V' and resid 44 through 72 Processing helix chain 'V' and resid 91 through 120 Processing helix chain 'V' and resid 122 through 133 Processing helix chain 'V' and resid 133 through 154 Processing helix chain 'V' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU V 163 " --> pdb=" O SER V 159 " (cutoff:3.500A) Processing helix chain 'W' and resid 9 through 38 Processing helix chain 'W' and resid 44 through 72 Processing helix chain 'W' and resid 91 through 120 Processing helix chain 'W' and resid 122 through 133 Processing helix chain 'W' and resid 133 through 154 Processing helix chain 'W' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU W 163 " --> pdb=" O SER W 159 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 38 Processing helix chain 'X' and resid 44 through 72 Processing helix chain 'X' and resid 91 through 120 Processing helix chain 'X' and resid 122 through 133 Processing helix chain 'X' and resid 133 through 154 Processing helix chain 'X' and resid 159 through 170 removed outlier: 3.806A pdb=" N GLU X 163 " --> pdb=" O SER X 159 " (cutoff:3.500A) 2637 hydrogen bonds defined for protein. 7911 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: 6.92 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10606 1.34 - 1.46: 4943 1.46 - 1.57: 18099 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 33912 Sorted by residual: bond pdb=" C ALA M 156 " pdb=" N PRO M 157 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.50e+00 bond pdb=" C ALA V 156 " pdb=" N PRO V 157 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.50e+00 bond pdb=" C ALA T 156 " pdb=" N PRO T 157 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.50e+00 bond pdb=" C ALA A 156 " pdb=" N PRO A 157 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.50e+00 bond pdb=" C ALA X 156 " pdb=" N PRO X 157 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.50e+00 ... (remaining 33907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 44655 2.57 - 5.14: 935 5.14 - 7.71: 135 7.71 - 10.28: 66 10.28 - 12.85: 1 Bond angle restraints: 45792 Sorted by residual: angle pdb=" C ALA W 156 " pdb=" N PRO W 157 " pdb=" CA PRO W 157 " ideal model delta sigma weight residual 119.84 129.45 -9.61 1.25e+00 6.40e-01 5.91e+01 angle pdb=" N GLU B 90 " pdb=" CA GLU B 90 " pdb=" C GLU B 90 " ideal model delta sigma weight residual 110.80 123.65 -12.85 2.13e+00 2.20e-01 3.64e+01 angle pdb=" N LYS S 45 " pdb=" CA LYS S 45 " pdb=" C LYS S 45 " ideal model delta sigma weight residual 111.28 117.33 -6.05 1.09e+00 8.42e-01 3.08e+01 angle pdb=" N THR U 131 " pdb=" CA THR U 131 " pdb=" C THR U 131 " ideal model delta sigma weight residual 111.82 117.22 -5.40 1.16e+00 7.43e-01 2.17e+01 angle pdb=" N THR B 131 " pdb=" CA THR B 131 " pdb=" C THR B 131 " ideal model delta sigma weight residual 111.82 117.22 -5.40 1.16e+00 7.43e-01 2.16e+01 ... (remaining 45787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 19381 17.57 - 35.14: 609 35.14 - 52.71: 287 52.71 - 70.28: 50 70.28 - 87.84: 25 Dihedral angle restraints: 20352 sinusoidal: 8112 harmonic: 12240 Sorted by residual: dihedral pdb=" CA TRP H 89 " pdb=" C TRP H 89 " pdb=" N GLU H 90 " pdb=" CA GLU H 90 " ideal model delta harmonic sigma weight residual 180.00 160.80 19.20 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA TRP A 89 " pdb=" C TRP A 89 " pdb=" N GLU A 90 " pdb=" CA GLU A 90 " ideal model delta harmonic sigma weight residual 180.00 160.80 19.20 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA TRP T 89 " pdb=" C TRP T 89 " pdb=" N GLU T 90 " pdb=" CA GLU T 90 " ideal model delta harmonic sigma weight residual 180.00 160.80 19.20 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 20349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 4699 0.118 - 0.236: 154 0.236 - 0.354: 19 0.354 - 0.472: 1 0.472 - 0.590: 23 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CG LEU K 151 " pdb=" CB LEU K 151 " pdb=" CD1 LEU K 151 " pdb=" CD2 LEU K 151 " both_signs ideal model delta sigma weight residual False -2.59 -2.00 -0.59 2.00e-01 2.50e+01 8.69e+00 chirality pdb=" CG LEU I 151 " pdb=" CB LEU I 151 " pdb=" CD1 LEU I 151 " pdb=" CD2 LEU I 151 " both_signs ideal model delta sigma weight residual False -2.59 -2.00 -0.59 2.00e-01 2.50e+01 8.69e+00 chirality pdb=" CG LEU J 151 " pdb=" CB LEU J 151 " pdb=" CD1 LEU J 151 " pdb=" CD2 LEU J 151 " both_signs ideal model delta sigma weight residual False -2.59 -2.00 -0.59 2.00e-01 2.50e+01 8.69e+00 ... (remaining 4893 not shown) Planarity restraints: 6024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 28 " -0.035 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" CG TYR H 28 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR H 28 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR H 28 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR H 28 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR H 28 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR H 28 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR H 28 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 28 " -0.035 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" CG TYR A 28 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR A 28 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 28 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 28 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 28 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 28 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 28 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 28 " -0.035 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" CG TYR B 28 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR B 28 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 28 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 28 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 28 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 28 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 28 " -0.006 2.00e-02 2.50e+03 ... (remaining 6021 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 92 2.52 - 3.12: 24800 3.12 - 3.71: 56422 3.71 - 4.31: 80819 4.31 - 4.90: 131955 Nonbonded interactions: 294088 Sorted by model distance: nonbonded pdb=" O GLY D 155 " pdb=" OG SER D 159 " model vdw 1.929 3.040 nonbonded pdb=" O GLY W 155 " pdb=" OG SER W 159 " model vdw 2.206 3.040 nonbonded pdb=" OD2 ASP B 40 " pdb=" OG SER D 2 " model vdw 2.305 3.040 nonbonded pdb=" OG SER Q 2 " pdb=" OD2 ASP W 40 " model vdw 2.305 3.040 nonbonded pdb=" OD2 ASP O 40 " pdb=" OG SER R 2 " model vdw 2.305 3.040 ... (remaining 294083 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: 0.01 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' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 29.100 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.130 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:9.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0489 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 : 0.006 0.059 33912 Z= 0.266 Angle : 1.018 12.850 45792 Z= 0.581 Chirality : 0.067 0.590 4896 Planarity : 0.006 0.026 6024 Dihedral : 12.145 87.844 12432 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.91 % Favored : 98.04 % Rotamer: Outliers : 2.07 % Allowed : 2.73 % Favored : 95.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.13), residues: 4080 helix: 1.80 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : -0.65 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.003 ARG O 75 TYR 0.063 0.006 TYR A 28 PHE 0.016 0.004 PHE N 37 TRP 0.013 0.003 TRP H 89 HIS 0.026 0.005 HIS M 147 Details of bonding type rmsd covalent geometry : bond 0.00567 (33912) covalent geometry : angle 1.01810 (45792) hydrogen bonds : bond 0.10263 ( 2637) hydrogen bonds : angle 4.19074 ( 7911) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 288 time to evaluate : 1.141 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: symmetry clash revert: symmetry clash REVERT: U 19 GLN cc_start: 0.2173 (tp40) cc_final: 0.1938 (mm-40) REVERT: A 19 GLN cc_start: 0.2205 (tp40) cc_final: 0.1933 (mm-40) REVERT: B 19 GLN cc_start: 0.2189 (tp40) cc_final: 0.1947 (mm-40) REVERT: C 19 GLN cc_start: 0.2198 (tp40) cc_final: 0.1934 (mm-40) REVERT: D 19 GLN cc_start: 0.2214 (tp40) cc_final: 0.1948 (mm-40) REVERT: E 19 GLN cc_start: 0.2198 (tp40) cc_final: 0.1926 (mm-40) REVERT: F 19 GLN cc_start: 0.2203 (tp40) cc_final: 0.1962 (mm-40) REVERT: G 19 GLN cc_start: 0.2191 (tp40) cc_final: 0.1926 (mm-40) REVERT: H 19 GLN cc_start: 0.2191 (tp40) cc_final: 0.1927 (mm-40) REVERT: I 19 GLN cc_start: 0.2188 (tp40) cc_final: 0.1919 (mm-40) REVERT: J 19 GLN cc_start: 0.2202 (tp40) cc_final: 0.1932 (mm-40) REVERT: K 19 GLN cc_start: 0.2201 (tp40) cc_final: 0.1936 (mm-40) REVERT: L 19 GLN cc_start: 0.2201 (tp40) cc_final: 0.1934 (mm-40) REVERT: M 19 GLN cc_start: 0.2166 (tp40) cc_final: 0.1933 (mm-40) REVERT: N 19 GLN cc_start: 0.2164 (tp40) cc_final: 0.1930 (mm-40) REVERT: O 19 GLN cc_start: 0.2194 (tp40) cc_final: 0.1928 (mm-40) REVERT: P 19 GLN cc_start: 0.2196 (tp40) cc_final: 0.1923 (mm-40) REVERT: Q 19 GLN cc_start: 0.2196 (tp40) cc_final: 0.1937 (mm-40) REVERT: R 19 GLN cc_start: 0.2202 (tp40) cc_final: 0.1939 (mm-40) REVERT: S 19 GLN cc_start: 0.2198 (tp40) cc_final: 0.1933 (mm-40) REVERT: T 19 GLN cc_start: 0.2204 (tp40) cc_final: 0.1939 (mm-40) REVERT: V 19 GLN cc_start: 0.2195 (tp40) cc_final: 0.1935 (mm-40) REVERT: W 19 GLN cc_start: 0.2197 (tp40) cc_final: 0.1928 (mm-40) REVERT: X 19 GLN cc_start: 0.2199 (tp40) cc_final: 0.1936 (mm-40) outliers start: 72 outliers final: 0 residues processed: 360 average time/residue: 0.4696 time to fit residues: 211.6634 Evaluate side-chains 264 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 94 ASN U 135 ASN A 7 ASN A 94 ASN ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 ASN B 7 ASN B 10 GLN B 94 ASN B 132 HIS B 135 ASN B 150 ASN C 7 ASN C 94 ASN C 132 HIS C 150 ASN D 7 ASN D 94 ASN D 132 HIS D 150 ASN E 7 ASN E 70 ASN E 94 ASN E 150 ASN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN F 132 HIS F 150 ASN G 7 ASN G 94 ASN G 132 HIS G 150 ASN ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 ASN H 132 HIS H 150 ASN I 7 ASN I 94 ASN I 132 HIS ** I 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 ASN ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 GLN J 94 ASN J 132 HIS J 150 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 ASN K 132 HIS K 150 ASN L 7 ASN L 94 ASN L 132 HIS L 150 ASN M 7 ASN M 94 ASN M 132 HIS M 150 ASN N 7 ASN N 94 ASN N 132 HIS N 150 ASN O 7 ASN O 94 ASN O 132 HIS O 150 ASN P 7 ASN P 94 ASN P 132 HIS P 150 ASN Q 7 ASN Q 94 ASN Q 132 HIS Q 150 ASN R 7 ASN R 94 ASN R 132 HIS ** R 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 ASN S 7 ASN S 94 ASN S 132 HIS S 150 ASN T 7 ASN T 94 ASN T 150 ASN V 7 ASN V 94 ASN V 132 HIS V 150 ASN ** W 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 94 ASN W 132 HIS W 150 ASN ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 94 ASN X 150 ASN Total number of N/Q/H flips: 88 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.198005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.187828 restraints weight = 199745.864| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 3.88 r_work: 0.3424 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0780 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33912 Z= 0.131 Angle : 0.596 10.730 45792 Z= 0.310 Chirality : 0.040 0.176 4896 Planarity : 0.003 0.025 6024 Dihedral : 4.487 20.582 4464 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.78 % Allowed : 6.35 % Favored : 91.87 % 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 aren not related in a simple way. whole: 3.82 (0.13), residues: 4080 helix: 3.18 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : -0.41 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 5 TYR 0.025 0.002 TYR Q 164 PHE 0.006 0.001 PHE U 37 TRP 0.007 0.002 TRP U 89 HIS 0.004 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00263 (33912) covalent geometry : angle 0.59638 (45792) hydrogen bonds : bond 0.03520 ( 2637) hydrogen bonds : angle 3.51516 ( 7911) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 198 time to evaluate : 1.154 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: symmetry clash revert: symmetry clash REVERT: B 44 LEU cc_start: -0.0470 (OUTLIER) cc_final: -0.1171 (mm) REVERT: C 44 LEU cc_start: -0.0420 (OUTLIER) cc_final: -0.1153 (mm) REVERT: D 44 LEU cc_start: -0.0453 (OUTLIER) cc_final: -0.1161 (mm) REVERT: F 44 LEU cc_start: -0.0446 (OUTLIER) cc_final: -0.1178 (mm) REVERT: G 44 LEU cc_start: -0.0416 (OUTLIER) cc_final: -0.1163 (mm) REVERT: H 44 LEU cc_start: -0.0446 (OUTLIER) cc_final: -0.1170 (mm) REVERT: I 44 LEU cc_start: -0.0448 (OUTLIER) cc_final: -0.1177 (mm) REVERT: J 44 LEU cc_start: -0.0455 (OUTLIER) cc_final: -0.1170 (mm) REVERT: L 44 LEU cc_start: -0.0450 (OUTLIER) cc_final: -0.1175 (mm) REVERT: M 44 LEU cc_start: -0.0459 (OUTLIER) cc_final: -0.1175 (mm) REVERT: N 44 LEU cc_start: -0.0456 (OUTLIER) cc_final: -0.1151 (mm) REVERT: O 44 LEU cc_start: -0.0454 (OUTLIER) cc_final: -0.1164 (mm) REVERT: P 44 LEU cc_start: -0.0459 (OUTLIER) cc_final: -0.1181 (mm) REVERT: Q 44 LEU cc_start: -0.0446 (OUTLIER) cc_final: -0.1162 (mm) REVERT: R 44 LEU cc_start: -0.0458 (OUTLIER) cc_final: -0.1158 (mm) REVERT: S 44 LEU cc_start: -0.0460 (OUTLIER) cc_final: -0.1194 (mm) REVERT: T 44 LEU cc_start: -0.0446 (OUTLIER) cc_final: -0.1151 (mm) REVERT: V 44 LEU cc_start: -0.0445 (OUTLIER) cc_final: -0.1186 (mm) REVERT: W 44 LEU cc_start: -0.0447 (OUTLIER) cc_final: -0.1174 (mm) outliers start: 62 outliers final: 17 residues processed: 257 average time/residue: 0.4487 time to fit residues: 146.8746 Evaluate side-chains 187 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain D residue 7 ASN Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain G residue 7 ASN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain I residue 7 ASN Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain M residue 7 ASN Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 7 ASN Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain O residue 7 ASN Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain P residue 7 ASN Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain Q residue 7 ASN Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain R residue 7 ASN Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain S residue 7 ASN Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain T residue 7 ASN Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain V residue 7 ASN Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain W residue 44 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 258 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 386 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 316 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 272 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 19 GLN U 54 GLN U 94 ASN U 108 GLN U 132 HIS ** U 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 137 GLN U 150 ASN A 19 GLN A 54 GLN A 108 GLN B 19 GLN B 54 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN C 54 GLN C 108 GLN D 54 GLN D 108 GLN E 54 GLN E 108 GLN E 132 HIS ** E 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN F 54 GLN F 108 GLN G 54 GLN G 108 GLN ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 GLN H 54 GLN H 108 GLN I 19 GLN I 54 GLN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 GLN ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 54 GLN J 108 GLN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 GLN K 108 GLN L 19 GLN L 54 GLN L 108 GLN M 19 GLN M 54 GLN M 108 GLN N 19 GLN N 54 GLN N 108 GLN N 137 GLN O 54 GLN O 108 GLN O 137 GLN P 54 GLN P 108 GLN Q 19 GLN Q 54 GLN Q 108 GLN R 19 GLN R 54 GLN R 108 GLN S 19 GLN S 54 GLN S 108 GLN ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 137 GLN T 54 GLN T 108 GLN T 132 HIS ** T 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN V 54 GLN V 108 GLN ** W 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 19 GLN W 54 GLN W 108 GLN ** W 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 54 GLN X 108 GLN X 132 HIS Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.254924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.246513 restraints weight = 236015.779| |-----------------------------------------------------------------------------| r_work (start): 0.4445 rms_B_bonded: 3.89 r_work (final): 0.4445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1402 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 33912 Z= 0.309 Angle : 0.960 10.092 45792 Z= 0.525 Chirality : 0.054 0.231 4896 Planarity : 0.007 0.059 6024 Dihedral : 5.835 20.468 4464 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.13 % Allowed : 6.47 % Favored : 90.40 % 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 aren not related in a simple way. whole: 0.42 (0.13), residues: 4080 helix: 0.81 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : -1.53 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 39 TYR 0.045 0.005 TYR E 164 PHE 0.017 0.004 PHE B 128 TRP 0.007 0.003 TRP B 89 HIS 0.016 0.003 HIS T 132 Details of bonding type rmsd covalent geometry : bond 0.00664 (33912) covalent geometry : angle 0.96035 (45792) hydrogen bonds : bond 0.06037 ( 2637) hydrogen bonds : angle 4.70968 ( 7911) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 199 time to evaluate : 1.292 Fit side-chains REVERT: U 61 HIS cc_start: 0.2855 (m170) cc_final: 0.2175 (m170) REVERT: U 96 MET cc_start: 0.1005 (mmp) cc_final: -0.0981 (mmp) REVERT: A 22 LEU cc_start: 0.3392 (OUTLIER) cc_final: 0.2821 (mp) REVERT: A 61 HIS cc_start: 0.2649 (m170) cc_final: 0.2190 (m170) REVERT: A 96 MET cc_start: 0.1062 (mmp) cc_final: -0.1182 (mmp) REVERT: A 134 LEU cc_start: -0.0331 (OUTLIER) cc_final: -0.0838 (mt) REVERT: B 44 LEU cc_start: -0.0258 (OUTLIER) cc_final: -0.1420 (mm) REVERT: B 61 HIS cc_start: 0.2796 (m170) cc_final: 0.2159 (m170) REVERT: B 96 MET cc_start: 0.1109 (mmp) cc_final: -0.1009 (mmp) REVERT: C 22 LEU cc_start: 0.3449 (OUTLIER) cc_final: 0.2780 (mp) REVERT: C 44 LEU cc_start: -0.0281 (OUTLIER) cc_final: -0.1307 (mm) REVERT: C 61 HIS cc_start: 0.2587 (m170) cc_final: 0.2074 (m170) REVERT: C 96 MET cc_start: 0.0908 (mmp) cc_final: -0.1034 (mmp) REVERT: D 22 LEU cc_start: 0.3677 (OUTLIER) cc_final: 0.3111 (mp) REVERT: D 44 LEU cc_start: -0.0208 (OUTLIER) cc_final: -0.1274 (mm) REVERT: D 61 HIS cc_start: 0.2830 (m170) cc_final: 0.2296 (m170) REVERT: D 96 MET cc_start: 0.0954 (mmp) cc_final: -0.1219 (mmp) REVERT: E 22 LEU cc_start: 0.3276 (OUTLIER) cc_final: 0.2725 (mp) REVERT: E 61 HIS cc_start: 0.2677 (m170) cc_final: 0.2127 (m170) REVERT: E 96 MET cc_start: 0.1073 (mmp) cc_final: -0.0998 (mmp) REVERT: F 44 LEU cc_start: -0.0258 (OUTLIER) cc_final: -0.1429 (mm) REVERT: F 61 HIS cc_start: 0.2627 (m170) cc_final: 0.2167 (m170) REVERT: F 96 MET cc_start: 0.0940 (mmp) cc_final: -0.1146 (mmp) REVERT: G 22 LEU cc_start: 0.3451 (OUTLIER) cc_final: 0.2793 (mp) REVERT: G 44 LEU cc_start: -0.0193 (OUTLIER) cc_final: -0.1487 (mm) REVERT: G 61 HIS cc_start: 0.2700 (m170) cc_final: 0.2180 (m170) REVERT: G 96 MET cc_start: 0.0971 (mmp) cc_final: -0.0934 (mmp) REVERT: H 22 LEU cc_start: 0.3717 (OUTLIER) cc_final: 0.3026 (mp) REVERT: H 44 LEU cc_start: -0.0226 (OUTLIER) cc_final: -0.1433 (mm) REVERT: H 61 HIS cc_start: 0.2703 (m170) cc_final: 0.2112 (m170) REVERT: H 96 MET cc_start: 0.0899 (mmp) cc_final: -0.1197 (mmp) REVERT: I 22 LEU cc_start: 0.3391 (OUTLIER) cc_final: 0.2788 (mp) REVERT: I 44 LEU cc_start: -0.0174 (OUTLIER) cc_final: -0.1316 (mm) REVERT: I 61 HIS cc_start: 0.2762 (m170) cc_final: 0.2199 (m170) REVERT: I 96 MET cc_start: 0.0860 (mmp) cc_final: -0.1104 (mmp) REVERT: J 22 LEU cc_start: 0.3394 (OUTLIER) cc_final: 0.2687 (mp) REVERT: J 44 LEU cc_start: -0.0328 (OUTLIER) cc_final: -0.1462 (mm) REVERT: J 61 HIS cc_start: 0.2668 (m170) cc_final: 0.2127 (m170) REVERT: J 96 MET cc_start: 0.0860 (mmp) cc_final: -0.1221 (mmp) REVERT: K 22 LEU cc_start: 0.3498 (OUTLIER) cc_final: 0.2859 (mp) REVERT: K 61 HIS cc_start: 0.2816 (m170) cc_final: 0.2091 (m170) REVERT: K 96 MET cc_start: 0.0917 (mmp) cc_final: -0.1132 (mmp) REVERT: L 22 LEU cc_start: 0.3424 (OUTLIER) cc_final: 0.2752 (mp) REVERT: L 44 LEU cc_start: -0.0155 (OUTLIER) cc_final: -0.1293 (mm) REVERT: L 61 HIS cc_start: 0.2635 (m170) cc_final: 0.2048 (m170) REVERT: L 96 MET cc_start: 0.1098 (mmp) cc_final: -0.0961 (mmp) REVERT: M 22 LEU cc_start: 0.3424 (OUTLIER) cc_final: 0.2829 (mp) REVERT: M 44 LEU cc_start: -0.0211 (OUTLIER) cc_final: -0.1353 (mm) REVERT: M 61 HIS cc_start: 0.2815 (m170) cc_final: 0.2169 (m170) REVERT: M 96 MET cc_start: 0.0923 (mmp) cc_final: -0.0971 (mmp) REVERT: N 22 LEU cc_start: 0.3675 (OUTLIER) cc_final: 0.2943 (mp) REVERT: N 44 LEU cc_start: -0.0323 (OUTLIER) cc_final: -0.1316 (mm) REVERT: N 61 HIS cc_start: 0.2596 (m170) cc_final: 0.2211 (m170) REVERT: N 96 MET cc_start: 0.1069 (mmp) cc_final: -0.1218 (mmp) REVERT: O 22 LEU cc_start: 0.3523 (OUTLIER) cc_final: 0.2854 (mp) REVERT: O 44 LEU cc_start: -0.0302 (OUTLIER) cc_final: -0.1353 (mm) REVERT: O 61 HIS cc_start: 0.2711 (m170) cc_final: 0.2226 (m170) REVERT: O 96 MET cc_start: 0.0841 (mmp) cc_final: -0.1045 (mmp) REVERT: P 22 LEU cc_start: 0.3412 (OUTLIER) cc_final: 0.2825 (mp) REVERT: P 44 LEU cc_start: -0.0151 (OUTLIER) cc_final: -0.1436 (mm) REVERT: P 61 HIS cc_start: 0.2741 (m170) cc_final: 0.2219 (m170) REVERT: P 96 MET cc_start: 0.0941 (mmp) cc_final: -0.0902 (mmp) REVERT: Q 22 LEU cc_start: 0.3421 (OUTLIER) cc_final: 0.2720 (mp) REVERT: Q 44 LEU cc_start: -0.0283 (OUTLIER) cc_final: -0.1379 (mm) REVERT: Q 61 HIS cc_start: 0.2688 (m170) cc_final: 0.2215 (m170) REVERT: Q 96 MET cc_start: 0.0997 (mmp) cc_final: -0.0999 (mmp) REVERT: R 22 LEU cc_start: 0.3439 (OUTLIER) cc_final: 0.2746 (mp) REVERT: R 44 LEU cc_start: -0.0350 (OUTLIER) cc_final: -0.1361 (mm) REVERT: R 61 HIS cc_start: 0.2594 (m170) cc_final: 0.2059 (m170) REVERT: R 96 MET cc_start: 0.0857 (mmp) cc_final: -0.0994 (mmp) REVERT: R 134 LEU cc_start: -0.0437 (OUTLIER) cc_final: -0.0886 (mt) REVERT: S 22 LEU cc_start: 0.3642 (OUTLIER) cc_final: 0.2959 (mp) REVERT: S 44 LEU cc_start: -0.0002 (OUTLIER) cc_final: -0.1416 (mm) REVERT: S 61 HIS cc_start: 0.2746 (m170) cc_final: 0.2153 (m170) REVERT: S 96 MET cc_start: 0.0849 (mmp) cc_final: -0.1004 (mmp) REVERT: T 22 LEU cc_start: 0.3616 (OUTLIER) cc_final: 0.2909 (mp) REVERT: T 44 LEU cc_start: -0.0232 (OUTLIER) cc_final: -0.1448 (mm) REVERT: T 61 HIS cc_start: 0.2852 (m170) cc_final: 0.2299 (m170) REVERT: T 96 MET cc_start: 0.0855 (mmp) cc_final: -0.1058 (mmp) REVERT: V 22 LEU cc_start: 0.3528 (OUTLIER) cc_final: 0.2870 (mp) REVERT: V 44 LEU cc_start: -0.0220 (OUTLIER) cc_final: -0.1362 (mm) REVERT: V 61 HIS cc_start: 0.2837 (m170) cc_final: 0.2164 (m170) REVERT: V 96 MET cc_start: 0.0825 (mmp) cc_final: -0.1159 (mmp) REVERT: W 22 LEU cc_start: 0.3583 (OUTLIER) cc_final: 0.2842 (mp) REVERT: W 44 LEU cc_start: -0.0157 (OUTLIER) cc_final: -0.1242 (mm) REVERT: W 61 HIS cc_start: 0.2774 (m170) cc_final: 0.2315 (m170) REVERT: W 96 MET cc_start: 0.0920 (mmp) cc_final: -0.0965 (mmp) REVERT: X 22 LEU cc_start: 0.3633 (OUTLIER) cc_final: 0.2927 (mp) REVERT: X 61 HIS cc_start: 0.2718 (m170) cc_final: 0.2272 (m170) REVERT: X 96 MET cc_start: 0.0980 (mmp) cc_final: -0.0944 (mmp) outliers start: 109 outliers final: 38 residues processed: 286 average time/residue: 0.5656 time to fit residues: 204.5516 Evaluate side-chains 279 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 199 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 134 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 134 LEU Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 134 LEU Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 134 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 361 optimal weight: 5.9990 chunk 308 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 158 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 373 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 350 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 241 optimal weight: 3.9990 chunk 286 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 19 GLN U 135 ASN U 150 ASN A 7 ASN A 19 GLN A 150 ASN B 7 ASN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN C 7 ASN C 19 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN D 19 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 ASN E 19 GLN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 7 ASN G 19 GLN ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 ASN I 19 GLN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN L 19 GLN M 7 ASN M 19 GLN N 7 ASN O 7 ASN O 19 GLN P 7 ASN P 19 GLN ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 7 ASN Q 19 GLN R 7 ASN R 19 GLN S 7 ASN S 19 GLN T 7 ASN T 19 GLN V 7 ASN V 19 GLN ** W 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 19 GLN ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.244824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.237150 restraints weight = 227155.634| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 3.87 r_work: 0.4011 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1117 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 33912 Z= 0.117 Angle : 0.548 8.524 45792 Z= 0.293 Chirality : 0.037 0.163 4896 Planarity : 0.003 0.035 6024 Dihedral : 4.537 18.623 4464 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.56 % Allowed : 7.21 % Favored : 89.22 % 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 aren not related in a simple way. whole: 2.71 (0.13), residues: 4080 helix: 2.52 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -1.04 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 5 TYR 0.014 0.002 TYR G 35 PHE 0.007 0.001 PHE N 51 TRP 0.003 0.001 TRP W 89 HIS 0.003 0.001 HIS P 169 Details of bonding type rmsd covalent geometry : bond 0.00231 (33912) covalent geometry : angle 0.54798 (45792) hydrogen bonds : bond 0.03402 ( 2637) hydrogen bonds : angle 3.53980 ( 7911) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 170 time to evaluate : 1.295 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: U 96 MET cc_start: 0.0192 (mmp) cc_final: -0.0937 (mmp) REVERT: U 149 THR cc_start: 0.5649 (OUTLIER) cc_final: 0.5339 (t) REVERT: B 44 LEU cc_start: -0.0372 (OUTLIER) cc_final: -0.1058 (mm) REVERT: B 61 HIS cc_start: 0.2453 (m170) cc_final: 0.2008 (m90) REVERT: B 96 MET cc_start: -0.0168 (mmp) cc_final: -0.1053 (mmp) REVERT: B 134 LEU cc_start: -0.0596 (OUTLIER) cc_final: -0.1292 (mm) REVERT: C 44 LEU cc_start: -0.0474 (OUTLIER) cc_final: -0.1105 (mm) REVERT: D 44 LEU cc_start: -0.0408 (OUTLIER) cc_final: -0.1075 (mm) REVERT: E 22 LEU cc_start: 0.2410 (OUTLIER) cc_final: 0.2169 (mt) REVERT: F 44 LEU cc_start: -0.0384 (OUTLIER) cc_final: -0.1059 (mm) REVERT: G 22 LEU cc_start: 0.2392 (OUTLIER) cc_final: 0.2119 (mt) REVERT: G 44 LEU cc_start: -0.0344 (OUTLIER) cc_final: -0.1028 (mm) REVERT: H 22 LEU cc_start: 0.2432 (OUTLIER) cc_final: 0.2145 (mt) REVERT: H 44 LEU cc_start: -0.0362 (OUTLIER) cc_final: -0.1051 (mm) REVERT: I 22 LEU cc_start: 0.2367 (OUTLIER) cc_final: 0.2114 (mt) REVERT: I 44 LEU cc_start: -0.0271 (OUTLIER) cc_final: -0.0972 (mm) REVERT: J 22 LEU cc_start: 0.2353 (OUTLIER) cc_final: 0.1998 (mt) REVERT: J 44 LEU cc_start: -0.0349 (OUTLIER) cc_final: -0.1052 (mm) REVERT: K 22 LEU cc_start: 0.2364 (OUTLIER) cc_final: 0.2153 (mt) REVERT: K 134 LEU cc_start: -0.0594 (OUTLIER) cc_final: -0.1314 (mm) REVERT: L 22 LEU cc_start: 0.2416 (OUTLIER) cc_final: 0.2137 (mt) REVERT: L 44 LEU cc_start: -0.0373 (OUTLIER) cc_final: -0.1049 (mm) REVERT: M 22 LEU cc_start: 0.2350 (OUTLIER) cc_final: 0.2110 (mt) REVERT: M 44 LEU cc_start: -0.0359 (OUTLIER) cc_final: -0.1034 (mm) REVERT: M 134 LEU cc_start: -0.0906 (OUTLIER) cc_final: -0.1108 (mt) REVERT: N 22 LEU cc_start: 0.2404 (OUTLIER) cc_final: 0.2198 (mt) REVERT: N 44 LEU cc_start: -0.0404 (OUTLIER) cc_final: -0.1067 (mm) REVERT: O 22 LEU cc_start: 0.2404 (OUTLIER) cc_final: 0.2153 (mt) REVERT: O 44 LEU cc_start: -0.0387 (OUTLIER) cc_final: -0.1078 (mm) REVERT: P 22 LEU cc_start: 0.2362 (OUTLIER) cc_final: 0.2128 (mt) REVERT: P 44 LEU cc_start: -0.0391 (OUTLIER) cc_final: -0.1080 (mm) REVERT: Q 22 LEU cc_start: 0.2376 (OUTLIER) cc_final: 0.2113 (mt) REVERT: Q 44 LEU cc_start: -0.0329 (OUTLIER) cc_final: -0.1014 (mm) REVERT: R 22 LEU cc_start: 0.2365 (OUTLIER) cc_final: 0.2138 (mt) REVERT: R 44 LEU cc_start: -0.0379 (OUTLIER) cc_final: -0.1040 (mm) REVERT: S 22 LEU cc_start: 0.2376 (OUTLIER) cc_final: 0.2104 (mt) REVERT: S 44 LEU cc_start: -0.0147 (OUTLIER) cc_final: -0.1152 (mm) REVERT: T 22 LEU cc_start: 0.2390 (OUTLIER) cc_final: 0.2160 (mt) REVERT: T 44 LEU cc_start: -0.0391 (OUTLIER) cc_final: -0.1034 (mm) REVERT: V 22 LEU cc_start: 0.2380 (OUTLIER) cc_final: 0.2146 (mt) REVERT: V 44 LEU cc_start: -0.0348 (OUTLIER) cc_final: -0.1021 (mm) REVERT: V 134 LEU cc_start: -0.0873 (OUTLIER) cc_final: -0.1121 (mt) REVERT: W 22 LEU cc_start: 0.2379 (OUTLIER) cc_final: 0.2141 (mt) REVERT: W 44 LEU cc_start: -0.0378 (OUTLIER) cc_final: -0.1060 (mm) REVERT: X 22 LEU cc_start: 0.2361 (OUTLIER) cc_final: 0.2134 (mt) outliers start: 124 outliers final: 55 residues processed: 275 average time/residue: 0.5243 time to fit residues: 184.9802 Evaluate side-chains 267 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 170 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 33 MET Chi-restraints excluded: chain U residue 83 LYS Chi-restraints excluded: chain U residue 149 THR Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 7 ASN Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain G residue 7 ASN Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 33 MET Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain I residue 7 ASN Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 33 MET Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain M residue 7 ASN Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain N residue 7 ASN Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 7 ASN Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 33 MET Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain P residue 7 ASN Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain Q residue 7 ASN Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 33 MET Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 7 ASN Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 33 MET Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain S residue 7 ASN Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain T residue 7 ASN Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 33 MET Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain V residue 7 ASN Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 33 MET Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 134 LEU Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 33 MET Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 65 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 51 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 222 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 312 optimal weight: 2.9990 chunk 327 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 282 optimal weight: 0.5980 chunk 244 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 266 optimal weight: 6.