Starting phenix.real_space_refine on Fri Jun 27 05:51:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v66_31736/06_2025/7v66_31736.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v66_31736/06_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_31736/06_2025/7v66_31736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v66_31736/06_2025/7v66_31736.map" model { file = "/net/cci-nas-00/data/ceres_data/7v66_31736/06_2025/7v66_31736.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v66_31736/06_2025/7v66_31736.cif" } resolution = 1.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, '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: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 23.39, per 1000 atoms: 0.70 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: 8.04 Conformation dependent library (CDL) restraints added in 4.0 seconds 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: 2.55 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: 11.41 Time building geometry restraints manager: 9.53 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: 5.170 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: 0.030 Extract box with map and model: 1.650 Check model and map are aligned: 0.290 Set scattering table: 0.350 Process input model: 76.070 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.270 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:14.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.820 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (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 TRP 0.013 0.003 TRP H 89 HIS 0.026 0.005 HIS M 147 PHE 0.016 0.004 PHE N 37 TYR 0.063 0.006 TYR A 28 ARG 0.009 0.003 ARG O 75 Details of bonding type rmsd hydrogen bonds : bond 0.10263 ( 2637) hydrogen bonds : angle 4.19074 ( 7911) covalent geometry : bond 0.00567 (33912) covalent geometry : angle 1.01810 (45792) *********************** 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 : 3.435 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: 1.1338 time to fit residues: 510.9834 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 : 3.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 2.9990 chunk 309 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 chunk 165 optimal weight: 8.9990 chunk 319 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 194 optimal weight: 0.0040 chunk 238 optimal weight: 10.0000 chunk 370 optimal weight: 0.9980 overall best weight: 0.9796 ------------------------------------------------------------------------------- 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 A 150 ASN B 7 ASN B 10 GLN B 94 ASN B 135 ASN B 150 ASN C 7 ASN C 94 ASN C 132 HIS C 150 ASN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN D 132 HIS D 150 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 ASN I 132 HIS I 135 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** L 94 ASN L 132 HIS L 150 ASN M 7 ASN M 94 ASN M 132 HIS M 150 ASN ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 94 ASN N 132 HIS N 150 ASN ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 94 ASN O 132 HIS O 150 ASN P 7 ASN P 94 ASN P 132 HIS P 150 ASN ** Q 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN Q 132 HIS Q 150 ASN ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 ASN R 132 HIS R 135 ASN R 150 ASN S 7 ASN S 94 ASN S 132 HIS S 150 ASN ** T 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 94 ASN T 150 ASN ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 78 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.197877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.187658 restraints weight = 199900.391| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 3.88 r_work: 0.3420 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0799 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33912 Z= 0.133 Angle : 0.603 10.369 45792 Z= 0.316 Chirality : 0.040 0.175 4896 Planarity : 0.003 0.022 6024 Dihedral : 4.504 20.615 4464 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.47 % Allowed : 6.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.77 (0.13), residues: 4080 helix: 3.14 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : -0.41 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP U 89 HIS 0.004 0.001 HIS A 114 PHE 0.007 0.001 PHE U 37 TYR 0.025 0.002 TYR Q 164 ARG 0.005 0.001 ARG A 5 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 2637) hydrogen bonds : angle 3.55002 ( 7911) covalent geometry : bond 0.00271 (33912) covalent geometry : angle 0.60340 (45792) *********************** 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 247 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 3.240 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 149 THR cc_start: 0.5800 (m) cc_final: 0.5596 (t) REVERT: B 44 LEU cc_start: -0.0427 (OUTLIER) cc_final: -0.1166 (mm) REVERT: C 44 LEU cc_start: -0.0407 (OUTLIER) cc_final: -0.1153 (mm) REVERT: D 44 LEU cc_start: -0.0444 (OUTLIER) cc_final: -0.1169 (mm) REVERT: E 19 GLN cc_start: 0.2069 (tp40) cc_final: 0.1867 (mm-40) REVERT: F 44 LEU cc_start: -0.0393 (OUTLIER) cc_final: -0.1161 (mm) REVERT: G 44 LEU cc_start: -0.0399 (OUTLIER) cc_final: -0.1179 (mm) REVERT: H 19 GLN cc_start: 0.2082 (tp40) cc_final: 0.1881 (mm-40) REVERT: H 44 LEU cc_start: -0.0402 (OUTLIER) cc_final: -0.1160 (mm) REVERT: I 44 LEU cc_start: -0.0396 (OUTLIER) cc_final: -0.1152 (mm) REVERT: J 44 LEU cc_start: -0.0409 (OUTLIER) cc_final: -0.1164 (mm) REVERT: K 19 GLN cc_start: 0.2072 (tp40) cc_final: 0.1870 (mm-40) REVERT: L 44 LEU cc_start: -0.0397 (OUTLIER) cc_final: -0.1154 (mm) REVERT: M 44 LEU cc_start: -0.0410 (OUTLIER) cc_final: -0.1157 (mm) REVERT: N 19 GLN cc_start: 0.2047 (tp40) cc_final: 0.1845 (mm-40) REVERT: N 44 LEU cc_start: -0.0449 (OUTLIER) cc_final: -0.1173 (mm) REVERT: O 44 LEU cc_start: -0.0407 (OUTLIER) cc_final: -0.1146 (mm) REVERT: P 44 LEU cc_start: -0.0407 (OUTLIER) cc_final: -0.1164 (mm) REVERT: Q 44 LEU cc_start: -0.0392 (OUTLIER) cc_final: -0.1143 (mm) REVERT: R 44 LEU cc_start: -0.0410 (OUTLIER) cc_final: -0.1133 (mm) REVERT: S 44 LEU cc_start: -0.0483 (OUTLIER) cc_final: -0.1227 (mm) REVERT: T 44 LEU cc_start: -0.0402 (OUTLIER) cc_final: -0.1139 (mm) REVERT: V 44 LEU cc_start: -0.0393 (OUTLIER) cc_final: -0.1171 (mm) REVERT: W 44 LEU cc_start: -0.0394 (OUTLIER) cc_final: -0.1161 (mm) outliers start: 51 outliers final: 6 residues processed: 246 average time/residue: 1.2911 time to fit residues: 400.8638 Evaluate side-chains 178 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 3.601 ------------------------------------------------------------------------------- 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 44 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain J residue 44 LEU 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 44 LEU 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 44 LEU 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 44 LEU 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 205 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 308 optimal weight: 10.0000 chunk 252 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 1.9990 chunk 400 optimal weight: 6.9990 chunk 330 optimal weight: 0.0970 chunk 368 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 297 optimal weight: 2.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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 108 GLN U 135 ASN U 137 GLN ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN A 54 GLN A 108 GLN A 135 ASN A 137 GLN ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN B 54 GLN B 108 GLN B 135 ASN B 137 GLN ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN C 108 GLN C 137 GLN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN D 54 GLN D 108 GLN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN E 108 GLN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN F 54 GLN F 108 GLN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN G 137 GLN ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN H 108 GLN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN I 54 GLN I 108 GLN I 137 GLN ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 54 GLN J 108 GLN J 137 GLN K 7 ASN K 54 GLN K 108 GLN K 137 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN L 54 GLN L 108 GLN ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN M 54 GLN M 108 GLN M 137 GLN ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 GLN N 108 GLN N 137 GLN ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 54 GLN O 108 GLN O 137 GLN ** P 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 GLN P 54 GLN P 108 GLN P 137 GLN ** Q 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN Q 108 GLN Q 137 GLN ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 GLN R 54 GLN R 108 GLN R 137 GLN ** S 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 19 GLN S 108 GLN S 137 GLN ** T 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 GLN T 108 GLN T 137 GLN ** V 7 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 ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 54 GLN X 108 GLN X 137 GLN Total number of N/Q/H flips: 80 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.234065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.225573 restraints weight = 222337.276| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 3.88 r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1141 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33912 Z= 0.188 Angle : 0.696 8.974 45792 Z= 0.374 Chirality : 0.043 0.175 4896 Planarity : 0.004 0.031 6024 Dihedral : 4.887 20.092 4464 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.93 % Allowed : 5.