Starting phenix.real_space_refine on Sat Feb 17 17:37:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgq_21199/02_2024/6vgq_21199_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgq_21199/02_2024/6vgq_21199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgq_21199/02_2024/6vgq_21199.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgq_21199/02_2024/6vgq_21199.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgq_21199/02_2024/6vgq_21199_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vgq_21199/02_2024/6vgq_21199_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.021 sd= 0.336 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 119 5.16 5 C 12194 2.51 5 N 3290 2.21 5 O 3745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19348 Number of models: 1 Model: "" Number of chains: 21 Chain: "N" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "H" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "I" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "J" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "K" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "L" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "M" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "A" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1383 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "B" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1383 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "C" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1383 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "D" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1383 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "E" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1383 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "F" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1383 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "G" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1383 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "U" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 24 Unusual residues: {'0QE': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'TRANS': 2, None: 1} Not linked: pdbres="PHE U 3 " pdbres="0QE U 4 " Unresolved non-hydrogen bonds: 1 Chain: "O" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 24 Unusual residues: {'0QE': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'TRANS': 2, None: 1} Not linked: pdbres="PHE O 3 " pdbres="0QE O 4 " Unresolved non-hydrogen bonds: 1 Chain: "P" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 24 Unusual residues: {'0QE': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'TRANS': 2, None: 1} Not linked: pdbres="PHE P 3 " pdbres="0QE P 4 " Unresolved non-hydrogen bonds: 1 Chain: "Q" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 24 Unusual residues: {'0QE': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'TRANS': 2, None: 1} Not linked: pdbres="PHE Q 3 " pdbres="0QE Q 4 " Unresolved non-hydrogen bonds: 1 Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 24 Unusual residues: {'0QE': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'TRANS': 2, None: 1} Not linked: pdbres="PHE R 3 " pdbres="0QE R 4 " Unresolved non-hydrogen bonds: 1 Chain: "S" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 24 Unusual residues: {'0QE': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'TRANS': 2, None: 1} Not linked: pdbres="PHE S 3 " pdbres="0QE S 4 " Unresolved non-hydrogen bonds: 1 Chain: "T" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 24 Unusual residues: {'0QE': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'TRANS': 2, None: 1} Not linked: pdbres="PHE T 3 " pdbres="0QE T 4 " Unresolved non-hydrogen bonds: 1 Time building chain proxies: 9.92, per 1000 atoms: 0.51 Number of scatterers: 19348 At special positions: 0 Unit cell: (112.36, 114.48, 108.12, 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 119 16.00 O 3745 8.00 N 3290 7.00 C 12194 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 - 3.50 Amino acid : False - 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.23 Conformation dependent library (CDL) restraints added in 3.8 seconds 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4690 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 28 sheets defined 49.0% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'N' and resid 16 through 27 removed