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 150 ASN A 7 ASN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 HIS B 7 ASN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN D 7 ASN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN E 7 ASN E 19 GLN E 137 GLN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 GLN G 7 ASN ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 GLN ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN I 7 ASN I 19 GLN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 GLN ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN L 7 ASN ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 ASN ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 137 GLN N 7 ASN ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 ASN ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 ASN ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 137 GLN Q 7 ASN Q 19 GLN ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 137 GLN R 7 ASN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 GLN S 7 ASN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 7 ASN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 137 GLN V 7 ASN V 19 GLN ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 137 GLN ** W 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 19 GLN ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 137 GLN ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.270415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.263009 restraints weight = 236333.891| |-----------------------------------------------------------------------------| r_work (start): 0.4596 rms_B_bonded: 3.85 r_work: 0.4288 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1445 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 33912 Z= 0.236 Angle : 0.844 14.853 45792 Z= 0.448 Chirality : 0.046 0.189 4896 Planarity : 0.005 0.036 6024 Dihedral : 5.374 19.270 4464 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.28 % Allowed : 9.14 % Favored : 86.58 % 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 aren not related in a simple way. whole: 0.89 (0.13), residues: 4080 helix: 1.29 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -1.93 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 152 TYR 0.030 0.003 TYR C 164 PHE 0.014 0.003 PHE N 51 TRP 0.009 0.003 TRP B 89 HIS 0.010 0.002 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00487 (33912) covalent geometry : angle 0.84398 (45792) hydrogen bonds : bond 0.05275 ( 2637) hydrogen bonds : angle 4.41176 ( 7911) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 207 time to evaluate : 1.410 Fit side-chains REVERT: U 33 MET cc_start: 0.0479 (mtt) cc_final: 0.0037 (mtp) REVERT: U 61 HIS cc_start: 0.2617 (m170) cc_final: 0.2186 (m170) REVERT: U 96 MET cc_start: 0.0745 (mmp) cc_final: -0.1173 (mmp) REVERT: A 22 LEU cc_start: 0.3085 (OUTLIER) cc_final: 0.2853 (mp) REVERT: A 61 HIS cc_start: 0.2657 (m170) cc_final: 0.2303 (m170) REVERT: A 96 MET cc_start: 0.0229 (mmp) cc_final: -0.1191 (mmp) REVERT: A 134 LEU cc_start: 0.0059 (OUTLIER) cc_final: -0.0231 (mt) REVERT: B 33 MET cc_start: 0.0430 (mtt) cc_final: 0.0000 (mtp) REVERT: B 44 LEU cc_start: -0.0095 (OUTLIER) cc_final: -0.1318 (mm) REVERT: B 61 HIS cc_start: 0.2705 (m170) cc_final: 0.2290 (m170) REVERT: B 96 MET cc_start: 0.0534 (mmp) cc_final: -0.1041 (mmp) REVERT: C 22 LEU cc_start: 0.3163 (OUTLIER) cc_final: 0.2742 (mp) REVERT: C 44 LEU cc_start: -0.0154 (OUTLIER) cc_final: -0.1370 (mm) REVERT: C 61 HIS cc_start: 0.2633 (m170) cc_final: 0.2238 (m170) REVERT: C 66 MET cc_start: 0.0422 (ttm) cc_final: 0.0171 (ptp) REVERT: C 96 MET cc_start: 0.0289 (mmp) cc_final: -0.1086 (mmp) REVERT: D 22 LEU cc_start: 0.3159 (OUTLIER) cc_final: 0.2771 (mp) REVERT: D 44 LEU cc_start: -0.0170 (OUTLIER) cc_final: -0.1333 (mm) REVERT: D 61 HIS cc_start: 0.2689 (m170) cc_final: 0.2232 (m170) REVERT: D 66 MET cc_start: 0.0414 (ttm) cc_final: 0.0147 (ptp) REVERT: D 96 MET cc_start: 0.0202 (mmp) cc_final: -0.1194 (mmp) REVERT: E 22 LEU cc_start: 0.3102 (OUTLIER) cc_final: 0.2727 (mp) REVERT: E 61 HIS cc_start: 0.2721 (m170) cc_final: 0.2199 (m170) REVERT: E 96 MET cc_start: 0.0357 (mmp) cc_final: -0.1125 (mmp) REVERT: F 44 LEU cc_start: -0.0103 (OUTLIER) cc_final: -0.1367 (mm) REVERT: F 61 HIS cc_start: 0.2707 (m170) cc_final: 0.2350 (m170) REVERT: F 96 MET cc_start: 0.0196 (mmp) cc_final: -0.1148 (mmp) REVERT: F 134 LEU cc_start: 0.0319 (OUTLIER) cc_final: -0.0011 (mt) REVERT: G 22 LEU cc_start: 0.2988 (OUTLIER) cc_final: 0.2653 (mp) REVERT: G 44 LEU cc_start: -0.0053 (OUTLIER) cc_final: -0.1266 (mm) REVERT: G 61 HIS cc_start: 0.2690 (m170) cc_final: 0.2306 (m170) REVERT: G 96 MET cc_start: 0.0165 (mmp) cc_final: -0.1153 (mmp) REVERT: H 22 LEU cc_start: 0.3030 (OUTLIER) cc_final: 0.2674 (mp) REVERT: H 44 LEU cc_start: -0.0034 (OUTLIER) cc_final: -0.1295 (mm) REVERT: H 61 HIS cc_start: 0.2644 (m170) cc_final: 0.2251 (m170) REVERT: H 96 MET cc_start: 0.0285 (mmp) cc_final: -0.1150 (mmp) REVERT: I 22 LEU cc_start: 0.3022 (OUTLIER) cc_final: 0.2625 (mp) REVERT: I 44 LEU cc_start: 0.0037 (OUTLIER) cc_final: -0.1246 (mm) REVERT: I 61 HIS cc_start: 0.2682 (m170) cc_final: 0.2312 (m170) REVERT: I 96 MET cc_start: 0.0239 (mmp) cc_final: -0.1231 (mmp) REVERT: J 22 LEU cc_start: 0.2994 (OUTLIER) cc_final: 0.2627 (mp) REVERT: J 44 LEU cc_start: -0.0059 (OUTLIER) cc_final: -0.1340 (mm) REVERT: J 61 HIS cc_start: 0.2662 (m170) cc_final: 0.2279 (m170) REVERT: J 66 MET cc_start: 0.0456 (ttm) cc_final: -0.0202 (tpp) REVERT: J 96 MET cc_start: 0.0226 (mmp) cc_final: -0.1200 (mmp) REVERT: K 22 LEU cc_start: 0.2968 (OUTLIER) cc_final: 0.2619 (mp) REVERT: K 61 HIS cc_start: 0.2663 (m170) cc_final: 0.2250 (m170) REVERT: K 96 MET cc_start: 0.0260 (mmp) cc_final: -0.1079 (mmp) REVERT: L 22 LEU cc_start: 0.3021 (OUTLIER) cc_final: 0.2658 (mp) REVERT: L 44 LEU cc_start: -0.0114 (OUTLIER) cc_final: -0.1368 (mm) REVERT: L 61 HIS cc_start: 0.2717 (m170) cc_final: 0.2306 (m170) REVERT: L 96 MET cc_start: 0.0316 (mmp) cc_final: -0.1124 (mmp) REVERT: L 134 LEU cc_start: 0.0100 (OUTLIER) cc_final: -0.0204 (mt) REVERT: M 22 LEU cc_start: 0.2993 (OUTLIER) cc_final: 0.2621 (mp) REVERT: M 44 LEU cc_start: -0.0084 (OUTLIER) cc_final: -0.1319 (mm) REVERT: M 61 HIS cc_start: 0.2692 (m170) cc_final: 0.2272 (m170) REVERT: M 96 MET cc_start: 0.0161 (mmp) cc_final: -0.1064 (mmp) REVERT: N 22 LEU cc_start: 0.3010 (OUTLIER) cc_final: 0.2687 (mp) REVERT: N 44 LEU cc_start: -0.0134 (OUTLIER) cc_final: -0.1356 (mm) REVERT: N 61 HIS cc_start: 0.2676 (m170) cc_final: 0.2244 (m170) REVERT: N 96 MET cc_start: 0.0435 (mmp) cc_final: -0.1216 (mmp) REVERT: N 154 MET cc_start: 0.2580 (mpt) cc_final: 0.2053 (mtt) REVERT: O 22 LEU cc_start: 0.3076 (OUTLIER) cc_final: 0.2660 (mp) REVERT: O 44 LEU cc_start: -0.0154 (OUTLIER) cc_final: -0.1362 (mm) REVERT: O 61 HIS cc_start: 0.2747 (m170) cc_final: 0.2268 (m170) REVERT: O 96 MET cc_start: 0.0364 (mmp) cc_final: -0.1101 (mmp) REVERT: O 134 LEU cc_start: 0.0056 (OUTLIER) cc_final: -0.0227 (mt) REVERT: P 22 LEU cc_start: 0.3060 (OUTLIER) cc_final: 0.2676 (mp) REVERT: P 44 LEU cc_start: -0.0115 (OUTLIER) cc_final: -0.1348 (mm) REVERT: P 61 HIS cc_start: 0.2706 (m170) cc_final: 0.2245 (m170) REVERT: P 96 MET cc_start: 0.0270 (mmp) cc_final: -0.1025 (mmp) REVERT: P 134 LEU cc_start: 0.0080 (OUTLIER) cc_final: -0.0209 (mt) REVERT: Q 22 LEU cc_start: 0.3026 (OUTLIER) cc_final: 0.2664 (mp) REVERT: Q 44 LEU cc_start: -0.0052 (OUTLIER) cc_final: -0.1294 (mm) REVERT: Q 61 HIS cc_start: 0.2749 (m170) cc_final: 0.2284 (m170) REVERT: Q 96 MET cc_start: 0.0274 (mmp) cc_final: -0.1102 (mmp) REVERT: R 22 LEU cc_start: 0.2965 (OUTLIER) cc_final: 0.2619 (mp) REVERT: R 44 LEU cc_start: -0.0107 (OUTLIER) cc_final: -0.1366 (mm) REVERT: R 61 HIS cc_start: 0.2692 (m170) cc_final: 0.2274 (m170) REVERT: R 96 MET cc_start: 0.0377 (mmp) cc_final: -0.1062 (mmp) REVERT: R 134 LEU cc_start: 0.0180 (OUTLIER) cc_final: -0.0121 (mt) REVERT: S 22 LEU cc_start: 0.3014 (OUTLIER) cc_final: 0.2633 (mp) REVERT: S 44 LEU cc_start: 0.0216 (OUTLIER) cc_final: -0.1091 (mm) REVERT: S 61 HIS cc_start: 0.2712 (m170) cc_final: 0.2273 (m170) REVERT: S 96 MET cc_start: 0.0291 (mmp) cc_final: -0.1102 (mmp) REVERT: S 134 LEU cc_start: 0.0096 (OUTLIER) cc_final: -0.0195 (mt) REVERT: T 22 LEU cc_start: 0.3047 (OUTLIER) cc_final: 0.2674 (mp) REVERT: T 44 LEU cc_start: -0.0144 (OUTLIER) cc_final: -0.1344 (mm) REVERT: T 61 HIS cc_start: 0.2641 (m170) cc_final: 0.2246 (m170) REVERT: T 96 MET cc_start: 0.0207 (mmp) cc_final: -0.1152 (mmp) REVERT: T 134 LEU cc_start: 0.0205 (OUTLIER) cc_final: -0.0123 (mt) REVERT: V 22 LEU cc_start: 0.2972 (OUTLIER) cc_final: 0.2617 (mp) REVERT: V 44 LEU cc_start: -0.0069 (OUTLIER) cc_final: -0.1348 (mm) REVERT: V 61 HIS cc_start: 0.2716 (m170) cc_final: 0.2184 (m170) REVERT: V 96 MET cc_start: 0.0259 (mmp) cc_final: -0.1237 (mmp) REVERT: V 134 LEU cc_start: -0.0608 (OUTLIER) cc_final: -0.0826 (mt) REVERT: W 22 LEU cc_start: 0.3015 (OUTLIER) cc_final: 0.2638 (mp) REVERT: W 44 LEU cc_start: -0.0146 (OUTLIER) cc_final: -0.1332 (mm) REVERT: W 61 HIS cc_start: 0.2711 (m170) cc_final: 0.2290 (m170) REVERT: W 96 MET cc_start: 0.0400 (mmp) cc_final: -0.1124 (mmp) REVERT: X 22 LEU cc_start: 0.3007 (OUTLIER) cc_final: 0.2640 (mp) REVERT: X 61 HIS cc_start: 0.2656 (m170) cc_final: 0.2228 (m170) REVERT: X 66 MET cc_start: 0.0536 (ttm) cc_final: -0.0195 (tpp) REVERT: X 96 MET cc_start: 0.0303 (mmp) cc_final: -0.1088 (mmp) outliers start: 149 outliers final: 42 residues processed: 325 average time/residue: 0.5695 time to fit residues: 233.9801 Evaluate side-chains 298 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 207 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 83 LYS Chi-restraints excluded: chain U residue 149 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 7 ASN Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain G residue 7 ASN Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 154 MET Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 154 MET Chi-restraints excluded: chain I residue 7 ASN Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain M residue 7 ASN Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain N residue 7 ASN Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain O residue 7 ASN Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain P residue 7 ASN Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 138 VAL Chi-restraints excluded: chain Q residue 7 ASN Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 138 VAL Chi-restraints excluded: chain R residue 7 ASN Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain S residue 7 ASN Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain T residue 7 ASN Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain T residue 134 LEU Chi-restraints excluded: chain T residue 138 VAL Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 134 LEU Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 138 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 133 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 280 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 368 optimal weight: 1.9990 chunk 204 optimal weight: 9.9990 chunk 363 optimal weight: 0.9990 chunk 401 optimal weight: 9.9990 chunk 342 optimal weight: 0.7980 chunk 320 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 7 ASN A 19 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN B 7 ASN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 ASN E 19 GLN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 7 ASN G 19 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 ASN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 ASN ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 ASN ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 ASN ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 7 ASN Q 19 GLN ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 ASN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 ASN V 19 GLN ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 19 GLN ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.263039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.255761 restraints weight = 240864.462| |-----------------------------------------------------------------------------| r_work (start): 0.4532 rms_B_bonded: 3.84 r_work: 0.4234 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1234 