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.13), residues: 4080 helix: 2.59 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : -0.48 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP N 89 HIS 0.006 0.001 HIS B 61 PHE 0.008 0.002 PHE W 37 TYR 0.032 0.003 TYR S 164 ARG 0.003 0.001 ARG T 72 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 2637) hydrogen bonds : angle 3.77475 ( 7911) covalent geometry : bond 0.00401 (33912) covalent geometry : angle 0.69583 (45792) *********************** 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 301 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 199 time to evaluate : 3.700 Fit side-chains REVERT: U 61 HIS cc_start: 0.2591 (m170) cc_final: 0.2089 (m170) REVERT: U 83 LYS cc_start: 0.2052 (OUTLIER) cc_final: 0.1844 (ptmm) REVERT: U 96 MET cc_start: 0.0722 (mmp) cc_final: -0.0998 (mmp) REVERT: A 22 LEU cc_start: 0.3275 (OUTLIER) cc_final: 0.2572 (mt) REVERT: A 61 HIS cc_start: 0.2407 (m170) cc_final: 0.2184 (m170) REVERT: A 96 MET cc_start: 0.0742 (mmp) cc_final: -0.1135 (mmp) REVERT: A 134 LEU cc_start: -0.0430 (OUTLIER) cc_final: -0.0787 (mt) REVERT: B 44 LEU cc_start: -0.0486 (OUTLIER) cc_final: -0.1506 (mm) REVERT: B 61 HIS cc_start: 0.2509 (m170) cc_final: 0.2080 (m170) REVERT: B 90 GLU cc_start: 0.0452 (OUTLIER) cc_final: 0.0237 (tp30) REVERT: B 96 MET cc_start: 0.0787 (mmp) cc_final: -0.1078 (mmp) REVERT: C 22 LEU cc_start: 0.3391 (OUTLIER) cc_final: 0.2559 (mt) REVERT: C 44 LEU cc_start: -0.0369 (OUTLIER) cc_final: -0.1308 (mm) REVERT: C 61 HIS cc_start: 0.2316 (m170) cc_final: 0.2023 (m170) REVERT: C 134 LEU cc_start: -0.0459 (OUTLIER) cc_final: -0.0818 (mt) REVERT: D 22 LEU cc_start: 0.3513 (OUTLIER) cc_final: 0.2759 (mt) REVERT: D 44 LEU cc_start: -0.0395 (OUTLIER) cc_final: -0.1340 (mm) REVERT: D 61 HIS cc_start: 0.2524 (m170) cc_final: 0.2179 (m170) REVERT: D 134 LEU cc_start: -0.0395 (OUTLIER) cc_final: -0.0764 (mt) REVERT: E 22 LEU cc_start: 0.3123 (OUTLIER) cc_final: 0.2416 (mt) REVERT: E 61 HIS cc_start: 0.2425 (m170) cc_final: 0.2040 (m170) REVERT: E 134 LEU cc_start: -0.0297 (OUTLIER) cc_final: -0.0757 (mt) REVERT: F 44 LEU cc_start: -0.0435 (OUTLIER) cc_final: -0.1497 (mm) REVERT: F 61 HIS cc_start: 0.2473 (m170) cc_final: 0.2203 (m170) REVERT: F 134 LEU cc_start: -0.0558 (OUTLIER) cc_final: -0.0889 (mt) REVERT: G 22 LEU cc_start: 0.3332 (OUTLIER) cc_final: 0.2512 (mt) REVERT: G 44 LEU cc_start: -0.0336 (OUTLIER) cc_final: -0.1429 (mm) REVERT: G 61 HIS cc_start: 0.2627 (m170) cc_final: 0.2309 (m170) REVERT: G 134 LEU cc_start: -0.0352 (OUTLIER) cc_final: -0.0868 (mt) REVERT: H 22 LEU cc_start: 0.3560 (OUTLIER) cc_final: 0.2774 (mt) REVERT: H 44 LEU cc_start: -0.0314 (OUTLIER) cc_final: -0.1322 (mm) REVERT: H 61 HIS cc_start: 0.2515 (m170) cc_final: 0.2041 (m170) REVERT: H 134 LEU cc_start: -0.0568 (OUTLIER) cc_final: -0.0967 (mt) REVERT: I 22 LEU cc_start: 0.3249 (OUTLIER) cc_final: 0.2499 (mt) REVERT: I 44 LEU cc_start: -0.0333 (OUTLIER) cc_final: -0.1377 (mm) REVERT: I 61 HIS cc_start: 0.2460 (m170) cc_final: 0.2127 (m170) REVERT: I 134 LEU cc_start: -0.0517 (OUTLIER) cc_final: -0.0854 (mt) REVERT: J 22 LEU cc_start: 0.3374 (OUTLIER) cc_final: 0.2505 (mt) REVERT: J 44 LEU cc_start: -0.0498 (OUTLIER) cc_final: -0.1484 (mm) REVERT: J 61 HIS cc_start: 0.2543 (m170) cc_final: 0.2158 (m170) REVERT: J 96 MET cc_start: 0.0611 (mmp) cc_final: -0.1102 (mmp) REVERT: J 134 LEU cc_start: -0.0438 (OUTLIER) cc_final: -0.0879 (mt) REVERT: K 22 LEU cc_start: 0.3392 (OUTLIER) cc_final: 0.2600 (mt) REVERT: K 61 HIS cc_start: 0.2522 (m170) cc_final: 0.1973 (m170) REVERT: K 96 MET cc_start: 0.0578 (mmp) cc_final: -0.1185 (mmp) REVERT: L 22 LEU cc_start: 0.3334 (OUTLIER) cc_final: 0.2507 (mt) REVERT: L 44 LEU cc_start: -0.0398 (OUTLIER) cc_final: -0.1423 (mm) REVERT: L 61 HIS cc_start: 0.2297 (m170) cc_final: 0.1960 (m170) REVERT: L 134 LEU cc_start: -0.0390 (OUTLIER) cc_final: -0.0879 (mt) REVERT: M 22 LEU cc_start: 0.3258 (OUTLIER) cc_final: 0.2499 (mt) REVERT: M 44 LEU cc_start: -0.0392 (OUTLIER) cc_final: -0.1428 (mm) REVERT: M 61 HIS cc_start: 0.2549 (m170) cc_final: 0.2081 (m170) REVERT: M 134 LEU cc_start: -0.0458 (OUTLIER) cc_final: -0.0880 (mt) REVERT: N 22 LEU cc_start: 0.3508 (OUTLIER) cc_final: 0.2651 (mt) REVERT: N 44 LEU cc_start: -0.0367 (OUTLIER) cc_final: -0.1383 (mm) REVERT: N 61 HIS cc_start: 0.2380 (m170) cc_final: 0.2174 (m170) REVERT: N 96 MET cc_start: 0.0737 (mmp) cc_final: -0.1107 (mmp) REVERT: O 22 LEU cc_start: 0.3334 (OUTLIER) cc_final: 0.2531 (mt) REVERT: O 44 LEU cc_start: -0.0485 (OUTLIER) cc_final: -0.1474 (mm) REVERT: O 61 HIS cc_start: 0.2492 (m170) cc_final: 0.2230 (m170) REVERT: O 134 LEU cc_start: -0.0597 (OUTLIER) cc_final: -0.0978 (mt) REVERT: P 22 LEU cc_start: 0.3228 (OUTLIER) cc_final: 0.2494 (mt) REVERT: P 44 LEU cc_start: -0.0309 (OUTLIER) cc_final: -0.1406 (mm) REVERT: P 61 HIS cc_start: 0.2466 (m170) cc_final: 0.2191 (m170) REVERT: P 96 MET cc_start: 0.0625 (mmp) cc_final: -0.1062 (mmp) REVERT: P 134 LEU cc_start: -0.0415 (OUTLIER) cc_final: -0.0799 (mt) REVERT: Q 22 LEU cc_start: 0.3299 (OUTLIER) cc_final: 0.2419 (mt) REVERT: Q 44 LEU cc_start: -0.0443 (OUTLIER) cc_final: -0.1431 (mm) REVERT: Q 61 HIS cc_start: 0.2448 (m170) cc_final: 0.2191 (m170) REVERT: Q 134 LEU cc_start: -0.0443 (OUTLIER) cc_final: -0.0807 (mt) REVERT: R 22 LEU cc_start: 0.3393 (OUTLIER) cc_final: 0.2540 (mt) REVERT: R 44 LEU cc_start: -0.0462 (OUTLIER) cc_final: -0.1517 (mm) REVERT: R 61 HIS cc_start: 0.2277 (m170) cc_final: 0.2005 (m170) REVERT: R 134 LEU cc_start: -0.0465 (OUTLIER) cc_final: -0.0794 (mt) REVERT: S 22 LEU cc_start: 0.3510 (OUTLIER) cc_final: 0.2660 (mt) REVERT: S 44 LEU cc_start: -0.0379 (OUTLIER) cc_final: -0.1421 (mm) REVERT: S 61 HIS cc_start: 0.2600 (m170) cc_final: 0.2236 (m170) REVERT: S 134 LEU cc_start: -0.0583 (OUTLIER) cc_final: -0.0964 (mt) REVERT: T 22 LEU cc_start: 0.3499 (OUTLIER) cc_final: 0.2613 (mt) REVERT: T 44 LEU cc_start: -0.0409 (OUTLIER) cc_final: -0.1510 (mm) REVERT: T 61 HIS cc_start: 0.2607 (m170) cc_final: 0.2244 (m170) REVERT: T 134 LEU cc_start: -0.0569 (OUTLIER) cc_final: -0.0971 (mt) REVERT: V 22 LEU cc_start: 0.3399 (OUTLIER) cc_final: 0.2578 (mt) REVERT: V 44 LEU cc_start: -0.0322 (OUTLIER) cc_final: -0.1369 (mm) REVERT: V 61 HIS cc_start: 0.2591 (m170) cc_final: 0.2146 (m170) REVERT: V 134 LEU cc_start: -0.0476 (OUTLIER) cc_final: -0.0897 (mt) REVERT: W 22 LEU cc_start: 0.3476 (OUTLIER) cc_final: 0.2586 (mt) REVERT: W 44 LEU cc_start: -0.0336 (OUTLIER) cc_final: -0.1297 (mm) REVERT: W 61 HIS cc_start: 0.2525 (m170) cc_final: 0.2287 (m170) REVERT: W 134 LEU cc_start: -0.0487 (OUTLIER) cc_final: -0.0843 (mt) REVERT: X 22 LEU cc_start: 0.3462 (OUTLIER) cc_final: 0.2610 (mt) REVERT: X 134 LEU cc_start: -0.0421 (OUTLIER) cc_final: -0.0754 (mt) REVERT: X 154 MET cc_start: 0.1191 (mmt) cc_final: 0.0965 (mpt) outliers start: 102 outliers final: 33 residues processed: 284 average time/residue: 1.1454 time to fit residues: 409.9098 Evaluate side-chains 289 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 194 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 83 LYS Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 33 MET Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 44 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 33 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 134 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 F residue 134 LEU 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 134 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 134 LEU 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 I residue 134 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 134 LEU Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 65 LEU 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 134 LEU 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 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 33 MET Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 33 MET Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 134 LEU 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 134 LEU 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 134 LEU Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 33 MET Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 134 LEU 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 T residue 134 LEU 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 134 LEU Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 33 MET 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 366 optimal weight: 10.0000 chunk 279 optimal weight: 0.5980 chunk 192 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 249 optimal weight: 8.9990 chunk 372 optimal weight: 0.9980 chunk 394 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 353 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 A 7 ASN A 19 GLN B 7 ASN B 19 GLN C 7 ASN C 