outlier: 3.505A pdb=" N GLU N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 54 Processing helix chain 'N' and resid 71 through 83 Processing helix chain 'N' and resid 99 through 105 Processing helix chain 'N' and resid 133 through 158 Processing helix chain 'N' and resid 162 through 170 removed outlier: 3.519A pdb=" N ASP N 170 " --> pdb=" O GLU N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 183 Processing helix chain 'H' and resid 16 through 27 removed outlier: 3.505A pdb=" N GLU H 27 " --> pdb=" O ARG H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 54 Processing helix chain 'H' and resid 71 through 83 Processing helix chain 'H' and resid 99 through 105 Processing helix chain 'H' and resid 133 through 158 Processing helix chain 'H' and resid 162 through 170 removed outlier: 3.519A pdb=" N ASP H 170 " --> pdb=" O GLU H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 183 Processing helix chain 'I' and resid 16 through 27 removed outlier: 3.505A pdb=" N GLU I 27 " --> pdb=" O ARG I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 54 Processing helix chain 'I' and resid 71 through 83 Processing helix chain 'I' and resid 99 through 105 Processing helix chain 'I' and resid 133 through 158 Processing helix chain 'I' and resid 162 through 170 removed outlier: 3.519A pdb=" N ASP I 170 " --> pdb=" O GLU I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 183 Processing helix chain 'J' and resid 16 through 27 removed outlier: 3.504A pdb=" N GLU J 27 " --> pdb=" O ARG J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 54 Processing helix chain 'J' and resid 71 through 83 Processing helix chain 'J' and resid 99 through 105 Processing helix chain 'J' and resid 133 through 158 Processing helix chain 'J' and resid 162 through 170 removed outlier: 3.519A pdb=" N ASP J 170 " --> pdb=" O GLU J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 183 Processing helix chain 'K' and resid 16 through 27 removed outlier: 3.506A pdb=" N GLU K 27 " --> pdb=" O ARG K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 54 Processing helix chain 'K' and resid 71 through 83 Processing helix chain 'K' and resid 99 through 105 Processing helix chain 'K' and resid 133 through 158 Processing helix chain 'K' and resid 162 through 170 removed outlier: 3.519A pdb=" N ASP K 170 " --> pdb=" O GLU K 166 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 183 Processing helix chain 'L' and resid 16 through 27 removed outlier: 3.505A pdb=" N GLU L 27 " --> pdb=" O ARG L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 54 Processing helix chain 'L' and resid 71 through 83 Processing helix chain 'L' and resid 99 through 105 Processing helix chain 'L' and resid 133 through 158 Processing helix chain 'L' and resid 162 through 170 removed outlier: 3.518A pdb=" N ASP L 170 " --> pdb=" O GLU L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 183 Processing helix chain 'M' and resid 16 through 27 removed outlier: 3.505A pdb=" N GLU M 27 " --> pdb=" O ARG M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 54 Processing helix chain 'M' and resid 71 through 83 Processing helix chain 'M' and resid 99 through 105 Processing helix chain 'M' and resid 133 through 158 Processing helix chain 'M' and resid 162 through 170 removed outlier: 3.519A pdb=" N ASP M 170 " --> pdb=" O GLU M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 183 Processing helix chain 'A' and resid 32 through 39 Processing helix chain 'A' and resid 50 through 66 Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 111 through 117 Processing helix chain 'A' and resid 147 through 172 removed outlier: 3.677A pdb=" N ILE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 184 removed outlier: 3.703A pdb=" N ASP A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 196 Processing helix chain 'B' and resid 32 through 39 Processing helix chain 'B' and resid 50 through 66 Processing helix chain 'B' and resid 83 through 95 Processing helix chain 'B' and resid 111 through 117 Processing helix chain 'B' and resid 147 through 172 removed outlier: 3.677A pdb=" N ILE B 152 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 184 removed outlier: 3.702A pdb=" N ASP B 184 " --> pdb=" O ARG B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 196 Processing helix chain 'C' and resid 32 through 39 Processing helix chain 'C' and resid 50 through 66 Processing