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 33912 Z= 0.126 Angle : 0.584 9.514 45792 Z= 0.307 Chirality : 0.037 0.167 4896 Planarity : 0.003 0.039 6024 Dihedral : 4.522 20.378 4464 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.87 % Allowed : 10.57 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.13), residues: 4080 helix: 2.36 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -1.46 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 5 TYR 0.025 0.002 TYR G 35 PHE 0.011 0.001 PHE N 51 TRP 0.003 0.001 TRP D 89 HIS 0.004 0.001 HIS C 124 Details of bonding type rmsd covalent geometry : bond 0.00244 (33912) covalent geometry : angle 0.58408 (45792) hydrogen bonds : bond 0.03580 ( 2637) hydrogen bonds : angle 3.70628 ( 7911) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 183 time to evaluate : 1.300 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: U 61 HIS cc_start: 0.2659 (m170) cc_final: 0.2179 (m170) REVERT: U 96 MET cc_start: 0.0333 (mmp) cc_final: -0.1042 (mmp) REVERT: U 149 THR cc_start: 0.5687 (OUTLIER) cc_final: 0.5426 (t) REVERT: A 61 HIS cc_start: 0.2669 (m170) cc_final: 0.2256 (m90) REVERT: B 44 LEU cc_start: -0.0227 (OUTLIER) cc_final: -0.1051 (mm) REVERT: B 61 HIS cc_start: 0.2705 (m170) cc_final: 0.2253 (m90) REVERT: B 96 MET cc_start: 0.0133 (mmp) cc_final: -0.1112 (mmp) REVERT: C 44 LEU cc_start: -0.0316 (OUTLIER) cc_final: -0.1065 (mm) REVERT: C 61 HIS cc_start: 0.2713 (m170) cc_final: 0.2160 (m90) REVERT: D 44 LEU cc_start: -0.0262 (OUTLIER) cc_final: -0.1006 (mm) REVERT: D 61 HIS cc_start: 0.2693 (m170) cc_final: 0.2188 (m90) REVERT: E 22 LEU cc_start: 0.2531 (OUTLIER) cc_final: 0.2247 (mt) REVERT: E 61 HIS cc_start: 0.2656 (m170) cc_final: 0.2150 (m170) REVERT: F 44 LEU cc_start: -0.0241 (OUTLIER) cc_final: -0.1028 (mm) REVERT: F 61 HIS cc_start: 0.2685 (m170) cc_final: 0.2212 (m90) REVERT: G 22 LEU cc_start: 0.2505 (OUTLIER) cc_final: 0.2189 (mt) REVERT: G 44 LEU cc_start: -0.0201 (OUTLIER) cc_final: -0.1065 (mm) REVERT: G 61 HIS cc_start: 0.2659 (m170) cc_final: 0.2251 (m90) REVERT: H 22 LEU cc_start: 0.2544 (OUTLIER) cc_final: 0.2211 (mt) REVERT: H 44 LEU cc_start: -0.0236 (OUTLIER) cc_final: -0.1093 (mm) REVERT: H 61 HIS cc_start: 0.2651 (m170) cc_final: 0.2204 (m90) REVERT: I 22 LEU cc_start: 0.2472 (OUTLIER) cc_final: 0.2201 (mt) REVERT: I 44 LEU cc_start: -0.0103 (OUTLIER) cc_final: -0.0952 (mm) REVERT: I 61 HIS cc_start: 0.2665 (m170) cc_final: 0.2265 (m90) REVERT: J 22 LEU cc_start: 0.2486 (OUTLIER) cc_final: 0.2285 (mp) REVERT: J 44 LEU cc_start: -0.0248 (OUTLIER) cc_final: -0.1079 (mm) REVERT: J 61 HIS cc_start: 0.2707 (m170) cc_final: 0.2225 (m90) REVERT: K 22 LEU cc_start: 0.2439 (OUTLIER) cc_final: 0.2206 (mt) REVERT: K 61 HIS cc_start: 0.2669 (m170) cc_final: 0.2168 (m90) REVERT: L 22 LEU cc_start: 0.2551 (OUTLIER) cc_final: 0.2269 (mp) REVERT: L 44 LEU cc_start: -0.0253 (OUTLIER) cc_final: -0.1041 (mm) REVERT: L 61 HIS cc_start: 0.2682 (m170) cc_final: 0.2197 (m90) REVERT: M 22 LEU cc_start: 0.2480 (OUTLIER) cc_final: 0.2178 (mt) REVERT: M 44 LEU cc_start: -0.0230 (OUTLIER) cc_final: -0.1014 (mm) REVERT: M 61 HIS cc_start: 0.2645 (m170) cc_final: 0.2188 (m90) REVERT: N 22 LEU cc_start: 0.2514 (OUTLIER) cc_final: 0.2300 (mt) REVERT: N 44 LEU cc_start: -0.0238 (OUTLIER) cc_final: -0.1022 (mm) REVERT: N 61 HIS cc_start: 0.2667 (m170) cc_final: 0.2220 (m90) REVERT: N 96 MET cc_start: 0.0023 (mmp) cc_final: -0.1083 (mmp) REVERT: O 22 LEU cc_start: 0.2580 (OUTLIER) cc_final: 0.2301 (mp) REVERT: O 44 LEU cc_start: -0.0262 (OUTLIER) cc_final: -0.1063 (mm) REVERT: O 61 HIS cc_start: 0.2716 (m170) cc_final: 0.2190 (m90) REVERT: P 22 LEU cc_start: 0.2583 (OUTLIER) cc_final: 0.2273 (mt) REVERT: P 44 LEU cc_start: -0.0208 (OUTLIER) cc_final: -0.0993 (mm) REVERT: P 61 HIS cc_start: 0.2763 (m170) cc_final: 0.2285 (m90) REVERT: P 66 MET cc_start: 0.0764 (OUTLIER) cc_final: 0.0305 (tpp) REVERT: P 96 MET cc_start: 0.0153 (mmp) cc_final: -0.1053 (mmp) REVERT: Q 22 LEU cc_start: 0.2540 (OUTLIER) cc_final: 0.2250 (mp) REVERT: Q 44 LEU cc_start: -0.0191 (OUTLIER) cc_final: -0.0989 (mm) REVERT: Q 61 HIS cc_start: 0.2718 (m170) cc_final: 0.2190 (m90) REVERT: R 22 LEU cc_start: 0.2494 (OUTLIER) cc_final: 0.2261 (mp) REVERT: R 44 LEU cc_start: -0.0226 (OUTLIER) cc_final: -0.1022 (mm) REVERT: R 61 HIS cc_start: 0.2689 (m170) cc_final: 0.2198 (m90) REVERT: S 22 LEU cc_start: 0.2550 (OUTLIER) cc_final: 0.2250 (mp) REVERT: S 44 LEU cc_start: -0.0039 (OUTLIER) cc_final: -0.1203 (mm) REVERT: S 61 HIS cc_start: 0.2739 (m170) cc_final: 0.2230 (m90) REVERT: T 22 LEU cc_start: 0.2517 (OUTLIER) cc_final: 0.2286 (mt) REVERT: T 44 LEU cc_start: -0.0265 (OUTLIER) cc_final: -0.1022 (mm) REVERT: T 61 HIS cc_start: 0.2656 (m170) cc_final: 0.2134 (m170) REVERT: V 22 LEU cc_start: 0.2501 (OUTLIER) cc_final: 0.2247 (mp) REVERT: V 44 LEU cc_start: -0.0214 (OUTLIER) cc_final: -0.1037 (mm) REVERT: V 61 HIS cc_start: 0.2676 (m170) cc_final: 0.2159 (m90) REVERT: W 22 LEU cc_start: 0.2551 (OUTLIER) cc_final: 0.2257 (mp) REVERT: W 44 LEU cc_start: -0.0232 (OUTLIER) cc_final: -0.1026 (mm) REVERT: W 61 HIS cc_start: 0.2668 (m170) cc_final: 0.2211 (m90) REVERT: X 22 LEU cc_start: 0.2441 (OUTLIER) cc_final: 0.2195 (mt) REVERT: X 61 HIS cc_start: 0.2660 (m170) cc_final: 0.2176 (m90) outliers start: 100 outliers final: 25 residues processed: 258 average time/residue: 0.5126 time to fit residues: 168.0837 Evaluate side-chains 241 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 177 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 83 LYS Chi-restraints excluded: chain U residue 149 THR Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 33 MET Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain G residue 7 ASN Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 154 MET Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 154 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain N residue 7 ASN Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain P residue 7 ASN Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain V residue 7 ASN Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain X residue 22 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 0 optimal weight: 10.0000 chunk 313 optimal weight: 0.8980 chunk 252 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 373 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 360 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 290 optimal weight: 9.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 94 ASN U 150 ASN A 7 ASN ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 ASN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 ASN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 7 ASN ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 ASN I 19 GLN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 150 ASN L 7 ASN ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 ASN ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 ASN ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 ASN ** P 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 7 ASN ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 ASN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 7 ASN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 ASN ** V 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 19 GLN ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.272602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.265297 restraints weight = 242288.645| |-----------------------------------------------------------------------------| r_work (start): 0.4614 rms_B_bonded: 3.85 r_work: 0.4334 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1355 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33912 Z= 0.157 Angle : 0.669 12.388 45792 Z= 0.349 Chirality : 0.038 0.172 4896 Planarity : 0.004 0.042 6024 Dihedral : 4.627 20.365 4464 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.56 % Allowed : 10.69 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.13), residues: 4080 helix: 2.26 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -1.68 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 152 TYR 0.025 0.003 TYR M 164 PHE 0.015 0.002 PHE E 51 TRP 0.004 0.001 TRP U 89 HIS 0.004 0.001 HIS I 169 Details of bonding type rmsd covalent geometry : bond 0.00317 (33912) covalent geometry : angle 0.66947 (45792) hydrogen bonds : bond 0.04028 ( 2637) hydrogen bonds : angle 3.80046 ( 7911) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 181 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 61 HIS cc_start: 0.2782 (m170) cc_final: 0.2276 (m170) REVERT: U 76 ILE cc_start: 0.2269 (OUTLIER) cc_final: 0.2056 (mt) REVERT: U 96 MET cc_start: 0.0608 (mmp) cc_final: -0.1063 (mmp) REVERT: A 61 HIS cc_start: 0.2765 (m170) cc_final: 0.2315 (m90) REVERT: A 66 MET cc_start: 0.0838 (OUTLIER) cc_final: 0.0171 (tpp) REVERT: A 96 MET cc_start: 0.0204 (mmp) cc_final: -0.1099 (mmp) REVERT: B 44 LEU cc_start: -0.0165 (OUTLIER) cc_final: -0.1141 (mm) REVERT: B 61 HIS cc_start: 0.2804 (m170) cc_final: 0.2335 (m90) REVERT: B 66 MET cc_start: 0.0735 (OUTLIER) cc_final: 0.0118 (tpp) REVERT: B 96 MET cc_start: 0.0414 (mmp) cc_final: -0.1306 (mmp) REVERT: C 33 MET cc_start: 0.0353 (mtt) cc_final: -0.0215 (mtp) REVERT: C 44 LEU cc_start: -0.0222 (OUTLIER) cc_final: -0.1168 (mm) REVERT: C 61 HIS cc_start: 0.2837 (m170) cc_final: 0.2269 (m90) REVERT: C 76 ILE cc_start: 0.2315 (OUTLIER) cc_final: 0.2089 (mt) REVERT: C 96 MET cc_start: 0.0368 (mmp) cc_final: -0.1152 (mmp) REVERT: D 44 LEU cc_start: -0.0187 (OUTLIER) cc_final: -0.1066 (mm) REVERT: D 61 HIS cc_start: 0.2796 (m170) cc_final: 0.2238 (m90) REVERT: E 22 LEU cc_start: 0.2822 (OUTLIER) cc_final: 0.2441 (mp) REVERT: E 61 HIS cc_start: 0.2719 (m170) cc_final: 0.2223 (m170) REVERT: E 96 MET cc_start: 0.0150 (mmp) cc_final: -0.1123 (mmp) REVERT: F 44 LEU cc_start: -0.0149 (OUTLIER) cc_final: -0.1107 (mm) REVERT: F 61 HIS cc_start: 0.2812 (m170) cc_final: 0.2252 (m90) REVERT: F 66 MET cc_start: 0.0710 (OUTLIER) cc_final: 0.0100 (tpp) REVERT: G 22 LEU cc_start: 0.2780 (OUTLIER) cc_final: 0.2457 (mp) REVERT: G 44 LEU cc_start: -0.0107 (OUTLIER) cc_final: -0.1134 (mm) REVERT: G 66 MET cc_start: 0.0812 (OUTLIER) cc_final: 0.0128 (tpp) REVERT: G 76 ILE cc_start: 0.2418 (OUTLIER) cc_final: 0.2203 (mt) REVERT: G 96 MET cc_start: 0.0103 (mmp) cc_final: -0.1117 (mmp) REVERT: G 154 MET cc_start: 0.2335 (OUTLIER) cc_final: 0.2006 (mpt) REVERT: H 22 LEU cc_start: 0.2813 (OUTLIER) cc_final: 0.2470 (mp) REVERT: H 44 LEU cc_start: -0.0087 (OUTLIER) cc_final: -0.1089 (mm) REVERT: H 61 HIS cc_start: 0.2739 (m170) cc_final: 0.2306 (m90) REVERT: H 66 MET cc_start: 0.0858 (OUTLIER) cc_final: 0.0164 (tpp) REVERT: H 96 MET cc_start: 0.0319 (mmp) cc_final: -0.1145 (mmp) REVERT: I 22 LEU cc_start: 0.2806 (OUTLIER) cc_final: 0.2475 (mp) REVERT: I 44 LEU cc_start: -0.0063 (OUTLIER) cc_final: -0.1066 (mm) REVERT: I 66 MET cc_start: 0.0894 (OUTLIER) cc_final: 0.0297 (tpp) REVERT: I 96 MET cc_start: 0.0271 (mmp) cc_final: -0.1207 (mmp) REVERT: J 22 LEU cc_start: 0.2768 (OUTLIER) cc_final: 0.2451 (mp) REVERT: J 44 LEU cc_start: -0.0066 (OUTLIER) cc_final: -0.1070 (mm) REVERT: J 61 HIS cc_start: 0.2797 (m170) cc_final: 0.2310 (m90) REVERT: K 22 LEU cc_start: 0.2748 (OUTLIER) cc_final: 0.2435 (mp) REVERT: K 33 MET cc_start: 0.0285 (mtt) cc_final: -0.0204 (mtp) REVERT: K 61 HIS cc_start: 0.2771 (m170) cc_final: 0.2274 (m170) REVERT: L 22 LEU cc_start: 0.2887 (OUTLIER) cc_final: 0.2530 (mp) REVERT: L 44 LEU cc_start: -0.0167 (OUTLIER) cc_final: -0.1098 (mm) REVERT: L 61 HIS cc_start: 0.2787 (m170) cc_final: 0.2322 (m90) REVERT: L 66 MET cc_start: 0.0847 (OUTLIER) cc_final: 0.0215 (tpp) REVERT: L 96 MET cc_start: 0.0230 (mmp) cc_final: -0.1104 (mmp) REVERT: M 22 LEU cc_start: 0.2854 (OUTLIER) cc_final: 0.2475 (mp) REVERT: M 44 LEU cc_start: -0.0135 (OUTLIER) cc_final: -0.1067 (mm) REVERT: M 61 HIS cc_start: 0.2756 (m170) cc_final: 0.2310 (m90) REVERT: M 66 MET cc_start: 0.0895 (OUTLIER) cc_final: 0.0188 (tpp) REVERT: M 76 ILE cc_start: 0.2472 (OUTLIER) cc_final: 0.2255 (mt) REVERT: M 96 MET cc_start: 0.0203 (mmp) cc_final: -0.1117 (mmp) REVERT: N 22 LEU cc_start: 0.2844 (OUTLIER) cc_final: 0.2525 (mp) REVERT: N 44 LEU cc_start: -0.0140 (OUTLIER) cc_final: -0.1106 (mm) REVERT: N 66 MET cc_start: 0.0862 (OUTLIER) cc_final: 0.0182 (tpp) REVERT: O 22 LEU cc_start: 0.2889 (OUTLIER) cc_final: 0.2503 (mp) REVERT: O 44 LEU cc_start: -0.0187 (OUTLIER) cc_final: -0.1114 (mm) REVERT: O 61 HIS cc_start: 0.2861 (m170) cc_final: 0.2307 (m90) REVERT: O 66 MET cc_start: 0.0839 (OUTLIER) cc_final: 0.0141 (tpp) REVERT: O 76 ILE cc_start: 0.2319 (OUTLIER) cc_final: 0.2111 (mt) REVERT: O 96 MET cc_start: 0.0254 (mmp) cc_final: -0.1081 (mmp) REVERT: P 22 LEU cc_start: 0.2864 (OUTLIER) cc_final: 0.2492 (mp) REVERT: P 44 LEU cc_start: -0.0156 (OUTLIER) cc_final: -0.1114 (mm) REVERT: P 61 HIS cc_start: 0.2824 (m170) cc_final: 0.2382 (m90) REVERT: P 66 MET cc_start: 0.0884 (OUTLIER) cc_final: 0.0226 (tpp) REVERT: Q 22 LEU cc_start: 0.2801 (OUTLIER) cc_final: 0.2467 (mp) REVERT: Q 44 LEU cc_start: -0.0130 (OUTLIER) cc_final: -0.1101 (mm) REVERT: Q 61 HIS cc_start: 0.2839 (m170) cc_final: 0.2292 (m90) REVERT: Q 66 MET cc_start: 0.0892 (OUTLIER) cc_final: 0.0190 (tpp) REVERT: Q 76 ILE cc_start: 0.2384 (OUTLIER) cc_final: 0.2182 (mt) REVERT: R 22 LEU cc_start: 0.2784 (OUTLIER) cc_final: 0.2468 (mp) REVERT: R 44 LEU cc_start: -0.0164 (OUTLIER) cc_final: -0.1091 (mm) REVERT: R 61 HIS cc_start: 0.2787 (m170) cc_final: 0.2343 (m90) REVERT: R 66 MET cc_start: 0.0833 (OUTLIER) cc_final: 0.0131 (tpp) REVERT: R 76 ILE cc_start: 0.2355 (OUTLIER) cc_final: 0.2149 (mt) REVERT: R 96 MET cc_start: 0.0321 (mmp) cc_final: -0.1128 (mmp) REVERT: S 22 LEU cc_start: 0.2887 (OUTLIER) cc_final: 0.2518 (mp) REVERT: S 33 MET cc_start: 0.0325 (mtt) cc_final: -0.0213 (mtp) REVERT: S 44 LEU cc_start: 0.0116 (OUTLIER) cc_final: -0.1129 (mm) REVERT: S 61 HIS cc_start: 0.2824 (m170) cc_final: 0.2326 (m90) REVERT: S 66 MET cc_start: 0.0872 (OUTLIER) cc_final: 0.0234 (tpp) REVERT: S 76 ILE cc_start: 0.2385 (OUTLIER) cc_final: 0.2139 (mt) REVERT: S 96 MET cc_start: 0.0345 (mmp) cc_final: -0.1132 (mmp) REVERT: T 22 LEU cc_start: 0.2797 (OUTLIER) cc_final: 0.2442 (mp) REVERT: T 44 LEU cc_start: -0.0198 (OUTLIER) cc_final: -0.1106 (mm) REVERT: T 61 HIS cc_start: 0.2751 (m170) cc_final: 0.2225 (m170) REVERT: T 96 MET cc_start: 0.0182 (mmp) cc_final: -0.1196 (mmp) REVERT: V 22 LEU cc_start: 0.2750 (OUTLIER) cc_final: 0.2429 (mp) REVERT: V 44 LEU cc_start: -0.0108 (OUTLIER) cc_final: -0.1098 (mm) REVERT: V 61 HIS cc_start: 0.2814 (m170) cc_final: 0.2263 (m90) REVERT: V 66 MET cc_start: 0.0769 (OUTLIER) cc_final: 0.0159 (tpp) REVERT: V 76 ILE cc_start: 0.2101 (OUTLIER) cc_final: 0.1896 (mt) REVERT: V 96 MET cc_start: 0.0340 (mmp) cc_final: -0.1181 (mmp) REVERT: W 22 LEU cc_start: 0.2837 (OUTLIER) cc_final: 0.2465 (mp) REVERT: W 44 LEU cc_start: -0.0168 (OUTLIER) cc_final: -0.1136 (mm) REVERT: W 66 MET cc_start: 0.0803 (OUTLIER) cc_final: 0.0195 (tpp) REVERT: X 22 LEU cc_start: 0.2802 (OUTLIER) cc_final: 0.2478 (mp) REVERT: X 61 HIS cc_start: 0.2728 (m170) cc_final: 0.2240 (m170) REVERT: X 96 MET cc_start: 0.0237 (mmp) cc_final: -0.1149 (mmp) outliers start: 124 outliers final: 31 residues processed: 269 average time/residue: 0.4538 time to fit residues: 156.0060 Evaluate side-chains 275 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 181 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 66 MET Chi-restraints excluded: chain U residue 76 ILE Chi-restraints excluded: chain U residue 83 LYS Chi-restraints excluded: chain U residue 149 THR Chi-restraints excluded: chain A residue 33 MET Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain G residue 7 ASN Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 154 MET Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 154 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 66 MET Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 66 MET Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain N residue 7 ASN Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 66 MET Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain P residue 7 ASN Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 76 ILE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 76 ILE Chi-restraints excluded: chain S residue 154 MET Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 66 MET Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain X residue 22 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 113 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 278 optimal weight: 0.9980 chunk 229 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 250 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 7 ASN A 19 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 ASN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 ASN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 7 ASN G 19 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 ASN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 ASN ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 7 ASN ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 ASN ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 ASN ** P 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 7 ASN ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 ASN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 7 ASN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 ASN ** V 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.274788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.267339 restraints weight = 240141.700| |-----------------------------------------------------------------------------| r_work (start): 0.4628 rms_B_bonded: 3.85 r_work: 0.4355 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.4355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1321 moved from start: 0.6131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33912 Z= 0.140 Angle : 0.622 8.625 45792 Z= 0.323 Chirality : 0.038 0.168 4896 Planarity : 0.003 0.043 6024 Dihedral : 4.469 20.547 4464 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.30 % Allowed : 11.12 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.13), residues: 4080 helix: 2.46 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : -1.79 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG V 152 TYR 0.025 0.002 TYR G 35 PHE 0.015 0.002 PHE D 51 TRP 0.003 0.001 TRP U 89 HIS 0.004 0.001 HIS N 169 Details of bonding type rmsd covalent geometry : bond 0.00280 (33912) covalent geometry : angle 0.62200 (45792) hydrogen bonds : bond 0.03677 ( 2637) hydrogen bonds : angle 3.68224 ( 7911) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 173 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 61 HIS cc_start: 0.2823 (m170) cc_final: 0.2251 (m170) REVERT: U 96 MET cc_start: 0.0414 (mmp) cc_final: -0.1004 (mmp) REVERT: A 61 HIS cc_start: 0.2799 (m170) cc_final: 0.2355 (m90) REVERT: A 96 MET cc_start: 0.0075 (mmp) cc_final: -0.1081 (mmp) REVERT: B 44 LEU cc_start: -0.0126 (OUTLIER) cc_final: -0.1068 (mm) REVERT: B 61 HIS cc_start: 0.2836 (m170) cc_final: 0.2321 (m90) REVERT: B 66 MET cc_start: 0.0716 (OUTLIER) cc_final: 0.0126 (tpp) REVERT: B 96 MET cc_start: 0.0274 (mmp) cc_final: -0.1268 (mmp) REVERT: C 33 MET cc_start: 0.0357 (mtt) cc_final: -0.0115 (mtp) REVERT: C 44 LEU cc_start: -0.0268 (OUTLIER) cc_final: -0.1117 (mm) REVERT: C 61 HIS cc_start: 0.2817 (m170) cc_final: 0.2276 (m90) REVERT: C 66 MET cc_start: 0.0822 (OUTLIER) cc_final: 0.0146 (tpp) REVERT: C 76 ILE cc_start: 0.2013 (OUTLIER) cc_final: 0.1724 (mt) REVERT: D 44 LEU cc_start: -0.0244 (OUTLIER) cc_final: -0.1045 (mm) REVERT: D 61 HIS cc_start: 0.2813 (m170) cc_final: 0.2258 (m90) REVERT: D 66 MET cc_start: 0.0838 (OUTLIER) cc_final: 0.0178 (tpp) REVERT: E 22 LEU cc_start: 0.2666 (OUTLIER) cc_final: 0.2378 (mp) REVERT: E 61 HIS cc_start: 0.2805 (m170) cc_final: 0.2228 (m170) REVERT: F 44 LEU cc_start: -0.0186 (OUTLIER) cc_final: -0.1071 (mm) REVERT: F 61 HIS cc_start: 0.2824 (m170) cc_final: 0.2265 (m90) REVERT: F 66 MET cc_start: 0.0751 (OUTLIER) cc_final: 0.0112 (tpp) REVERT: G 22 LEU cc_start: 0.2625 (OUTLIER) cc_final: 0.2330 (mp) REVERT: G 44 LEU cc_start: -0.0044 (OUTLIER) cc_final: -0.1052 (mm) REVERT: G 66 MET cc_start: 0.0862 (OUTLIER) cc_final: 0.0053 (tpp) REVERT: H 22 LEU cc_start: 0.2656 (OUTLIER) cc_final: 0.2352 (mp) REVERT: H 44 LEU cc_start: -0.0011 (OUTLIER) cc_final: -0.1001 (mm) REVERT: H 61 HIS cc_start: 0.2781 (m170) cc_final: 0.2319 (m90) REVERT: H 66 MET cc_start: 0.0824 (OUTLIER) cc_final: 0.0089 (tpp) REVERT: I 22 LEU cc_start: 0.2695 (OUTLIER) cc_final: 0.2392 (mp) REVERT: I 44 LEU cc_start: -0.0100 (OUTLIER) cc_final: -0.1080 (mm) REVERT: I 66 MET cc_start: 0.0911 (OUTLIER) cc_final: 0.0281 (tpp) REVERT: J 22 LEU cc_start: 0.2620 (OUTLIER) cc_final: 0.2339 (mp) REVERT: J 44 LEU cc_start: -0.0073 (OUTLIER) cc_final: -0.1021 (mm) REVERT: J 66 MET cc_start: 0.0919 (OUTLIER) cc_final: 0.0225 (tpp) REVERT: K 22 LEU cc_start: 0.2602 (OUTLIER) cc_final: 0.2350 (mp) REVERT: K 61 HIS cc_start: 0.2768 (m170) cc_final: 0.2246 (m90) REVERT: L 22 LEU cc_start: 0.2690 (OUTLIER) cc_final: 0.2388 (mp) REVERT: L 44 LEU cc_start: -0.0211 (OUTLIER) cc_final: -0.1082 (mm) REVERT: L 66 MET cc_start: 0.0778 (OUTLIER) cc_final: 0.0057 (tpp) REVERT: M 22 LEU cc_start: 0.2599 (OUTLIER) cc_final: 0.2307 (mp) REVERT: M 44 LEU cc_start: -0.0162 (OUTLIER) cc_final: -0.1029 (mm) REVERT: M 66 MET cc_start: 0.0806 (OUTLIER) cc_final: 0.0033 (tpp) REVERT: N 22 LEU cc_start: 0.2625 (OUTLIER) cc_final: 0.2391 (mp) REVERT: N 44 LEU cc_start: -0.0195 (OUTLIER) cc_final: -0.1087 (mm) REVERT: N 66 MET cc_start: 0.0814 (OUTLIER) cc_final: 0.0197 (tpp) REVERT: N 76 ILE cc_start: 0.2085 (OUTLIER) cc_final: 0.1828 (mt) REVERT: O 22 LEU cc_start: 0.2700 (OUTLIER) cc_final: 0.2401 (mp) REVERT: O 44 LEU cc_start: -0.0219 (OUTLIER) cc_final: -0.1097 (mm) REVERT: O 61 HIS cc_start: 0.2861 (m170) cc_final: 0.2311 (m90) REVERT: O 66 MET cc_start: 0.0817 (OUTLIER) cc_final: 0.0045 (tpp) REVERT: P 44 LEU cc_start: -0.0193 (OUTLIER) cc_final: -0.1090 (mm) REVERT: P 61 HIS cc_start: 0.2810 (m170) cc_final: 0.2343 (m90) REVERT: P 66 MET cc_start: 0.0946 (OUTLIER) cc_final: 0.0254 (tpp) REVERT: P 76 ILE cc_start: 0.2268 (OUTLIER) cc_final: 0.2047 (mt) REVERT: Q 22 LEU cc_start: 0.2606 (OUTLIER) cc_final: 0.2346 (mp) REVERT: Q 44 LEU cc_start: -0.0171 (OUTLIER) cc_final: -0.1063 (mm) REVERT: Q 61 HIS cc_start: 0.2857 (m170) cc_final: 0.2309 (m90) REVERT: Q 66 MET cc_start: 0.0825 (OUTLIER) cc_final: 0.0043 (tpp) REVERT: R 22 LEU cc_start: 0.2633 (OUTLIER) cc_final: 0.2390 (mp) REVERT: R 44 LEU cc_start: -0.0191 (OUTLIER) cc_final: -0.1074 (mm) REVERT: R 61 HIS cc_start: 0.2819 (m170) cc_final: 0.2361 (m90) REVERT: R 66 MET cc_start: 0.0787 (OUTLIER) cc_final: 0.0046 (tpp) REVERT: S 22 LEU cc_start: 0.2699 (OUTLIER) cc_final: 0.2411 (mp) REVERT: S 44 LEU cc_start: 0.0094 (OUTLIER) cc_final: -0.1122 (mm) REVERT: S 61 HIS cc_start: 0.2861 (m170) cc_final: 0.2327 (m90) REVERT: S 66 MET cc_start: 0.0790 (OUTLIER) cc_final: 0.0025 (tpp) REVERT: T 22 LEU cc_start: 0.2631 (OUTLIER) cc_final: 0.2378 (mp) REVERT: T 44 LEU cc_start: -0.0300 (OUTLIER) cc_final: -0.1119 (mm) REVERT: T 61 HIS cc_start: 0.2733 (m170) cc_final: 0.2209 (m170) REVERT: V 22 LEU cc_start: 0.2607 (OUTLIER) cc_final: 0.2345 (mp) REVERT: V 44 LEU cc_start: -0.0143 (OUTLIER) cc_final: -0.1070 (mm) REVERT: V 61 HIS cc_start: 0.2860 (m170) cc_final: 0.2231 (m90) REVERT: V 66 MET cc_start: 0.0745 (OUTLIER) cc_final: 0.0082 (tpp) REVERT: W 22 LEU cc_start: 0.2682 (OUTLIER) cc_final: 0.2383 (mp) REVERT: W 44 LEU cc_start: -0.0178 (OUTLIER) cc_final: -0.1043 (mm) REVERT: W 66 MET cc_start: 0.0708 (OUTLIER) cc_final: 0.0006 (tpp) REVERT: X 22 LEU cc_start: 0.2593 (OUTLIER) cc_final: 0.2323 (mp) REVERT: X 66 MET cc_start: 0.0837 (OUTLIER) cc_final: 0.0155 (tpp) outliers start: 115 outliers final: 32 residues processed: 258 average time/residue: 0.4899 time to fit residues: 161.6187 Evaluate side-chains 259 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 169 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 83 LYS Chi-restraints excluded: chain U residue 149 THR Chi-restraints excluded: chain A residue 33 MET Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain G residue 154 MET Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 154 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 66 MET Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 66 MET Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain M residue 7 ASN Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 66 MET Chi-restraints excluded: chain N residue 7 ASN Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 154 MET Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 66 MET Chi-restraints excluded: chain P residue 7 ASN Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 76 ILE Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 154 MET Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain V residue 7 ASN Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 66 MET Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 66 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 154 optimal weight: 8.9990 chunk 282 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 361 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 280 optimal weight: 9.9990 chunk 170 optimal weight: 0.8980 chunk 276 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 308 optimal weight: 5.9990 chunk 300 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 7 ASN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN E 7 ASN F 7 ASN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 ASN ** H 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 ASN ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 ASN ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 ASN ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 ASN ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 7 ASN ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 ASN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 7 ASN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 ASN ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.279077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.271739 restraints weight = 243676.968| |-----------------------------------------------------------------------------| r_work (start): 0.4667 rms_B_bonded: 3.88 r_work: 0.4406 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.4406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1366 moved from start: 0.6332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33912 Z= 0.148 Angle : 0.653 8.696 45792 Z= 0.338 Chirality : 0.038 0.169 4896 Planarity : 0.003 0.044 6024 Dihedral : 4.534 20.620 4464 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.48 % Allowed : 11.03 % Favored : 85.49 % 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 aren not related in a simple way. whole: 2.23 (0.13), residues: 4080 helix: 2.34 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : -1.82 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 152 TYR 0.026 0.002 TYR B 164 PHE 0.017 0.002 PHE S 51 TRP 0.004 0.001 TRP U 89 HIS 0.004 0.001 HIS V 124 Details of bonding type rmsd covalent geometry : bond 0.00300 (33912) covalent geometry : angle 0.65274 (45792) hydrogen bonds : bond 0.03821 ( 2637) hydrogen bonds : angle 3.79334 ( 7911) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 166 time to evaluate : 1.397 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: U 61 HIS cc_start: 0.2832 (m170) cc_final: 0.2254 (m170) REVERT: U 96 MET cc_start: 0.0456 (mmp) cc_final: -0.1028 (mmp) REVERT: A 61 HIS cc_start: 0.2871 (m170) cc_final: 0.2380 (m90) REVERT: A 66 MET cc_start: 0.0950 (OUTLIER) cc_final: 0.0130 (tpp) REVERT: B 44 LEU cc_start: -0.0134 (OUTLIER) cc_final: -0.1085 (mm) REVERT: B 61 HIS cc_start: 0.2859 (m170) cc_final: 0.2337 (m90) REVERT: B 66 MET cc_start: 0.0890 (OUTLIER) cc_final: 0.0179 (tpp) REVERT: B 96 MET cc_start: 0.0354 (mmp) cc_final: -0.1204 (mmp) REVERT: C 44 LEU cc_start: -0.0228 (OUTLIER) cc_final: -0.1126 (mm) REVERT: C 66 MET cc_start: 0.1074 (OUTLIER) cc_final: 0.0208 (tpp) REVERT: C 76 ILE cc_start: 0.2102 (OUTLIER) cc_final: 0.1850 (mt) REVERT: D 44 LEU cc_start: -0.0207 (OUTLIER) cc_final: -0.1072 (mm) REVERT: D 66 MET cc_start: 0.1004 (OUTLIER) cc_final: 0.0248 (tpp) REVERT: D 96 MET cc_start: 0.0194 (mmp) cc_final: -0.1189 (mmp) REVERT: E 22 LEU cc_start: 0.2756 (OUTLIER) cc_final: 0.2433 (mp) REVERT: E 61 HIS cc_start: 0.2817 (m170) cc_final: 0.2248 (m90) REVERT: E 66 MET cc_start: 0.0754 (OUTLIER) cc_final: 0.0264 (tpp) REVERT: F 44 LEU cc_start: -0.0147 (OUTLIER) cc_final: -0.1073 (mm) REVERT: F 61 HIS cc_start: 0.2877 (m170) cc_final: 0.2299 (m90) REVERT: F 66 MET cc_start: 0.0902 (OUTLIER) cc_final: 0.0168 (tpp) REVERT: G 22 LEU cc_start: 0.2680 (OUTLIER) cc_final: 0.2383 (mp) REVERT: G 44 LEU cc_start: -0.0038 (OUTLIER) cc_final: -0.1071 (mm) REVERT: G 66 MET cc_start: 0.1003 (OUTLIER) cc_final: 0.0158 (tpp) REVERT: H 22 LEU cc_start: 0.2754 (OUTLIER) cc_final: 0.2425 (mp) REVERT: H 44 LEU cc_start: 0.0006 (OUTLIER) cc_final: -0.1056 (mm) REVERT: H 66 MET cc_start: 0.0967 (OUTLIER) cc_final: 0.0141 (tpp) REVERT: I 22 LEU cc_start: 0.2784 (OUTLIER) cc_final: 0.2463 (mp) REVERT: I 44 LEU cc_start: 0.0027 (OUTLIER) cc_final: -0.1036 (mm) REVERT: I 66 MET cc_start: 0.1001 (OUTLIER) cc_final: 0.0263 (tpp) REVERT: J 22 LEU cc_start: 0.2730 (OUTLIER) cc_final: 0.2421 (mp) REVERT: J 44 LEU cc_start: 0.0002 (OUTLIER) cc_final: -0.1008 (mm) REVERT: J 66 MET cc_start: 0.1071 (OUTLIER) cc_final: 0.0234 (tpp) REVERT: K 22 LEU cc_start: 0.2644 (OUTLIER) cc_final: 0.2382 (mp) REVERT: K 61 HIS cc_start: 0.2826 (m170) cc_final: 0.2275 (m170) REVERT: L 22 LEU cc_start: 0.2908 (OUTLIER) cc_final: 0.2520 (mp) REVERT: L 44 LEU cc_start: -0.0142 (OUTLIER) cc_final: -0.1082 (mm) REVERT: L 66 MET cc_start: 0.0921 (OUTLIER) cc_final: 0.0158 (tpp) REVERT: M 22 LEU cc_start: 0.2684 (OUTLIER) cc_final: 0.2368 (mp) REVERT: M 44 LEU cc_start: -0.0056 (OUTLIER) cc_final: -0.1040 (mm) REVERT: M 66 MET cc_start: 0.1006 (OUTLIER) cc_final: 0.0127 (tpp) REVERT: M 76 ILE cc_start: 0.2265 (OUTLIER) cc_final: 0.1973 (mt) REVERT: M 154 MET cc_start: 0.2650 (tpp) cc_final: 0.2164 (mmt) REVERT: N 22 LEU cc_start: 0.2736 (OUTLIER) cc_final: 0.2483 (mp) REVERT: N 33 MET cc_start: 0.0287 (mtt) cc_final: -0.0306 (mtt) REVERT: N 44 LEU cc_start: -0.0168 (OUTLIER) cc_final: -0.1074 (mm) REVERT: N 66 MET cc_start: 0.0996 (OUTLIER) cc_final: 0.0205 (tpp) REVERT: O 22 LEU cc_start: 0.2786 (OUTLIER) cc_final: 0.2463 (mp) REVERT: O 44 LEU cc_start: -0.0171 (OUTLIER) cc_final: -0.1120 (mm) REVERT: O 66 MET cc_start: 0.0985 (OUTLIER) cc_final: 0.0136 (tpp) REVERT: O 76 ILE cc_start: 0.2096 (OUTLIER) cc_final: 0.1867 (mt) REVERT: P 44 LEU cc_start: -0.0148 (OUTLIER) cc_final: -0.1097 (mm) REVERT: P 61 HIS cc_start: 0.2863 (m170) cc_final: 0.2386 (m90) REVERT: P 66 MET cc_start: 0.1053 (OUTLIER) cc_final: 0.0307 (tpp) REVERT: P 76 ILE cc_start: 0.2263 (OUTLIER) cc_final: 0.2030 (mt) REVERT: Q 22 LEU cc_start: 0.2710 (OUTLIER) cc_final: 0.2417 (mp) REVERT: Q 44 LEU cc_start: -0.0098 (OUTLIER) cc_final: -0.1076 (mm) REVERT: Q 66 MET cc_start: 0.0967 (OUTLIER) cc_final: 0.0160 (tpp) REVERT: Q 76 ILE cc_start: 0.2182 (OUTLIER) cc_final: 0.1915 (mt) REVERT: R 22 LEU cc_start: 0.2779 (OUTLIER) cc_final: 0.2486 (mp) REVERT: R 44 LEU cc_start: -0.0174 (OUTLIER) cc_final: -0.1067 (mm) REVERT: R 66 MET cc_start: 0.0963 (OUTLIER) cc_final: 0.0125 (tpp) REVERT: R 76 ILE cc_start: 0.2145 (OUTLIER) cc_final: 0.1895 (mt) REVERT: S 22 LEU cc_start: 0.2805 (OUTLIER) cc_final: 0.2465 (mp) REVERT: S 44 LEU cc_start: 0.0086 (OUTLIER) cc_final: -0.1096 (mm) REVERT: S 61 HIS cc_start: 0.2909 (m170) cc_final: 0.2372 (m90) REVERT: S 66 MET cc_start: 0.0930 (OUTLIER) cc_final: 0.0173 (tpp) REVERT: S 76 ILE cc_start: 0.2198 (OUTLIER) cc_final: 0.1880 (mt) REVERT: T 22 LEU cc_start: 0.2774 (OUTLIER) cc_final: 0.2469 (mp) REVERT: T 44 LEU cc_start: -0.0211 (OUTLIER) cc_final: -0.1107 (mm) REVERT: T 61 HIS cc_start: 0.2799 (m170) cc_final: 0.2270 (m90) REVERT: V 22 LEU cc_start: 0.2678 (OUTLIER) cc_final: 0.2404 (mp) REVERT: V 44 LEU cc_start: -0.0088 (OUTLIER) cc_final: -0.1050 (mm) REVERT: V 66 MET cc_start: 0.0922 (OUTLIER) cc_final: 0.0138 (tpp) REVERT: W 22 LEU cc_start: 0.2783 (OUTLIER) cc_final: 0.2450 (mp) REVERT: W 44 LEU cc_start: -0.0050 (OUTLIER) cc_final: -0.1022 (mm) REVERT: W 66 MET cc_start: 0.0876 (OUTLIER) cc_final: 0.0076 (tpp) REVERT: X 22 LEU cc_start: 0.2728 (OUTLIER) cc_final: 0.2442 (mp) REVERT: X 66 