19 GLN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 GLN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN K 19 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN M 7 ASN M 19 GLN N 7 ASN N 19 GLN ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 GLN P 7 ASN P 19 GLN ** Q 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 GLN S 7 ASN S 19 GLN ** T 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 GLN ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN ** W 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 19 GLN ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.234359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.226313 restraints weight = 222951.676| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 3.89 r_work: 0.3889 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1012 moved from start: 0.4366 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= 0.120 Angle : 0.573 11.152 45792 Z= 0.292 Chirality : 0.037 0.165 4896 Planarity : 0.003 0.036 6024 Dihedral : 4.383 19.475 4464 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.33 % Allowed : 5.20 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.13), residues: 4080 helix: 3.18 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : -0.32 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP I 89 HIS 0.005 0.001 HIS X 61 PHE 0.008 0.001 PHE W 37 TYR 0.022 0.002 TYR M 164 ARG 0.004 0.000 ARG M 5 Details of bonding type rmsd hydrogen bonds : bond 0.03196 ( 2637) hydrogen bonds : angle 3.45088 ( 7911) covalent geometry : bond 0.00240 (33912) covalent geometry : angle 0.57319 (45792) *********************** 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 298 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 182 time to evaluate : 3.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 61 HIS cc_start: 0.2215 (m170) cc_final: 0.1897 (m170) REVERT: U 96 MET cc_start: 0.0168 (mmp) cc_final: -0.0920 (mmp) REVERT: U 149 THR cc_start: 0.5750 (OUTLIER) cc_final: 0.5495 (t) REVERT: A 22 LEU cc_start: 0.2289 (OUTLIER) cc_final: 0.2066 (mt) REVERT: A 61 HIS cc_start: 0.2226 (m170) cc_final: 0.1878 (m170) REVERT: B 44 LEU cc_start: -0.0317 (OUTLIER) cc_final: -0.0973 (mm) REVERT: B 61 HIS cc_start: 0.2273 (m170) cc_final: 0.1911 (m170) REVERT: C 22 LEU cc_start: 0.2406 (OUTLIER) cc_final: 0.2114 (mt) REVERT: C 44 LEU cc_start: -0.0408 (OUTLIER) cc_final: -0.1032 (mm) REVERT: C 61 HIS cc_start: 0.2266 (m170) cc_final: 0.1932 (m170) REVERT: D 44 LEU cc_start: -0.0395 (OUTLIER) cc_final: -0.1019 (mm) REVERT: E 22 LEU cc_start: 0.2351 (OUTLIER) cc_final: 0.1927 (mt) REVERT: F 44 LEU cc_start: -0.0366 (OUTLIER) cc_final: -0.1002 (mm) REVERT: F 61 HIS cc_start: 0.2194 (m170) cc_final: 0.1864 (m170) REVERT: G 22 LEU cc_start: 0.2396 (OUTLIER) cc_final: 0.2136 (mt) REVERT: G 44 LEU cc_start: -0.0379 (OUTLIER) cc_final: -0.1047 (mm) REVERT: G 61 HIS cc_start: 0.2313 (m170) cc_final: 0.1954 (m170) REVERT: H 22 LEU cc_start: 0.2405 (OUTLIER) cc_final: 0.1925 (mt) REVERT: H 44 LEU cc_start: -0.0350 (OUTLIER) cc_final: -0.1011 (mm) REVERT: I 22 LEU cc_start: 0.2310 (OUTLIER) cc_final: 0.2063 (mt) REVERT: I 44 LEU cc_start: -0.0307 (OUTLIER) cc_final: -0.0972 (mm) REVERT: I 61 HIS cc_start: 0.2242 (m170) cc_final: 0.1881 (m170) REVERT: J 22 LEU cc_start: 0.2385 (OUTLIER) cc_final: 0.2114 (mt) REVERT: J 44 LEU cc_start: -0.0370 (OUTLIER) cc_final: -0.1012 (mm) REVERT: J 61 HIS cc_start: 0.2293 (m170) cc_final: 0.1988 (m170) REVERT: K 22 LEU cc_start: 0.2322 (OUTLIER) cc_final: 0.1913 (mt) REVERT: L 22 LEU cc_start: 0.2444 (OUTLIER) cc_final: 0.2160 (mt) REVERT: L 44 LEU cc_start: -0.0340 (OUTLIER) cc_final: -0.0994 (mm) REVERT: L 61 HIS cc_start: 0.2301 (m170) cc_final: 0.1971 (m170) REVERT: M 22 LEU cc_start: 0.2362 (OUTLIER) cc_final: 0.2087 (mt) REVERT: M 44 LEU cc_start: -0.0311 (OUTLIER) cc_final: -0.0946 (mm) REVERT: N 22 LEU cc_start: 0.2364 (OUTLIER) cc_final: 0.2104 (mt) REVERT: N 44 LEU cc_start: -0.0354 (OUTLIER) cc_final: -0.1006 (mm) REVERT: O 22 LEU cc_start: 0.2408 (OUTLIER) cc_final: 0.2140 (mt) REVERT: O 44 LEU cc_start: -0.0364 (OUTLIER) cc_final: -0.0993 (mm) REVERT: O 61 HIS cc_start: 0.2304 (m170) cc_final: 0.1920 (m170) REVERT: P 22 LEU cc_start: 0.2324 (OUTLIER) cc_final: 0.2049 (mt) REVERT: P 44 LEU cc_start: -0.0350 (OUTLIER) cc_final: -0.0985 (mm) REVERT: Q 22 LEU cc_start: 0.2425 (OUTLIER) cc_final: 0.2146 (mt) REVERT: Q 44 LEU cc_start: -0.0339 (OUTLIER) cc_final: -0.0984 (mm) REVERT: Q 61 HIS cc_start: 0.2293 (m170) cc_final: 0.1949 (m170) REVERT: R 22 LEU cc_start: 0.2400 (OUTLIER) cc_final: 0.2132 (mt) REVERT: R 44 LEU cc_start: -0.0338 (OUTLIER) cc_final: -0.0977 (mm) REVERT: R 61 HIS cc_start: 0.2325 (m170) cc_final: 0.1973 (m170) REVERT: S 22 LEU cc_start: 0.2391 (OUTLIER) cc_final: 0.2117 (mt) REVERT: S 44 LEU cc_start: -0.0213 (OUTLIER) cc_final: -0.1097 (mm) REVERT: S 61 HIS cc_start: 0.2281 (m170) cc_final: 0.1956 (m170) REVERT: T 22 LEU cc_start: 0.2369 (OUTLIER) cc_final: 0.2101 (mt) REVERT: T 44 LEU cc_start: -0.0386 (OUTLIER) cc_final: -0.1009 (mm) REVERT: T 134 LEU cc_start: -0.0794 (OUTLIER) cc_final: -0.1000 (mt) REVERT: V 22 LEU cc_start: 0.2328 (OUTLIER) cc_final: 0.2067 (mt) REVERT: V 44 LEU cc_start: -0.0326 (OUTLIER) cc_final: -0.0978 (mm) REVERT: W 22 LEU cc_start: 0.2406 (OUTLIER) cc_final: 0.2151 (mt) REVERT: W 44 LEU cc_start: -0.0309 (OUTLIER) cc_final: -0.0959 (mm) REVERT: W 61 HIS cc_start: 0.2321 (m170) cc_final: 0.1944 (m170) REVERT: W 134 LEU cc_start: -0.0861 (OUTLIER) cc_final: -0.1061 (mt) REVERT: X 22 LEU cc_start: 0.2366 (OUTLIER) cc_final: 0.2108 (mt) REVERT: X 61 HIS cc_start: 0.2533 (m170) cc_final: 0.2293 (m90) outliers start: 116 outliers final: 42 residues processed: 272 average time/residue: 1.0904 time to fit residues: 379.4487 Evaluate side-chains 257 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 173 time to evaluate : 3.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 149 THR Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 22 LEU 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 33 MET Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 68 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 D residue 44 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 33 MET Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 68 LEU 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 H residue 22 LEU Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain H residue 44 LEU 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 I residue 68 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 K residue 22 LEU Chi-restraints excluded: chain K residue 33 MET 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 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 68 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 33 MET Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain P residue 7 ASN Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 33 MET Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 68 LEU 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 R residue 22 LEU Chi-restraints excluded: chain R residue 33 MET Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain S residue 7 ASN Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 33 MET Chi-restraints excluded: chain S residue 44 LEU 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 68 LEU Chi-restraints excluded: chain T residue 134 LEU 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 68 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 134 LEU Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 33 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 293 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 336 optimal weight: 0.9990 chunk 272 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 6.9990 chunk 353 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 overall best weight: 0.7596 ------------------------------------------------------------------------------- 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** A 7 ASN A 19 GLN B 7 ASN B 19 GLN C 7 ASN C 19 GLN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN F 7 ASN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN K 7 ASN K 19 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN M 19 GLN ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 19 GLN ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 GLN P 7 ASN P 19 GLN ** Q 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 GLN S 7 ASN S 19 GLN ** T 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 GLN ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN ** W 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 19 GLN ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.238505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.230459 restraints weight = 223831.053| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 3.86 r_work: 0.3949 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1011 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 33912 Z= 0.112 Angle : 0.548 11.075 45792 Z= 0.279 Chirality : 0.036 0.161 4896 Planarity : 0.003 0.038 6024 Dihedral : 4.207 17.515 4464 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.25 % Allowed : 6.03 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.04 (0.13), residues: 4080 helix: 3.38 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : -0.29 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 89 HIS 0.004 0.001 HIS X 61 PHE 0.009 0.001 PHE B 37 TYR 0.021 0.002 TYR D 164 ARG 0.003 0.000 ARG M 5 Details of bonding type rmsd hydrogen bonds : bond 0.03096 ( 2637) hydrogen bonds : angle 3.40606 ( 7911) covalent geometry : bond 0.00224 (33912) covalent geometry : angle 0.54847 (45792) *********************** 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 299 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 186 time to evaluate : 3.