helix chain 'C' and resid 83 through 95 Processing helix chain 'C' and resid 111 through 117 Processing helix chain 'C' and resid 147 through 172 removed outlier: 3.678A pdb=" N ILE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 184 removed outlier: 3.703A pdb=" N ASP C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 Processing helix chain 'D' and resid 32 through 39 Processing helix chain 'D' and resid 50 through 66 Processing helix chain 'D' and resid 83 through 95 Processing helix chain 'D' and resid 111 through 117 Processing helix chain 'D' and resid 147 through 172 removed outlier: 3.677A pdb=" N ILE D 152 " --> pdb=" O SER D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 removed outlier: 3.703A pdb=" N ASP D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 196 Processing helix chain 'E' and resid 32 through 39 Processing helix chain 'E' and resid 50 through 66 Processing helix chain 'E' and resid 83 through 95 Processing helix chain 'E' and resid 111 through 117 Processing helix chain 'E' and resid 147 through 172 removed outlier: 3.678A pdb=" N ILE E 152 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 184 removed outlier: 3.703A pdb=" N ASP E 184 " --> pdb=" O ARG E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 196 Processing helix chain 'F' and resid 32 through 39 Processing helix chain 'F' and resid 50 through 66 Processing helix chain 'F' and resid 83 through 95 Processing helix chain 'F' and resid 111 through 117 Processing helix chain 'F' and resid 147 through 172 removed outlier: 3.677A pdb=" N ILE F 152 " --> pdb=" O SER F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 184 removed outlier: 3.703A pdb=" N ASP F 184 " --> pdb=" O ARG F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 Processing helix chain 'G' and resid 32 through 39 Processing helix chain 'G' and resid 50 through 66 Processing helix chain 'G' and resid 83 through 95 Processing helix chain 'G' and resid 111 through 117 Processing helix chain 'G' and resid 147 through 172 removed outlier: 3.678A pdb=" N ILE G 152 " --> pdb=" O SER G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 184 removed outlier: 3.703A pdb=" N ASP G 184 " --> pdb=" O ARG G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 196 Processing sheet with id= A, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.228A pdb=" N SER N 61 " --> pdb=" O ILE N 30 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LEU N 32 " --> pdb=" O SER N 61 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR N 63 " --> pdb=" O LEU N 32 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS N 188 " --> pdb=" O ALA N 114 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 95 through 97 removed outlier: 6.761A pdb=" N ARG N 119 " --> pdb=" O ALA N 96 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 29 through 32 removed outlier: 6.228A pdb=" N SER H 61 " --> pdb=" O ILE H 30 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU H 32 " --> pdb=" O SER H 61 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR H 63 " --> pdb=" O LEU H 32 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS H 188 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 95 through 97 removed outlier: 6.761A pdb=" N ARG H 119 " --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'I' and resid 29 through 32 removed outlier: 6.228A pdb=" N SER I 61 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU I 32 " --> pdb=" O SER I 61 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR I 63 " --> pdb=" O LEU I 32 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS I 188 " --> pdb=" O ALA I 114 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'I' and resid 95 through 97 removed outlier: 6.760A pdb=" N ARG I 119 " --> pdb=" O ALA I 96 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 29 through 32 removed outlier: 6.228A pdb=" N SER J 61 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU J 32 " --> pdb=" O SER J 61 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR J 63 " --> pdb=" O LEU J 32 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS J 188 " --> pdb=" O ALA J 114 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 95 through 97 removed outlier: 6.761A pdb=" N ARG J 119 " --> pdb=" O ALA J 96 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.227A pdb=" N SER K 61 " --> pdb=" O ILE K 30 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU K 32 " --> pdb=" O SER K 61 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR K 63 " --> pdb=" O LEU K 32 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS K 188 " --> pdb=" O ALA K 114 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 95 through 97 removed outlier: 6.761A pdb=" N ARG K 119 " --> pdb=" O ALA K 96 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 29 through 32 removed outlier: 6.228A pdb=" N SER L 61 " --> pdb=" O ILE L 30 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU L 32 " --> pdb=" O SER L 61 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TYR L 63 " --> pdb=" O LEU L 32 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS L 188 " --> pdb=" O ALA L 114 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 95 through 97 removed outlier: 6.761A pdb=" N ARG L 119 " --> pdb=" O ALA L 96 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.228A pdb=" N SER M 61 " --> pdb=" O ILE M 30 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU M 32 " --> pdb=" O SER M 61 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR M 63 " --> pdb=" O LEU M 32 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS M 188 " --> pdb=" O ALA M 114 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'M' and resid 95 through 97 removed outlier: 6.761A pdb=" N ARG M 119 " --> pdb=" O ALA M 96 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 41 through 44 removed outlier: 6.489A pdb=" N THR A 73 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU A 44 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR A 75 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 107 through 109 removed outlier: 6.797A pdb=" N ARG A 131 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.490A pdb=" N THR B 73 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU B 44 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TYR B 75 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 107 through 109 removed outlier: 6.796A pdb=" N ARG B 131 " --> pdb=" O ALA B 108 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 41 through 44 removed outlier: 6.490A pdb=" N THR C 73 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU C 44 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TYR C 75 " --> pdb=" O LEU C 44 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 107 through 109 removed outlier: 6.796A pdb=" N ARG C 131 " --> pdb=" O ALA C 108 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 41 through 44 removed outlier: 6.490A pdb=" N THR D 73 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU D 44 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR D 75 " --> pdb=" O LEU D 44 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 107 through 109 removed outlier: 6.796A pdb=" N ARG D 131 " --> pdb=" O ALA D 108 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 41 through 44 removed outlier: 6.490A pdb=" N THR E 73 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU E 44 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR E 75 " --> pdb=" O LEU E 44 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 107 through 109 removed outlier: 6.796A pdb=" N ARG E 131 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 41 through 44 removed outlier: 6.490A pdb=" N THR F 73 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU F 44 " --> pdb=" O THR F 73 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR F 75 " --> pdb=" O LEU F 44 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 107 through 109 removed outlier: 6.796A pdb=" N ARG F 131 " --> pdb=" O ALA F 108 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 41 through 44 removed outlier: 6.490A pdb=" N THR G 73 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU G 44 " --> pdb=" O THR G 73 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR G 75 " --> pdb=" O LEU G 44 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 107 through 109 removed outlier: 6.796A pdb=" N ARG G 131 " --> pdb=" O ALA G 108 " (cutoff:3.500A) 966 hydrogen bonds defined for protein. 2856 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.22 Time building geometry restraints manager: 7.