MET cc_start: 0.1012 (OUTLIER) cc_final: 0.0156 (tpp) outliers start: 121 outliers final: 28 residues processed: 253 average time/residue: 0.4789 time to fit residues: 154.2464 Evaluate side-chains 255 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 163 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 66 MET Chi-restraints excluded: chain U residue 83 LYS Chi-restraints excluded: chain U residue 149 THR Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain G residue 154 MET Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 154 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 66 MET Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 66 MET Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain M residue 7 ASN Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 66 MET Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain N residue 7 ASN Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 66 MET Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 76 ILE Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 76 ILE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 76 ILE Chi-restraints excluded: chain S residue 154 MET Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 66 MET Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 66 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 147 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 305 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 162 optimal weight: 0.5980 chunk 294 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 19 GLN ** U 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 7 ASN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN E 7 ASN F 7 ASN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 ASN ** H 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 ASN I 19 GLN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 150 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 ASN ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 ASN ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 ASN ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 ASN ** P 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 7 ASN ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 ASN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 7 ASN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 ASN ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 7 ASN ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.288127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.281162 restraints weight = 251499.477| |-----------------------------------------------------------------------------| r_work (start): 0.4748 rms_B_bonded: 3.85 r_work: 0.4494 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.4494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1499 moved from start: 0.6763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 33912 Z= 0.192 Angle : 0.769 10.796 45792 Z= 0.401 Chirality : 0.041 0.191 4896 Planarity : 0.004 0.044 6024 Dihedral : 4.929 21.039 4464 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.42 % Allowed : 11.49 % Favored : 85.09 % 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 aren not related in a simple way. whole: 1.38 (0.13), residues: 4080 helix: 1.75 (0.09), residues: 3168 sheet: None (None), residues: 0 loop : -2.15 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 5 TYR 0.028 0.003 TYR J 35 PHE 0.023 0.003 PHE S 51 TRP 0.009 0.002 TRP S 89 HIS 0.006 0.002 HIS Q 169 Details of bonding type rmsd covalent geometry : bond 0.00397 (33912) covalent geometry : angle 0.76940 (45792) hydrogen bonds : bond 0.04560 ( 2637) hydrogen bonds : angle 4.19094 ( 7911) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 186 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 61 HIS cc_start: 0.2927 (m170) cc_final: 0.2348 (m170) REVERT: A 61 HIS cc_start: 0.2857 (m170) cc_final: 0.2397 (m170) REVERT: B 44 LEU cc_start: 0.0081 (OUTLIER) cc_final: -0.1129 (mm) REVERT: B 61 HIS cc_start: 0.2854 (m170) cc_final: 0.2383 (m90) REVERT: C 31 LEU cc_start: 0.3254 (tp) cc_final: 0.2992 (tp) REVERT: C 33 MET cc_start: 0.0240 (mtt) cc_final: -0.0325 (mtt) REVERT: C 44 LEU cc_start: 0.0014 (OUTLIER) cc_final: -0.1121 (mm) REVERT: D 31 LEU cc_start: 0.3216 (tp) cc_final: 0.2978 (tp) REVERT: D 33 MET cc_start: 0.0280 (mtt) cc_final: -0.0208 (mtt) REVERT: D 44 LEU cc_start: 0.0014 (OUTLIER) cc_final: -0.1105 (mm) REVERT: D 96 MET cc_start: 0.0453 (mmp) cc_final: -0.1302 (mmp) REVERT: E 22 LEU cc_start: 0.2993 (OUTLIER) cc_final: 0.2621 (mp) REVERT: E 61 HIS cc_start: 0.2888 (m170) cc_final: 0.2418 (m90) REVERT: E 66 MET cc_start: 0.0864 (OUTLIER) cc_final: 0.0250 (tpp) REVERT: F 44 LEU cc_start: 0.0156 (OUTLIER) cc_final: -0.1063 (mm) REVERT: F 61 HIS cc_start: 0.2953 (m170) cc_final: 0.2448 (m90) REVERT: F 66 MET cc_start: 0.1168 (OUTLIER) cc_final: 0.0511 (tpp) REVERT: G 22 LEU cc_start: 0.2933 (OUTLIER) cc_final: 0.2573 (mp) REVERT: G 44 LEU cc_start: 0.0170 (OUTLIER) cc_final: -0.1074 (mm) REVERT: G 96 MET cc_start: 0.0260 (mmm) cc_final: -0.1009 (mmm) REVERT: H 22 LEU cc_start: 0.2937 (OUTLIER) cc_final: 0.2520 (mp) REVERT: H 44 LEU cc_start: 0.0244 (OUTLIER) cc_final: -0.1010 (mm) REVERT: I 22 LEU cc_start: 0.3012 (OUTLIER) cc_final: 0.2672 (mp) REVERT: I 44 LEU cc_start: 0.0296 (OUTLIER) cc_final: -0.0946 (mm) REVERT: J 22 LEU cc_start: 0.2971 (OUTLIER) cc_final: 0.2642 (mp) REVERT: J 44 LEU cc_start: 0.0220 (OUTLIER) cc_final: -0.1051 (mm) REVERT: K 22 LEU cc_start: 0.2894 (OUTLIER) cc_final: 0.2568 (mp) REVERT: K 31 LEU cc_start: 0.3197 (tp) cc_final: 0.2993 (tp) REVERT: K 61 HIS cc_start: 0.2912 (m170) cc_final: 0.2409 (m170) REVERT: L 44 LEU cc_start: 0.0071 (OUTLIER) cc_final: -0.1104 (mm) REVERT: M 22 LEU cc_start: 0.2980 (OUTLIER) cc_final: 0.2563 (mp) REVERT: M 44 LEU cc_start: 0.0174 (OUTLIER) cc_final: -0.1014 (mm) REVERT: N 22 LEU cc_start: 0.3013 (OUTLIER) cc_final: 0.2720 (mp) REVERT: N 31 LEU cc_start: 0.3219 (tp) cc_final: 0.2970 (tp) REVERT: N 33 MET cc_start: 0.0391 (mtt) cc_final: -0.0197 (mtt) REVERT: N 44 LEU cc_start: 0.0041 (OUTLIER) cc_final: -0.1153 (mm) REVERT: N 96 MET cc_start: 0.0247 (mmp) cc_final: -0.1200 (mmp) REVERT: O 44 LEU cc_start: 0.0165 (OUTLIER) cc_final: -0.1046 (mm) REVERT: P 44 LEU cc_start: 0.0182 (OUTLIER) cc_final: -0.1020 (mm) REVERT: Q 22 LEU cc_start: 0.2888 (OUTLIER) cc_final: 0.2518 (mp) REVERT: Q 44 LEU cc_start: 0.0171 (OUTLIER) cc_final: -0.1059 (mm) REVERT: Q 61 HIS cc_start: 0.2961 (m170) cc_final: 0.2377 (m90) REVERT: R 44 LEU cc_start: 0.0086 (OUTLIER) cc_final: -0.1092 (mm) REVERT: S 22 LEU cc_start: 0.3007 (OUTLIER) cc_final: 0.2633 (mp) REVERT: S 44 LEU cc_start: 0.0233 (OUTLIER) cc_final: -0.1038 (mm) REVERT: T 22 LEU cc_start: 0.2962 (OUTLIER) cc_final: 0.2620 (mp) REVERT: T 44 LEU cc_start: 0.0110 (OUTLIER) cc_final: -0.1073 (mm) REVERT: T 61 HIS cc_start: 0.2821 (m170) cc_final: 0.2316 (m170) REVERT: T 66 MET cc_start: 0.0875 (OUTLIER) cc_final: 0.0369 (tpp) REVERT: V 22 LEU cc_start: 0.2881 (OUTLIER) cc_final: 0.2511 (mp) REVERT: V 44 LEU cc_start: 0.0148 (OUTLIER) cc_final: -0.1049 (mm) REVERT: V 61 HIS cc_start: 0.3032 (m170) cc_final: 0.2359 (m90) REVERT: W 22 LEU cc_start: 0.3015 (OUTLIER) cc_final: 0.2658 (mp) REVERT: W 44 LEU cc_start: 0.0151 (OUTLIER) cc_final: -0.1010 (mm) REVERT: X 22 LEU cc_start: 0.2989 (OUTLIER) cc_final: 0.2595 (mp) REVERT: X 154 MET cc_start: 0.2679 (tpp) cc_final: 0.1534 (mmt) outliers start: 119 outliers final: 35 residues processed: 257 average time/residue: 0.4682 time to fit residues: 154.2036 Evaluate side-chains 259 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 188 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 66 MET Chi-restraints excluded: chain U residue 83 LYS Chi-restraints excluded: chain U residue 149 THR Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain G residue 154 MET Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 154 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 66 MET Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 66 MET Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain M residue 7 ASN Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 66 MET Chi-restraints excluded: chain M residue 154 MET Chi-restraints excluded: chain N residue 7 ASN Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 66 MET Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 154 MET Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 66 MET Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 66 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 95 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 313 optimal weight: 6.9990 chunk 336 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 243 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 347 optimal weight: 5.9990 chunk 387 optimal weight: 5.9990 chunk 66 optimal weight: 0.0970 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 7 ASN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN D 19 GLN E 7 ASN F 7 ASN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 ASN ** H 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 ASN I 19 GLN ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 ASN N 7 ASN O 7 ASN ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 ASN P 19 GLN Q 7 ASN ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 ASN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 7 ASN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 ASN ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 7 ASN W 19 GLN ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.287005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.279927 restraints weight = 251331.824| |-----------------------------------------------------------------------------| r_work (start): 0.4738 rms_B_bonded: 3.84 r_work: 0.4489 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.4489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1408 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 33912 Z= 0.150 Angle : 0.678 8.745 45792 Z= 0.349 Chirality : 0.039 0.222 4896 Planarity : 0.003 0.045 6024 Dihedral : 4.679 20.743 4464 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.67 % Allowed : 12.53 % Favored : 84.80 % 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 aren not related in a simple way. whole: 1.76 (0.13), residues: 4080 helix: 2.05 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : -2.12 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 152 TYR 0.030 0.002 TYR J 35 PHE 0.017 0.002 PHE S 51 TRP 0.007 0.001 TRP E 89 HIS 0.005 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00310 (33912) covalent geometry : angle 0.67790 (45792) hydrogen bonds : bond 0.03966 ( 2637) hydrogen bonds : angle 3.95797 ( 7911) =============================================================================== Job complete usr+sys time: 10045.77 seconds wall clock time: 172 minutes 43.61 seconds (10363.61 seconds total)