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 96 MET cc_start: 0.0120 (mmp) cc_final: -0.1026 (mmp) REVERT: A 22 LEU cc_start: 0.2358 (OUTLIER) cc_final: 0.2088 (mt) REVERT: B 44 LEU cc_start: -0.0308 (OUTLIER) cc_final: -0.0946 (mm) REVERT: C 22 LEU cc_start: 0.2462 (OUTLIER) cc_final: 0.2129 (mt) REVERT: C 44 LEU cc_start: -0.0356 (OUTLIER) cc_final: -0.0942 (mm) REVERT: D 44 LEU cc_start: -0.0343 (OUTLIER) cc_final: -0.0916 (mm) REVERT: E 22 LEU cc_start: 0.2413 (OUTLIER) cc_final: 0.1940 (mt) REVERT: E 66 MET cc_start: 0.0594 (ttm) cc_final: 0.0365 (ptp) REVERT: F 44 LEU cc_start: -0.0329 (OUTLIER) cc_final: -0.0937 (mm) REVERT: G 22 LEU cc_start: 0.2452 (OUTLIER) cc_final: 0.2167 (mt) REVERT: G 44 LEU cc_start: -0.0334 (OUTLIER) cc_final: -0.0995 (mm) REVERT: H 22 LEU cc_start: 0.2474 (OUTLIER) cc_final: 0.2127 (mt) REVERT: H 44 LEU cc_start: -0.0318 (OUTLIER) cc_final: -0.0934 (mm) REVERT: I 22 LEU cc_start: 0.2339 (OUTLIER) cc_final: 0.2055 (mt) REVERT: I 44 LEU cc_start: -0.0329 (OUTLIER) cc_final: -0.0947 (mm) REVERT: J 22 LEU cc_start: 0.2434 (OUTLIER) cc_final: 0.2125 (mt) REVERT: J 44 LEU cc_start: -0.0348 (OUTLIER) cc_final: -0.0957 (mm) REVERT: K 22 LEU cc_start: 0.2372 (OUTLIER) cc_final: 0.1917 (mt) REVERT: L 22 LEU cc_start: 0.2464 (OUTLIER) cc_final: 0.2151 (mt) REVERT: L 44 LEU cc_start: -0.0301 (OUTLIER) cc_final: -0.0911 (mm) REVERT: M 22 LEU cc_start: 0.2400 (OUTLIER) cc_final: 0.2091 (mt) REVERT: M 44 LEU cc_start: -0.0297 (OUTLIER) cc_final: -0.0894 (mm) REVERT: N 22 LEU cc_start: 0.2433 (OUTLIER) cc_final: 0.2101 (mt) REVERT: N 44 LEU cc_start: -0.0333 (OUTLIER) cc_final: -0.0932 (mm) REVERT: O 22 LEU cc_start: 0.2466 (OUTLIER) cc_final: 0.2166 (mt) REVERT: O 44 LEU cc_start: -0.0336 (OUTLIER) cc_final: -0.0943 (mm) REVERT: P 22 LEU cc_start: 0.2401 (OUTLIER) cc_final: 0.2059 (mt) REVERT: P 44 LEU cc_start: -0.0334 (OUTLIER) cc_final: -0.0928 (mm) REVERT: Q 22 LEU cc_start: 0.2466 (OUTLIER) cc_final: 0.2155 (mt) REVERT: Q 44 LEU cc_start: -0.0318 (OUTLIER) cc_final: -0.0913 (mm) REVERT: R 22 LEU cc_start: 0.2451 (OUTLIER) cc_final: 0.2153 (mt) REVERT: R 44 LEU cc_start: -0.0301 (OUTLIER) cc_final: -0.0910 (mm) REVERT: S 22 LEU cc_start: 0.2447 (OUTLIER) cc_final: 0.2135 (mt) REVERT: S 44 LEU cc_start: -0.0258 (OUTLIER) cc_final: -0.1075 (mm) REVERT: T 22 LEU cc_start: 0.2430 (OUTLIER) cc_final: 0.2119 (mt) REVERT: T 44 LEU cc_start: -0.0393 (OUTLIER) cc_final: -0.0939 (mm) REVERT: T 134 LEU cc_start: -0.0754 (OUTLIER) cc_final: -0.1010 (mt) REVERT: V 22 LEU cc_start: 0.2382 (OUTLIER) cc_final: 0.2083 (mt) REVERT: V 44 LEU cc_start: -0.0299 (OUTLIER) cc_final: -0.0915 (mm) REVERT: W 22 LEU cc_start: 0.2444 (OUTLIER) cc_final: 0.2153 (mt) REVERT: W 44 LEU cc_start: -0.0293 (OUTLIER) cc_final: -0.0913 (mm) REVERT: W 134 LEU cc_start: -0.0825 (OUTLIER) cc_final: -0.1027 (mt) REVERT: X 22 LEU cc_start: 0.2386 (OUTLIER) cc_final: 0.2106 (mt) REVERT: X 61 HIS cc_start: 0.2609 (m170) cc_final: 0.2228 (m90) outliers start: 113 outliers final: 27 residues processed: 266 average time/residue: 1.0214 time to fit residues: 347.5481 Evaluate side-chains 242 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 174 time to evaluate : 3.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 149 THR Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 22 LEU 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 68 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 D residue 44 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 154 MET Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 44 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 68 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain K residue 7 ASN 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 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 68 LEU 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 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 P residue 68 LEU Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 44 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 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 68 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 65 LEU Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 22 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 3.9990 chunk 355 optimal weight: 0.4980 chunk 77 optimal weight: 10.0000 chunk 231 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 394 optimal weight: 8.9990 chunk 327 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 32 optimal weight: 0.0470 chunk 130 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 overall best weight: 2.1084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 7 ASN U 19 GLN ** U 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 132 HIS ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 GLN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 ASN ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN K 7 ASN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN M 19 GLN ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 GLN ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 ASN P 19 GLN ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 GLN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 135 ASN ** S 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 19 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 GLN ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 137 GLN ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 GLN X 150 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.257126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.249733 restraints weight = 234610.588| |-----------------------------------------------------------------------------| r_work (start): 0.4473 rms_B_bonded: 3.86 r_work: 0.4156 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1246 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 33912 Z= 0.178 Angle : 0.689 12.045 45792 Z= 0.361 Chirality : 0.040 0.253 4896 Planarity : 0.004 0.038 6024 Dihedral : 4.596 17.151 4464 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.27 % Allowed : 8.33 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.13), residues: 4080 helix: 2.75 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -1.03 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 89 HIS 0.006 0.001 HIS T 132 PHE 0.010 0.002 PHE B 37 TYR 0.026 0.003 TYR V 164 ARG 0.004 0.001 ARG K 152 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 2637) hydrogen bonds : angle 3.74780 ( 7911) covalent geometry : bond 0.00374 (33912) covalent geometry : angle 0.68874 (45792) *********************** 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 268 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 189 time to evaluate : 3.288 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: U 61 HIS cc_start: 0.2391 (m170) cc_final: 0.2066 (m170) REVERT: A 22 LEU cc_start: 0.2801 (OUTLIER) cc_final: 0.2422 (mt) REVERT: A 61 HIS cc_start: 0.2403 (m170) cc_final: 0.2120 (m170) REVERT: B 44 LEU cc_start: -0.0113 (OUTLIER) cc_final: -0.1167 (mm) REVERT: B 61 HIS cc_start: 0.2394 (m170) cc_final: 0.2128 (m90) REVERT: B 96 MET cc_start: 0.0037 (mmp) cc_final: -0.1069 (mmp) REVERT: C 22 LEU cc_start: 0.2799 (OUTLIER) cc_final: 0.2381 (mp) REVERT: C 44 LEU cc_start: -0.0095 (OUTLIER) cc_final: -0.1134 (mm) REVERT: C 61 HIS cc_start: 0.2468 (m170) cc_final: 0.2211 (m90) REVERT: D 22 LEU cc_start: 0.2716 (OUTLIER) cc_final: 0.2499 (mp) REVERT: D 44 LEU cc_start: -0.0149 (OUTLIER) cc_final: -0.1154 (mm) REVERT: D 61 HIS cc_start: 0.2404 (m170) cc_final: 0.2081 (m170) REVERT: E 22 LEU cc_start: 0.2794 (OUTLIER) cc_final: 0.2337 (mp) REVERT: E 61 HIS cc_start: 0.2400 (m170) cc_final: 0.2087 (m170) REVERT: F 44 LEU cc_start: -0.0075 (OUTLIER) cc_final: -0.1134 (mm) REVERT: F 61 HIS cc_start: 0.2368 (m170) cc_final: 0.2088 (m170) REVERT: G 22 LEU cc_start: 0.2778 (OUTLIER) cc_final: 0.2402 (mp) REVERT: G 44 LEU cc_start: -0.0065 (OUTLIER) cc_final: -0.1190 (mm) REVERT: G 61 HIS cc_start: 0.2457 (m170) cc_final: 0.2158 (m170) REVERT: H 22 LEU cc_start: 0.2863 (OUTLIER) cc_final: 0.2406 (mp) REVERT: H 44 LEU cc_start: -0.0082 (OUTLIER) cc_final: -0.1161 (mm) REVERT: H 61 HIS cc_start: 0.2476 (m170) cc_final: 0.2130 (m170) REVERT: I 22 LEU cc_start: 0.2879 (OUTLIER) cc_final: 0.2431 (mt) REVERT: I 44 LEU cc_start: -0.0102 (OUTLIER) cc_final: -0.1137 (mm) REVERT: I 61 HIS cc_start: 0.2403 (m170) cc_final: 0.2139 (m170) REVERT: J 22 LEU cc_start: 0.2812 (OUTLIER) cc_final: 0.2382 (mt) REVERT: J 44 LEU cc_start: -0.0061 (OUTLIER) cc_final: -0.1111 (mm) REVERT: J 61 HIS cc_start: 0.2448 (m170) cc_final: 0.2161 (m170) REVERT: K 22 LEU cc_start: 