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6538 1.34 - 1.46: 3863 1.46 - 1.58: 8996 1.58 - 1.70: 0 1.70 - 1.81: 217 Bond restraints: 19614 Sorted by residual: bond pdb=" C PHE O 3 " pdb=" O PHE O 3 " ideal model delta sigma weight residual 1.231 1.429 -0.198 2.00e-02 2.50e+03 9.84e+01 bond pdb=" C PHE P 3 " pdb=" O PHE P 3 " ideal model delta sigma weight residual 1.231 1.429 -0.198 2.00e-02 2.50e+03 9.83e+01 bond pdb=" C PHE U 3 " pdb=" O PHE U 3 " ideal model delta sigma weight residual 1.231 1.429 -0.198 2.00e-02 2.50e+03 9.82e+01 bond pdb=" C PHE T 3 " pdb=" O PHE T 3 " ideal model delta sigma weight residual 1.231 1.429 -0.198 2.00e-02 2.50e+03 9.81e+01 bond pdb=" C PHE Q 3 " pdb=" O PHE Q 3 " ideal model delta sigma weight residual 1.231 1.429 -0.198 2.00e-02 2.50e+03 9.77e+01 ... (remaining 19609 not shown) Histogram of bond angle deviations from ideal: 100.20 - 107.08: 540 107.08 - 113.96: 11172 113.96 - 120.84: 9152 120.84 - 127.72: 5562 127.72 - 134.60: 83 Bond angle restraints: 26509 Sorted by residual: angle pdb=" CA PHE S 3 " pdb=" C PHE S 3 " pdb=" O PHE S 3 " ideal model delta sigma weight residual 120.80 104.72 16.08 1.70e+00 3.46e-01 8.95e+01 angle pdb=" CA PHE O 3 " pdb=" C PHE O 3 " pdb=" O PHE O 3 " ideal model delta sigma weight residual 120.80 104.72 16.08 1.70e+00 3.46e-01 8.94e+01 angle pdb=" CA PHE P 3 " pdb=" C PHE P 3 " pdb=" O PHE P 3 " ideal model delta sigma weight residual 120.80 104.73 16.07 1.70e+00 3.46e-01 8.93e+01 angle pdb=" CA PHE Q 3 " pdb=" C PHE Q 3 " pdb=" O PHE Q 3 " ideal model delta sigma weight residual 120.80 104.74 16.06 1.70e+00 3.46e-01 8.93e+01 angle pdb=" CA PHE T 3 " pdb=" C PHE T 3 " pdb=" O PHE T 3 " ideal model delta sigma weight residual 120.80 104.75 16.05 1.70e+00 3.46e-01 8.92e+01 ... (remaining 26504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.28: 11361 14.28 - 28.57: 448 28.57 - 42.85: 77 42.85 - 57.13: 35 57.13 - 71.41: 28 Dihedral angle restraints: 11949 sinusoidal: 4669 harmonic: 7280 Sorted by residual: dihedral pdb=" CA MET J 99 " pdb=" C MET J 99 " pdb=" N GLY J 100 " pdb=" CA GLY J 100 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA MET I 99 " pdb=" C MET I 99 " pdb=" N GLY I 100 " pdb=" CA GLY I 100 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA MET N 99 " pdb=" C MET N 99 " pdb=" N GLY N 100 " pdb=" CA GLY N 100 " ideal model delta harmonic sigma weight residual 180.00 161.31 18.69 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 11946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1869 0.033 - 0.066: 792 0.066 - 0.099: 323 0.099 - 0.132: 62 0.132 - 0.165: 34 Chirality restraints: 3080 Sorted by residual: chirality pdb=" CA ILE G 72 " pdb=" N ILE G 72 " pdb=" C ILE G 72 " pdb=" CB ILE G 72 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CA ILE E 72 " pdb=" N ILE E 72 " pdb=" C ILE E 72 " pdb=" CB ILE E 72 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA ILE A 72 " pdb=" N ILE A 72 " pdb=" C ILE A 72 " pdb=" CB ILE A 72 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.76e-01 ... (remaining 3077 not shown) Planarity restraints: 3444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 110 " -0.032 2.00e-02 2.50e+03 6.35e-02 4.03e+01 pdb=" C SER B 110 " 0.110 2.00e-02 2.50e+03 pdb=" O SER B 110 " -0.040 2.00e-02 2.50e+03 pdb=" N ALA B 111 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 110 " -0.032 2.00e-02 2.50e+03 6.34e-02 4.02e+01 pdb=" C SER C 110 " 0.110 2.00e-02 2.50e+03 pdb=" O SER C 110 " -0.040 2.00e-02 2.50e+03 pdb=" N ALA C 111 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 110 " -0.032 2.00e-02 2.50e+03 6.33e-02 4.00e+01 pdb=" C SER F 110 " 0.110 2.00e-02 2.50e+03 pdb=" O SER F 110 " -0.040 2.00e-02 2.50e+03 pdb=" N ALA F 111 " -0.038 2.00e-02 2.50e+03 ... (remaining 3441 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 14 2.05 - 2.76: 3125 2.76 - 3.47: 27951 3.47 - 4.19: 48436 4.19 - 4.90: 86046 Nonbonded interactions: 165572 Sorted by model distance: nonbonded pdb=" OG SER N 98 " pdb=" C PHE U 3 " model vdw 1.335 3.270 nonbonded pdb=" OG SER I 98 " pdb=" C PHE P 3 " model vdw 1.335 3.270 nonbonded pdb=" OG SER H 98 " pdb=" C PHE O 3 " model vdw 1.335 3.270 nonbonded pdb=" OG SER K 98 " pdb=" C PHE R 3 " model vdw 1.335 3.270 nonbonded pdb=" OG SER M 98 " pdb=" C PHE T 3 " model vdw 1.335 3.270 ... (remaining 165567 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 2.460 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 52.140 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.190 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.198 19614 Z= 0.374 Angle : 0.882 16.082 26509 Z= 0.526 Chirality : 0.044 0.165 3080 Planarity : 0.005 0.064 3444 Dihedral : 9.856 71.415 7259 Min Nonbonded Distance : 1.335 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.15), residues: 2485 helix: 0.66 (0.12), residues: 1407 sheet: 2.31 (0.32), residues: 168 loop : -0.04 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP N 174 HIS 0.008 0.003 HIS I 123 PHE 0.021 0.002 PHE C 83 TYR 0.011 0.001 TYR B 33 ARG 0.003 0.000 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 558 time to evaluate : 2.