0.2783 (OUTLIER) cc_final: 0.2355 (mp) REVERT: K 61 HIS cc_start: 0.2414 (m170) cc_final: 0.2069 (m170) REVERT: L 22 LEU cc_start: 0.2788 (OUTLIER) cc_final: 0.2401 (mp) REVERT: L 44 LEU cc_start: -0.0065 (OUTLIER) cc_final: -0.1103 (mm) REVERT: L 61 HIS cc_start: 0.2481 (m170) cc_final: 0.2179 (m170) REVERT: M 22 LEU cc_start: 0.2844 (OUTLIER) cc_final: 0.2435 (mt) REVERT: M 44 LEU cc_start: -0.0060 (OUTLIER) cc_final: -0.1095 (mm) REVERT: M 61 HIS cc_start: 0.2392 (m170) cc_final: 0.2123 (m170) REVERT: N 22 LEU cc_start: 0.2652 (OUTLIER) cc_final: 0.2313 (mp) REVERT: N 44 LEU cc_start: -0.0080 (OUTLIER) cc_final: -0.1113 (mm) REVERT: N 61 HIS cc_start: 0.2455 (m170) cc_final: 0.2200 (m170) REVERT: O 22 LEU cc_start: 0.2867 (OUTLIER) cc_final: 0.2463 (mp) REVERT: O 44 LEU cc_start: -0.0059 (OUTLIER) cc_final: -0.1102 (mm) REVERT: O 61 HIS cc_start: 0.2451 (m170) cc_final: 0.2095 (m170) REVERT: P 22 LEU cc_start: 0.2850 (OUTLIER) cc_final: 0.2458 (mp) REVERT: P 44 LEU cc_start: -0.0063 (OUTLIER) cc_final: -0.1103 (mm) REVERT: P 61 HIS cc_start: 0.2420 (m170) cc_final: 0.2105 (m170) REVERT: Q 22 LEU cc_start: 0.2834 (OUTLIER) cc_final: 0.2426 (mp) REVERT: Q 44 LEU cc_start: -0.0113 (OUTLIER) cc_final: -0.1157 (mm) REVERT: Q 61 HIS cc_start: 0.2529 (m170) cc_final: 0.2156 (m170) REVERT: R 22 LEU cc_start: 0.2755 (OUTLIER) cc_final: 0.2390 (mp) REVERT: R 44 LEU cc_start: -0.0010 (OUTLIER) cc_final: -0.1096 (mm) REVERT: R 61 HIS cc_start: 0.2505 (m170) cc_final: 0.2191 (m170) REVERT: S 22 LEU cc_start: 0.2783 (OUTLIER) cc_final: 0.2393 (mp) REVERT: S 44 LEU cc_start: 0.0128 (OUTLIER) cc_final: -0.1105 (mm) REVERT: S 61 HIS cc_start: 0.2476 (m170) cc_final: 0.2194 (m170) REVERT: T 22 LEU cc_start: 0.2864 (OUTLIER) cc_final: 0.2449 (mp) REVERT: T 44 LEU cc_start: -0.0131 (OUTLIER) cc_final: -0.1137 (mm) REVERT: T 61 HIS cc_start: 0.2373 (m170) cc_final: 0.2026 (m170) REVERT: V 22 LEU cc_start: 0.2815 (OUTLIER) cc_final: 0.2448 (mp) REVERT: V 44 LEU cc_start: -0.0018 (OUTLIER) cc_final: -0.1076 (mm) REVERT: V 61 HIS cc_start: 0.2389 (m170) cc_final: 0.2091 (m170) REVERT: W 22 LEU cc_start: 0.2829 (OUTLIER) cc_final: 0.2426 (mp) REVERT: W 44 LEU cc_start: -0.0038 (OUTLIER) cc_final: -0.1094 (mm) REVERT: W 61 HIS cc_start: 0.2493 (m170) cc_final: 0.2140 (m170) REVERT: W 134 LEU cc_start: -0.0677 (OUTLIER) cc_final: -0.0919 (mt) REVERT: X 22 LEU cc_start: 0.2722 (OUTLIER) cc_final: 0.2349 (mt) REVERT: X 61 HIS cc_start: 0.2999 (m170) cc_final: 0.2530 (m90) REVERT: X 66 MET cc_start: 0.0533 (ttm) cc_final: 0.0202 (ptt) outliers start: 79 outliers final: 24 residues processed: 253 average time/residue: 1.1007 time to fit residues: 352.5036 Evaluate side-chains 254 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 189 time to evaluate : 3.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 7 ASN Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 149 THR 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 E residue 22 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 154 MET Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 44 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 J residue 22 LEU Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain K residue 7 ASN 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 149 THR Chi-restraints excluded: chain L residue 154 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 68 LEU 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 149 THR 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 P residue 149 THR Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 44 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 68 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 W residue 22 LEU Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 149 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 288 optimal weight: 2.9990 chunk 223 optimal weight: 0.9990 chunk 332 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 393 optimal weight: 4.9990 chunk 246 optimal weight: 0.9990 chunk 239 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN ** 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 ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 19 GLN ** 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 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 ASN ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 ASN P 19 GLN ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 7 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 GLN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.269222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.262159 restraints weight = 245076.871| |-----------------------------------------------------------------------------| r_work (start): 0.4582 rms_B_bonded: 3.86 r_work: 0.4287 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1312 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33912 Z= 0.167 Angle : 0.671 9.773 45792 Z= 0.352 Chirality : 0.040 0.209 4896 Planarity : 0.004 0.043 6024 Dihedral : 4.580 19.510 4464 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.53 % Allowed : 9.34 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.13), residues: 4080 helix: 2.46 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -1.34 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP U 89 HIS 0.006 0.001 HIS T 132 PHE 0.013 0.002 PHE C 51 TYR 0.026 0.003 TYR E 164 ARG 0.003 0.000 ARG K 152 Details of bonding type rmsd hydrogen bonds : bond 0.03871 ( 2637) hydrogen bonds : angle 3.76116 ( 7911) covalent geometry : bond 0.00349 (33912) covalent geometry : angle 0.67127 (45792) *********************** 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 290 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 202 time to evaluate : 3.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 61 HIS cc_start: 0.2454 (m170) cc_final: 0.2165 (m90) REVERT: U 66 MET cc_start: 0.0534 (ttm) cc_final: 0.0210 (ptt) REVERT: U 96 MET cc_start: 0.0522 (mmp) cc_final: -0.1460 (mmp) REVERT: A 22 LEU cc_start: 0.2760 (OUTLIER) cc_final: 0.2457 (mt) REVERT: A 61 HIS cc_start: 0.2509 (m170) cc_final: 0.2209 (m90) REVERT: A 66 MET cc_start: 0.0665 (ttm) cc_final: 0.0276 (ptp) REVERT: B 44 LEU cc_start: 0.0063 (OUTLIER) cc_final: -0.1099 (mm) REVERT: B 61 HIS cc_start: 0.2522 (m170) cc_final: 0.2235 (m90) REVERT: B 66 MET cc_start: 0.0505 (ttm) cc_final: 0.0259 (ptp) REVERT: C 22 LEU cc_start: 0.2798 (OUTLIER) cc_final: 0.2442 (mp) REVERT: C 44 LEU cc_start: -0.0072 (OUTLIER) cc_final: -0.1110 (mm) REVERT: C 61 HIS cc_start: 0.2620 (m170) cc_final: 0.2263 (m90) REVERT: D 44 LEU cc_start: -0.0055 (OUTLIER) cc_final: -0.1106 (mm) REVERT: D 61 HIS cc_start: 0.2504 (m170) cc_final: 0.2183 (m90) REVERT: E 22 LEU cc_start: 0.2644 (OUTLIER) cc_final: 0.2138 (mt) REVERT: E 61 HIS cc_start: 0.2498 (m170) cc_final: 0.2220 (m170) REVERT: E 71 GLN cc_start: 0.1098 (OUTLIER) cc_final: 0.0315 (pt0) REVERT: F 44 LEU cc_start: -0.0003 (OUTLIER) cc_final: -0.1058 (mm) REVERT: F 61 HIS cc_start: 0.2479 (m170) cc_final: 0.2233 (m90) REVERT: G 22 LEU cc_start: 0.2848 (OUTLIER) cc_final: 0.2515 (mp) REVERT: G 44 LEU cc_start: 0.0171 (OUTLIER) cc_final: -0.0969 (mm) REVERT: G 61 HIS cc_start: 0.2634 (m170) cc_final: 0.2268 (m90) REVERT: G 66 MET cc_start: 0.0477 (ttm) cc_final: 0.0270 (ttm) REVERT: H 22 LEU cc_start: 0.2924 (OUTLIER) cc_final: 0.2532 (mt) REVERT: H 44 LEU cc_start: 0.0078 (OUTLIER) cc_final: -0.1061 (mm) REVERT: H 61 HIS cc_start: 0.2607 (m170) cc_final: 0.2239 (m90) REVERT: I 22 LEU cc_start: 0.2851 (OUTLIER) cc_final: 0.2483 (mp) REVERT: I 44 LEU cc_start: 0.0051 (OUTLIER) cc_final: -0.1026 (mm) REVERT: I 61 HIS cc_start: 0.2497 (m170) cc_final: 0.2233 (m90) REVERT: J 22 LEU cc_start: 0.2838 (OUTLIER) cc_final: 0.2471 (mp) REVERT: J 44 LEU cc_start: 0.0076 (OUTLIER) cc_final: -0.1077 (mm) REVERT: J 61 HIS cc_start: 0.2595 (m170) cc_final: 0.2281 (m90) REVERT: K 22 LEU cc_start: 0.2754 (OUTLIER) cc_final: 0.2403 (mp) REVERT: K 61 HIS cc_start: 0.2598 (m170) cc_final: 0.2183 (m170) REVERT: L 22 LEU cc_start: 0.2821 (OUTLIER) cc_final: 0.2470 (mp) REVERT: L 44 LEU cc_start: 0.0015 (OUTLIER) cc_final: -0.1087 (mm) REVERT: L 61 HIS cc_start: 0.2575 (m170) cc_final: 0.2334 (m90) REVERT: L 66 MET cc_start: 0.0461 (ttm) cc_final: 0.0261 (ttm) REVERT: M 22 LEU cc_start: 0.2778 (OUTLIER) cc_final: 0.2417 (mp) REVERT: M 44 LEU cc_start: 0.0015 (OUTLIER) cc_final: -0.1048 (mm) REVERT: M 61 HIS cc_start: 0.2479 (m170) cc_final: 0.2199 (m90) REVERT: N 22 LEU cc_start: 0.2751 (OUTLIER) cc_final: 0.2362 (mp) REVERT: N 33 MET cc_start: 0.0190 (mtt) cc_final: -0.0318 (mtp) REVERT: N 44 LEU cc_start: -0.0058 (OUTLIER) cc_final: -0.1138 (mm) REVERT: N 61 HIS cc_start: 0.2638 (m170) cc_final: 0.2288 (m90) REVERT: O 22 LEU cc_start: 0.2872 (OUTLIER) cc_final: 0.2494 (mp) REVERT: O 44 LEU cc_start: -0.0035 (OUTLIER) cc_final: -0.1137 (mm) REVERT: O 61 HIS cc_start: 0.2613 (m170) cc_final: 0.2254 (m90) REVERT: O 66 MET cc_start: 0.0485 (ttm) cc_final: 0.0268 (ttm) REVERT: P 22 LEU cc_start: 0.2792 (OUTLIER) cc_final: 0.2450 (mp) REVERT: P 44 LEU cc_start: 0.0048 (OUTLIER) cc_final: -0.1054 (mm) REVERT: P 61 HIS cc_start: 0.2536 (m170) cc_final: 0.2252 (m90) REVERT: Q 22 LEU cc_start: 0.2835 (OUTLIER) cc_final: 0.2481 (mp) REVERT: Q 44 LEU cc_start: -0.0022 (OUTLIER) cc_final: -0.1119 (mm) REVERT: Q 61 HIS cc_start: 0.2642 (m170) cc_final: 0.2268 (m90) REVERT: R 22 LEU cc_start: 0.2776 (OUTLIER) cc_final: 0.2473 (mp) REVERT: R 44 LEU cc_start: 0.0031 (OUTLIER) cc_final: -0.1079 (mm) REVERT: R 61 HIS cc_start: 0.2568 (m170) cc_final: 0.2281 (m90) REVERT: S 22 LEU cc_start: 0.2846 (OUTLIER) cc_final: 0.2457 (mp) REVERT: S 44 LEU cc_start: 0.0193 (OUTLIER) cc_final: -0.1006 (mm) REVERT: S 61 HIS cc_start: 0.2582 (m170) cc_final: 0.2320 (m170) REVERT: T 22 LEU cc_start: 0.2809 (OUTLIER) cc_final: 0.2469 (mp) REVERT: T 44 LEU cc_start: -0.0087 (OUTLIER) cc_final: -0.1147 (mm) REVERT: T 61 HIS cc_start: 0.2466 (m170) cc_final: 0.2140 (m90) REVERT: T 71 GLN cc_start: 0.1041 (OUTLIER) cc_final: 0.0373 (pt0) REVERT: V 22 LEU cc_start: 0.2809 (OUTLIER) cc_final: 0.2471 (mp) REVERT: V 44 LEU cc_start: 0.0036 (OUTLIER) cc_final: -0.1082 (mm) REVERT: V 61 HIS cc_start: 0.2522 (m170) cc_final: 0.2223 (m90) REVERT: W 22 LEU cc_start: 0.2828 (OUTLIER) cc_final: 0.2464 (mp) REVERT: W 44 LEU cc_start: 0.0021 (OUTLIER) cc_final: -0.1053 (mm) REVERT: W 61 HIS cc_start: 0.2653 (m170) cc_final: 0.2232 (m90) REVERT: W 66 MET cc_start: 0.0493 (ttm) cc_final: 0.0263 (ttm) REVERT: X 22 LEU cc_start: 0.2773 (OUTLIER) cc_final: 0.2442 (mp) REVERT: X 61 HIS cc_start: 0.3018 (m90) cc_final: 0.2470 (m90) REVERT: X 66 MET cc_start: 0.0385 (ttm) cc_final: -0.0251 (tpp) outliers start: 88 outliers final: 18 residues processed: 273 average time/residue: 1.0607 time to fit residues: 367.2768 Evaluate side-chains 260 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 201 time to evaluate : 3.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 149 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 154 MET Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 44 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 J residue 22 LEU Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 65 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 154 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 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 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 22 LEU Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 44 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 71 GLN 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 X residue 22 LEU Chi-restraints excluded: chain X residue 33 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 10.0000 chunk 157 optimal weight: 8.9990 chunk 234 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 250 optimal weight: 0.9980 chunk 267 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 309 optimal weight: 0.8980 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 ASN B 10 GLN B 19 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN ** 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** ** 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** ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 150 ASN N 7 ASN ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 GLN ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 7 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 7 ASN T 19 GLN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN ** 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** ** W 135 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.277749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.270658 restraints weight = 244278.065| |-----------------------------------------------------------------------------| r_work (start): 0.4653 rms_B_bonded: 3.84 r_work: 0.4379 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1379 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33912 Z= 0.183 Angle : 0.721 9.988 45792 Z= 0.375 Chirality : 0.042 0.339 4896 Planarity : 0.004 0.043 6024 Dihedral : 4.740 17.756 4464 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.98 % Allowed : 10.69 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.13), residues: 4080 helix: 2.24 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : -1.81 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP U 89 HIS 0.007 0.002 HIS T 132 PHE 0.014 0.002 PHE D 51 TYR 0.028 0.003 TYR A 164 ARG 0.005 0.000 ARG L 5 Details of bonding type rmsd hydrogen bonds : bond 0.04092 ( 2637) hydrogen bonds : angle 3.96338 ( 7911) covalent geometry : bond 0.00389 (33912) covalent geometry : angle 0.72105 (45792) *********************** 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 270 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 201 time to evaluate : 3.272 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: 0.2572 (m170) cc_final: 0.2266 (m90) REVERT: U 96 MET cc_start: 0.0588 (mmp) cc_final: -0.1443 (mmp) REVERT: A 22 LEU cc_start: 0.3000 (OUTLIER) cc_final: 0.2656 (mp) REVERT: A 61 HIS cc_start: 0.2612 (m170) cc_final: 0.2270 (m90) REVERT: A 66 MET cc_start: 0.0724 (ttm) cc_final: 0.0246 (ptp) REVERT: B 44 LEU cc_start: 0.0208 (OUTLIER) cc_final: -0.0989 (mm) REVERT: B 61 HIS cc_start: 0.2625 (m170) cc_final: 0.2305 (m90) REVERT: B 66 MET cc_start: 0.0426 (ttm) cc_final: 0.0176 (ptp) REVERT: B 96 MET cc_start: 0.0265 (mmp) cc_final: -0.1441 (mmp) REVERT: C 22 LEU cc_start: 0.2951 (OUTLIER) cc_final: 0.2574 (mp) REVERT: C 44 LEU cc_start: 0.0070 (OUTLIER) cc_final: -0.1115 (mm) REVERT: C 61 HIS cc_start: 0.2720 (m170) cc_final: 0.2342 (m90) REVERT: D 44 LEU cc_start: 0.0085 (OUTLIER) cc_final: -0.1035 (mm) REVERT: D 61 HIS cc_start: 0.2614 (m170) cc_final: 0.2235 (m90) REVERT: E 22 LEU cc_start: 0.2809 (OUTLIER) cc_final: 0.2368 (mp) REVERT: E 61 HIS cc_start: 0.2673 (m170) cc_final: 0.2321 (m170) REVERT: E 71 GLN cc_start: 0.1252 (OUTLIER) cc_final: 0.0427 (pt0) REVERT: F 44 LEU cc_start: 0.0139 (OUTLIER) cc_final: -0.0990 (mm) REVERT: F 61 HIS cc_start: 0.2584 (m170) cc_final: 0.2342 (m90) REVERT: G 22 LEU cc_start: 0.3003 (OUTLIER) cc_final: 0.2597 (mp) REVERT: G 44 LEU cc_start: 0.0203 (OUTLIER) cc_final: -0.0960 (mm) REVERT: G 61 HIS cc_start: 0.2700 (m170) cc_final: 0.2322 (m90) REVERT: H 22 LEU cc_start: 0.3024 (OUTLIER) cc_final: 0.2659 (mp) REVERT: H 44 LEU cc_start: 0.0272 (OUTLIER) cc_final: -0.1021 (mm) REVERT: H 61 HIS cc_start: 0.2673 (m170) cc_final: 0.2307 (m90) REVERT: I 22 LEU cc_start: 0.2909 (OUTLIER) cc_final: 0.2522 (mp) REVERT: I 44 LEU cc_start: 0.0158 (OUTLIER) cc_final: -0.1003 (mm) REVERT: I 61 HIS cc_start: 0.2581 (m170) cc_final: 0.2353 (m90) REVERT: J 22 LEU cc_start: 0.2864 (OUTLIER) cc_final: 0.2476 (mp) REVERT: J 44 LEU cc_start: 0.0220 (OUTLIER) cc_final: -0.1024 (mm) REVERT: J 61 HIS cc_start: 0.2688 (m170) cc_final: 0.2343 (m90) REVERT: K 22 LEU cc_start: 0.2707 (OUTLIER) cc_final: 0.2251 (mp) REVERT: K 61 HIS cc_start: 0.2600 (m170) cc_final: 0.2232 (m170) REVERT: L 22 LEU cc_start: 0.2898 (OUTLIER) cc_final: 0.2542 (mp) REVERT: L 44 LEU cc_start: 0.0185 (OUTLIER) cc_final: -0.0989 (mm) REVERT: L 61 HIS cc_start: 0.2676 (m170) cc_final: 0.2405 (m90) REVERT: M 22 LEU cc_start: 0.2709 (OUTLIER) cc_final: 0.2311 (mp) REVERT: M 44 LEU cc_start: 0.0205 (OUTLIER) cc_final: -0.0984 (mm) REVERT: M 61 HIS cc_start: 0.2663 (m170) cc_final: 0.2370 (m90) REVERT: M 66 MET cc_start: 0.1017 (ttm) cc_final: 0.0792 (ttm) REVERT: N 22 LEU cc_start: 0.2875 (OUTLIER) cc_final: 0.2472 (mp) REVERT: N 33 MET cc_start: 0.0375 (mtt) cc_final: -0.0198 (mtp) REVERT: N 44 LEU cc_start: 0.0129 (OUTLIER) cc_final: -0.1039 (mm) REVERT: N 61 HIS cc_start: 0.2662 (m170) cc_final: 0.2279 (m170) REVERT: O 22 LEU cc_start: 0.2939 (OUTLIER) cc_final: 0.2562 (mp) REVERT: O 44 LEU cc_start: 0.0121 (OUTLIER) cc_final: -0.1058 (mm) REVERT: O 61 HIS cc_start: 0.2673 (m170) cc_final: 0.2321 (m90) REVERT: P 22 LEU cc_start: 0.2880 (OUTLIER) cc_final: 0.2673 (mp) REVERT: P 44 LEU cc_start: 0.0218 (OUTLIER) cc_final: -0.0996 (mm) REVERT: P 61 HIS cc_start: 0.2615 (m170) cc_final: 0.2363 (m90) REVERT: Q 22 LEU cc_start: 0.2910 (OUTLIER) cc_final: 0.2529 (mp) REVERT: Q 44 LEU cc_start: 0.0181 (OUTLIER) cc_final: -0.1049 (mm) REVERT: Q 61 HIS cc_start: 0.2687 (m170) cc_final: 0.2327 (m90) REVERT: R 22 LEU cc_start: 0.2880 (OUTLIER) cc_final: 0.2533 (mp) REVERT: R 44 LEU cc_start: 0.0243 (OUTLIER) cc_final: -0.0950 (mm) REVERT: R 61 HIS cc_start: 0.2643 (m170) cc_final: 0.2368 (m90) REVERT: S 22 LEU cc_start: 0.2869 (OUTLIER) cc_final: 0.2483 (mp) REVERT: S 44 LEU cc_start: 0.0190 (OUTLIER) cc_final: -0.1047 (mm) REVERT: S 61 HIS cc_start: 0.2664 (m170) cc_final: 0.2378 (m90) REVERT: T 22 LEU cc_start: 0.2943 (OUTLIER) cc_final: 0.2564 (mp) REVERT: T 44 LEU cc_start: 0.0158 (OUTLIER) cc_final: -0.0973 (mm) REVERT: T 61 HIS cc_start: 0.2528 (m170) cc_final: 0.2200 (m90) REVERT: T 71 GLN cc_start: 0.1164 (OUTLIER) cc_final: 0.0534 (pt0) REVERT: V 22 LEU cc_start: 0.2902 (OUTLIER) cc_final: 0.2559 (mp) REVERT: V 44 LEU cc_start: 0.0211 (OUTLIER) cc_final: -0.0982 (mm) REVERT: V 61 HIS cc_start: 0.2637 (m170) cc_final: 0.2349 (m90) REVERT: W 22 LEU cc_start: 0.2907 (OUTLIER) cc_final: 0.2525 (mp) REVERT: W 44 LEU cc_start: 0.0181 (OUTLIER) cc_final: -0.0976 (mm) REVERT: W 61 HIS cc_start: 0.2779 (m170) cc_final: 0.2345 (m90) REVERT: X 22 LEU cc_start: 0.2886 (OUTLIER) cc_final: 0.2507 (mp) REVERT: X 61 HIS cc_start: 0.3137 (m90) cc_final: 0.2523 (m90) outliers start: 69 outliers final: 12 residues processed: 252 average time/residue: 1.1481 time to fit residues: 362.1496 Evaluate side-chains 253 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 200 time to evaluate : 3.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU 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 C residue 22 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 71 GLN Chi-restraints excluded: chain E residue 154 MET Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 LEU 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 I residue 7 ASN 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 154 MET Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 44 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 154 MET Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 154 MET Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 44 LEU 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 65 LEU Chi-restraints excluded: chain T residue 71 GLN Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain X residue 22 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 3.9990 chunk 376 optimal weight: 6.9990 chunk 343 optimal weight: 0.8980 chunk 366 optimal weight: 10.0000 chunk 220 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 287 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 331 optimal weight: 7.9990 chunk 346 optimal weight: 5.9990 chunk 365 optimal weight: 0.0270 overall best weight: 1.3640 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 ASN B 10 GLN B 19 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN ** 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** G 150 ASN 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** ** 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** M 7 ASN ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 7 ASN T 19 GLN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN ** 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** ** W 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 GLN ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.278878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.271915 restraints weight = 245566.719| |-----------------------------------------------------------------------------| r_work (start): 0.4673 rms_B_bonded: 3.85 r_work: 0.4394 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1311 moved from start: 0.6285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33912 Z= 0.145 Angle : 0.663 8.655 45792 Z= 0.338 Chirality : 0.040 0.337 4896 Planarity : 0.003 0.044 6024 Dihedral : 4.526 17.390 4464 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.33 % Allowed : 10.55 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.13), residues: 4080 helix: 2.50 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : -1.67 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP U 89 HIS 0.004 0.001 HIS T 132 PHE 0.009 0.001 PHE N 51 TYR 0.026 0.002 TYR A 35 ARG 0.002 0.000 ARG N 5 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 2637) hydrogen bonds : angle 3.79079 ( 7911) covalent geometry : bond 0.00300 (33912) covalent geometry : angle 0.66283 (45792) *********************** 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 278 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 197 time to evaluate : 3.592 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: U 61 HIS cc_start: 0.2589 (m170) cc_final: 0.2178 (m170) REVERT: U 96 MET cc_start: 0.0329 (mmp) cc_final: -0.1292 (mmp) REVERT: A 22 LEU cc_start: 0.2720 (OUTLIER) cc_final: 0.2487 (mp) REVERT: A 61 HIS cc_start: 0.2540 (m170) cc_final: 0.2206 (m90) REVERT: B 44 LEU cc_start: 0.0132 (OUTLIER) cc_final: -0.0952 (mm) REVERT: B 61 HIS cc_start: 0.2566 (m170) cc_final: 0.2222 (m90) REVERT: B 66 MET cc_start: 0.0379 (ttm) cc_final: 0.0117 (ptp) REVERT: B 154 MET cc_start: 0.2221 (mmt) cc_final: 0.0371 (mmt) REVERT: C 22 LEU cc_start: 0.2793 (OUTLIER) cc_final: 0.2494 (mp) REVERT: C 44 LEU cc_start: -0.0005 (OUTLIER) cc_final: -0.1036 (mm) REVERT: C 61 HIS cc_start: 0.2656 (m170) cc_final: 0.2247 (m90) REVERT: D 44 LEU cc_start: 0.0049 (OUTLIER) cc_final: -0.0938 (mm) REVERT: D 61 HIS cc_start: 0.2562 (m170) cc_final: 0.2264 (m90) REVERT: D 66 MET cc_start: 0.0859 (OUTLIER) cc_final: 0.0244 (tpp) REVERT: E 22 LEU cc_start: 0.2688 (OUTLIER) cc_final: 0.2257 (mp) REVERT: E 61 HIS cc_start: 0.2703 (m170) cc_final: 0.2236 (m170) REVERT: E 66 MET cc_start: 0.0764 (ttm) cc_final: 0.0443 (ptp) REVERT: F 44 LEU cc_start: 0.0025 (OUTLIER) cc_final: -0.0981 (mm) REVERT: F 61 HIS cc_start: 0.2518 (m170) cc_final: 0.2294 (m90) REVERT: F 66 MET cc_start: 0.1012 (OUTLIER) cc_final: 0.0368 (tpp) REVERT: G 22 LEU cc_start: 0.2750 (OUTLIER) cc_final: 0.2491 (mp) REVERT: G 44 LEU cc_start: 0.0127 (OUTLIER) cc_final: -0.0882 (mm) REVERT: G 61 HIS cc_start: 0.2645 (m170) cc_final: 0.2354 (m90) REVERT: H 22 LEU cc_start: 0.2786 (OUTLIER) cc_final: 0.2471 (mp) REVERT: H 44 LEU cc_start: 0.0220 (OUTLIER) cc_final: -0.0943 (mm) REVERT: H 61 HIS cc_start: 0.2638 (m170) cc_final: 0.2290 (m90) REVERT: I 22 LEU cc_start: 0.2757 (OUTLIER) cc_final: 0.2413 (mp) REVERT: I 44 LEU cc_start: 0.0092 (OUTLIER) cc_final: -0.0941 (mm) REVERT: I 61 HIS cc_start: 0.2573 (m170) cc_final: 0.2289 (m90) REVERT: I 66 MET cc_start: 0.0802 (OUTLIER) cc_final: 0.0310 (tpp) REVERT: J 22 LEU cc_start: 0.2825 (OUTLIER) cc_final: 0.2441 (mp) REVERT: J 44 LEU cc_start: 0.0168 (OUTLIER) cc_final: -0.0990 (mm) REVERT: J 61 HIS cc_start: 0.2663 (m170) cc_final: 0.2325 (m90) REVERT: K 22 LEU cc_start: 0.2475 (OUTLIER) cc_final: 0.2137 (mp) REVERT: K 61 HIS cc_start: 0.2578 (m170) cc_final: 0.2160 (m170) REVERT: L 22 LEU cc_start: 0.2825 (OUTLIER) cc_final: 0.2469 (mp) REVERT: L 44 LEU cc_start: 0.0058 (OUTLIER) cc_final: -0.0946 (mm) REVERT: L 61 HIS cc_start: 0.2636 (m170) cc_final: 0.2401 (m90) REVERT: M 22 LEU cc_start: 0.2613 (OUTLIER) cc_final: 0.2203 (mt) REVERT: M 44 LEU cc_start: 0.0083 (OUTLIER) cc_final: -0.0970 (mm) REVERT: M 61 HIS cc_start: 0.2645 (m170) cc_final: 0.2356 (m90) REVERT: N 22 LEU cc_start: 0.2749 (OUTLIER) cc_final: 0.2367 (mp) REVERT: N 44 LEU cc_start: 0.0027 (OUTLIER) cc_final: -0.0973 (mm) REVERT: N 61 HIS cc_start: 0.2699 (m170) cc_final: 0.2266 (m170) REVERT: O 22 LEU cc_start: 0.2818 (OUTLIER) cc_final: 0.2496 (mp) REVERT: O 44 LEU cc_start: -0.0010 (OUTLIER) cc_final: -0.1008 (mm) REVERT: O 61 HIS cc_start: 0.2652 (m170) cc_final: 0.2286 (m90) REVERT: P 22 LEU cc_start: 0.2753 (OUTLIER) cc_final: 0.2447 (mp) REVERT: P 44 LEU cc_start: 0.0102 (OUTLIER) cc_final: -0.0898 (mm) REVERT: P 61 HIS cc_start: 0.2625 (m170) cc_final: 0.2297 (m90) REVERT: Q 22 LEU cc_start: 0.2876 (OUTLIER) cc_final: 0.2490 (mp) REVERT: Q 44 LEU cc_start: 0.0122 (OUTLIER) cc_final: -0.0935 (mm) REVERT: Q 61 HIS cc_start: 0.2682 (m170) cc_final: 0.2233 (m90) REVERT: R 22 LEU cc_start: 0.2792 (OUTLIER) cc_final: 0.2483 (mp) REVERT: R 44 LEU cc_start: 0.0092 (OUTLIER) cc_final: -0.0910 (mm) REVERT: R 61 HIS cc_start: 0.2623 (m170) cc_final: 0.2314 (m90) REVERT: S 22 LEU cc_start: 0.2879 (OUTLIER) cc_final: 0.2514 (mp) REVERT: S 44 LEU cc_start: 0.0059 (OUTLIER) cc_final: -0.1045 (mm) REVERT: S 61 HIS cc_start: 0.2686 (m170) cc_final: 0.2337 (m90) REVERT: T 22 LEU cc_start: 0.2703 (OUTLIER) cc_final: 0.2414 (mp) REVERT: T 44 LEU cc_start: -0.0000 (OUTLIER) cc_final: -0.1028 (mm) REVERT: T 61 HIS cc_start: 0.2501 (m170) cc_final: 0.2147 (m90) REVERT: T 71 GLN cc_start: 0.1025 (OUTLIER) cc_final: 0.0331 (pt0) REVERT: V 22 LEU cc_start: 0.2784 (OUTLIER) cc_final: 0.2436 (mp) REVERT: V 44 LEU cc_start: 0.0081 (OUTLIER) cc_final: -0.0981 (mm) REVERT: V 61 HIS cc_start: 0.2589 (m170) cc_final: 0.2181 (m90) REVERT: W 22 LEU cc_start: 0.2847 (OUTLIER) cc_final: 0.2497 (mp) REVERT: W 44 LEU cc_start: 0.0077 (OUTLIER) cc_final: -0.0930 (mm) REVERT: W 61 HIS cc_start: 0.2731 (m170) cc_final: 0.2343 (m90) REVERT: X 22 LEU cc_start: 0.2741 (OUTLIER) cc_final: 0.2410 (mp) REVERT: X 61 HIS cc_start: 0.3056 (m90) cc_final: 0.2413 (m90) outliers start: 81 outliers final: 13 residues processed: 241 average time/residue: 1.6948 time to fit residues: 502.2324 Evaluate side-chains 252 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 196 time to evaluate : 3.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 149 THR Chi-restraints excluded: chain A residue 22 LEU 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 C residue 22 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 154 MET Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 LEU 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 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 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 154 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 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 P residue 22 LEU Chi-restraints excluded: chain P residue 44 LEU 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 R residue 22 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 44 LEU 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 65 LEU Chi-restraints excluded: chain T residue 71 GLN Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 154 MET Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain X residue 22 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 8.9990 chunk 387 optimal weight: 3.9990 chunk 236 optimal weight: 0.2980 chunk 183 optimal weight: 5.9990 chunk 269 optimal weight: 1.9990 chunk 406 optimal weight: 1.9990 chunk 374 optimal weight: 0.5980 chunk 323 optimal weight: 0.9980 chunk 33 optimal weight: 0.0980 chunk 250 optimal weight: 0.9990 chunk 198 optimal weight: 7.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 ASN B 19 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 7 ASN T 19 GLN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN ** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.272517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.270226 restraints weight = 22967.082| |-----------------------------------------------------------------------------| r_work (start): 0.4713 rms_B_bonded: 0.13 r_work: 0.4645 rms_B_bonded: 0.71 restraints_weight: 0.5000 r_work: 0.4564 rms_B_bonded: 1.82 restraints_weight: 0.2500 r_work: 0.4482 rms_B_bonded: 3.31 restraints_weight: 0.1250 r_work (final): 0.4482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1225 moved from start: 0.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 33912 Z= 0.121 Angle : 0.639 9.173 45792 Z= 0.321 Chirality : 0.038 0.310 4896 Planarity : 0.003 0.046 6024 Dihedral : 4.341 19.573 4464 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.87 % Allowed : 11.47 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.13), residues: 4080 helix: 2.84 (0.09), residues: 3168 sheet: None (None), residues: 0 loop : -1.46 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP V 89 HIS 0.004 0.001 HIS B 124 PHE 0.008 0.001 PHE Q 37 TYR 0.020 0.002 TYR A 35 ARG 0.004 0.000 ARG Q 5 Details of bonding type rmsd hydrogen bonds : bond 0.03270 ( 2637) hydrogen bonds : angle 3.71499 ( 7911) covalent geometry : bond 0.00241 (33912) covalent geometry : angle 0.63866 (45792) ********************** 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 250 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 185 time to evaluate : 3.341 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: U 61 HIS cc_start: 0.2543 (m170) cc_final: 0.2091 (m170) REVERT: U 96 MET cc_start: 0.0611 (mmp) cc_final: -0.1325 (mmp) REVERT: A 22 LEU cc_start: 0.2614 (OUTLIER) cc_final: 0.2342 (mt) REVERT: A 61 HIS cc_start: 0.2531 (m170) cc_final: 0.2101 (m90) REVERT: B 44 LEU cc_start: -0.0042 (OUTLIER) cc_final: -0.0908 (mm) REVERT: B 61 HIS cc_start: 0.2541 (m170) cc_final: 0.2163 (m90) REVERT: B 66 MET cc_start: 0.0373 (ttm) cc_final: 0.0157 (ptp) REVERT: B 154 MET cc_start: 0.2058 (mmt) cc_final: 0.0198 (mmt) REVERT: C 22 LEU cc_start: 0.2636 (OUTLIER) cc_final: 0.2320 (mp) REVERT: C 44 LEU cc_start: -0.0258 (OUTLIER) cc_final: -0.0986 (mm) REVERT: D 44 LEU cc_start: -0.0257 (OUTLIER) cc_final: -0.0951 (mm) REVERT: D 61 HIS cc_start: 0.2565 (m170) cc_final: 0.2199 (m90) REVERT: D 66 MET cc_start: 0.1022 (OUTLIER) cc_final: 0.0326 (tpp) REVERT: D 96 MET cc_start: -0.0136 (mmp) cc_final: -0.1108 (mmp) REVERT: E 22 LEU cc_start: 0.2579 (OUTLIER) cc_final: 0.2127 (mp) REVERT: F 44 LEU cc_start: -0.0128 (OUTLIER) cc_final: -0.0920 (mm) REVERT: F 61 HIS cc_start: 0.2563 (m170) cc_final: 0.2216 (m90) REVERT: G 22 LEU cc_start: 0.2492 (OUTLIER) cc_final: 0.2141 (mt) REVERT: G 44 LEU cc_start: -0.0007 (OUTLIER) cc_final: -0.0829 (mm) REVERT: G 61 HIS cc_start: 0.2695 (m170) cc_final: 0.2277 (m90) REVERT: H 22 LEU cc_start: 0.2515 (OUTLIER) cc_final: 0.2142 (mt) REVERT: H 44 LEU cc_start: -0.0016 (OUTLIER) cc_final: -0.0896 (mm) REVERT: H 61 HIS cc_start: 0.2678 (m170) cc_final: 0.2280 (m90) REVERT: I 22 LEU cc_start: 0.2555 (OUTLIER) cc_final: 0.2264 (mt) REVERT: I 44 LEU cc_start: -0.0074 (OUTLIER) cc_final: -0.0920 (mm) REVERT: I 61 HIS cc_start: 0.2557 (m170) cc_final: 0.2230 (m90) REVERT: J 22 LEU cc_start: 0.2635 (OUTLIER) cc_final: 0.2288 (mt) REVERT: J 44 LEU cc_start: -0.0037 (OUTLIER) cc_final: -0.0918 (mm) REVERT: K 22 LEU cc_start: 0.2463 (OUTLIER) cc_final: 0.2047 (mt) REVERT: L 22 LEU cc_start: 0.2650 (OUTLIER) cc_final: 0.2316 (mp) REVERT: L 44 LEU cc_start: -0.0128 (OUTLIER) cc_final: -0.0910 (mm) REVERT: M 22 LEU cc_start: 0.2615 (OUTLIER) cc_final: 0.2180 (mt) REVERT: M 44 LEU cc_start: -0.0099 (OUTLIER) cc_final: -0.0918 (mm) REVERT: M 61 HIS cc_start: 0.2676 (m170) cc_final: 0.2203 (m90) REVERT: N 22 LEU cc_start: 0.2592 (OUTLIER) cc_final: 0.2233 (mp) REVERT: N 44 LEU cc_start: -0.0314 (OUTLIER) cc_final: -0.1003 (mm) REVERT: N 61 HIS cc_start: 0.2730 (m170) cc_final: 0.2214 (m170) REVERT: N 65 LEU cc_start: 0.0525 (OUTLIER) cc_final: 0.0312 (mp) REVERT: O 22 LEU cc_start: 0.2655 (OUTLIER) cc_final: 0.2336 (mp) REVERT: O 44 LEU cc_start: -0.0077 (OUTLIER) cc_final: -0.0907 (mm) REVERT: P 44 LEU cc_start: -0.0026 (OUTLIER) cc_final: -0.0855 (mm) REVERT: P 61 HIS cc_start: 0.2558 (m170) cc_final: 0.2201 (m90) REVERT: Q 22 LEU cc_start: 0.2652 (OUTLIER) cc_final: 0.2354 (mp) REVERT: Q 44 LEU cc_start: -0.0059 (OUTLIER) cc_final: -0.0901 (mm) REVERT: R 22 LEU cc_start: 0.2648 (OUTLIER) cc_final: 0.2352 (mp) REVERT: R 44 LEU cc_start: -0.0122 (OUTLIER) cc_final: -0.0905 (mm) REVERT: R 61 HIS cc_start: 0.2660 (m170) cc_final: 0.2302 (m90) REVERT: S 22 LEU cc_start: 0.2620 (OUTLIER) cc_final: 0.2296 (mt) REVERT: S 44 LEU cc_start: -0.0076 (OUTLIER) cc_final: -0.1002 (mm) REVERT: T 22 LEU cc_start: 0.2580 (OUTLIER) cc_final: 0.2258 (mt) REVERT: T 44 LEU cc_start: -0.0270 (OUTLIER) cc_final: -0.1011 (mm) REVERT: T 61 HIS cc_start: 0.2485 (m170) cc_final: 0.2083 (m90) REVERT: V 22 LEU cc_start: 0.2614 (OUTLIER) cc_final: 0.2302 (mt) REVERT: V 44 LEU cc_start: -0.0126 (OUTLIER) cc_final: -0.0932 (mm) REVERT: V 61 HIS cc_start: 0.2554 (m170) cc_final: 0.2099 (m90) REVERT: V 154 MET cc_start: 0.2202 (OUTLIER) cc_final: 0.1507 (mmt) REVERT: W 22 LEU cc_start: 0.2684 (OUTLIER) cc_final: 0.2348 (mp) REVERT: W 44 LEU cc_start: -0.0116 (OUTLIER) cc_final: -0.0896 (mm) REVERT: X 22 LEU cc_start: 0.2424 (OUTLIER) cc_final: 0.2078 (mt) REVERT: X 61 HIS cc_start: 0.3116 (m90) cc_final: 0.2422 (m90) outliers start: 65 outliers final: 12 residues processed: 231 average time/residue: 1.1681 time to fit residues: 338.6871 Evaluate side-chains 234 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 181 time to evaluate : 3.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 149 THR Chi-restraints excluded: chain A residue 22 LEU 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 C residue 22 LEU Chi-restraints excluded: chain C residue 44 LEU 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 E residue 22 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 LEU 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 I residue 7 ASN 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 154 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 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 P residue 44 LEU 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 R residue 22 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 44 LEU 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 65 LEU Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 154 MET Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain X residue 22 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 44 optimal weight: 1.9990 chunk 267 optimal weight: 0.9990 chunk 343 optimal weight: 0.8980 chunk 386 optimal weight: 0.9980 chunk 210 optimal weight: 0.9980 chunk 281 optimal weight: 8.9990 chunk 211 optimal weight: 0.7980 chunk 368 optimal weight: 2.9990 chunk 237 optimal weight: 0.5980 chunk 345 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 ASN B 19 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 ** 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 3 GLN ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 7 ASN ** T 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 ASN ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.274193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.271852 restraints weight = 23036.727| |-----------------------------------------------------------------------------| r_work (start): 0.4727 rms_B_bonded: 0.13 r_work: 0.4661 rms_B_bonded: 0.69 restraints_weight: 0.5000 r_work: 0.4583 rms_B_bonded: 1.73 restraints_weight: 0.2500 r_work: 0.4500 rms_B_bonded: 3.23 restraints_weight: 0.1250 r_work (final): 0.4500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1247 moved from start: 0.6397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33912 Z= 0.127 Angle : 0.652 9.295 45792 Z= 0.330 Chirality : 0.038 0.284 4896 Planarity : 0.003 0.045 6024 Dihedral : 4.292 18.254 4464 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.87 % Allowed : 11.72 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.13), residues: 4080 helix: 2.97 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -1.25 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 89 HIS 0.004 0.001 HIS B 124 PHE 0.008 0.001 PHE D 51 TYR 0.020 0.002 TYR K 35 ARG 0.004 0.000 ARG M 5 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 2637) hydrogen bonds : angle 3.72997 ( 7911) covalent geometry : bond 0.00260 (33912) covalent geometry : angle 0.65248 (45792) =============================================================================== Job complete usr+sys time: 24414.11 seconds wall clock time: 424 minutes 29.65 seconds (25469.65 seconds total)