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 70 SER cc_start: 0.9120 (t) cc_final: 0.8886 (m) REVERT: H 55 ASP cc_start: 0.8491 (t0) cc_final: 0.8268 (t0) REVERT: H 70 SER cc_start: 0.8855 (t) cc_final: 0.8587 (m) REVERT: H 168 ASP cc_start: 0.8655 (m-30) cc_final: 0.8429 (m-30) REVERT: I 55 ASP cc_start: 0.8386 (t0) cc_final: 0.8110 (t0) REVERT: I 179 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6597 (mt-10) REVERT: J 55 ASP cc_start: 0.8333 (t0) cc_final: 0.7691 (t0) REVERT: J 75 MET cc_start: 0.9101 (mmp) cc_final: 0.8729 (mmt) REVERT: L 183 TYR cc_start: 0.8778 (t80) cc_final: 0.8318 (t80) REVERT: M 35 GLU cc_start: 0.7897 (tt0) cc_final: 0.7675 (tt0) REVERT: B 184 ASP cc_start: 0.7264 (t70) cc_final: 0.6933 (t0) REVERT: C 184 ASP cc_start: 0.7380 (t70) cc_final: 0.7147 (t0) REVERT: C 206 TYR cc_start: 0.6915 (m-80) cc_final: 0.6597 (m-10) REVERT: D 69 ASP cc_start: 0.7621 (m-30) cc_final: 0.7367 (m-30) REVERT: D 74 MET cc_start: 0.8421 (ttm) cc_final: 0.8201 (ttt) REVERT: D 129 ASN cc_start: 0.8555 (m-40) cc_final: 0.8229 (m110) REVERT: D 184 ASP cc_start: 0.7929 (t70) cc_final: 0.7664 (t0) REVERT: E 87 MET cc_start: 0.8314 (mmm) cc_final: 0.7924 (mmt) REVERT: F 34 ASN cc_start: 0.7889 (m-40) cc_final: 0.7576 (m110) REVERT: F 87 MET cc_start: 0.8493 (mmm) cc_final: 0.7994 (mmt) outliers start: 0 outliers final: 0 residues processed: 558 average time/residue: 0.2864 time to fit residues: 250.7484 Evaluate side-chains 405 residues out of total 2023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 7.9990 chunk 185 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 222 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 124 GLN H 160 GLN J 160 GLN K 160 GLN L 124 GLN M 124 GLN M 160 GLN C 101 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN E 101 GLN F 136 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19614 Z= 0.258 Angle : 0.578 9.797 26509 Z= 0.294 Chirality : 0.043 0.168 3080 Planarity : 0.004 0.049 3444 Dihedral : 4.665 20.814 2737 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.27 % Allowed : 8.11 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.87 (0.16), residues: 2485 helix: 1.95 (0.13), residues: 1393 sheet: 2.43 (0.37), residues: 168 loop : -0.06 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 174 HIS 0.007 0.001 HIS M 123 PHE 0.018 0.002 PHE T 3 TYR 0.012 0.001 TYR A 90 ARG 0.006 0.001 ARG C 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 419 time to evaluate : 2.135 Fit side-chains revert: symmetry clash REVERT: N 168 ASP cc_start: 0.8731 (m-30) cc_final: 0.8316 (m-30) REVERT: H 168 ASP cc_start: 0.8817 (m-30) cc_final: 0.8174 (m-30) REVERT: I 55 ASP cc_start: 0.8636 (t0) cc_final: 0.8141 (t0) REVERT: I 168 ASP cc_start: 0.8649 (m-30) cc_final: 0.8432 (m-30) REVERT: J 99 MET cc_start: 0.8226 (mmm) cc_final: 0.7885 (tpt) REVERT: J 163 GLU cc_start: 0.8565 (tp30) cc_final: 0.8274 (tp30) REVERT: L 183 TYR cc_start: 0.8721 (t80) cc_final: 0.8441 (t80) REVERT: A 164 MET cc_start: 0.7373 (ttp) cc_final: 0.7047 (ttt) REVERT: B 38 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7401 (mt-10) REVERT: B 86 LEU cc_start: 0.8608 (tp) cc_final: 0.8331 (tp) REVERT: C 146 GLN cc_start: 0.8371 (mt0) cc_final: 0.7924 (mt0) REVERT: C 149 ASP cc_start: 0.8213 (t0) cc_final: 0.7877 (t0) REVERT: D 74 MET cc_start: 0.8585 (ttm) cc_final: 0.8320 (ttt) REVERT: D 93 MET cc_start: 0.9213 (mtp) cc_final: 0.8990 (mtm) REVERT: D 136 GLN cc_start: 0.8481 (pm20) cc_final: 0.8143 (pt0) REVERT: E 37 PHE cc_start: 0.8243 (t80) cc_final: 0.7933 (t80) REVERT: E 95 TYR cc_start: 0.8450 (t80) cc_final: 0.8201 (t80) REVERT: F 74 MET cc_start: 0.8057 (ttm) cc_final: 0.7856 (ttp) REVERT: G 91 ASP cc_start: 0.8561 (m-30) cc_final: 0.8134 (m-30) REVERT: G 201 ASP cc_start: 0.8679 (m-30) cc_final: 0.8455 (m-30) outliers start: 46 outliers final: 30 residues processed: 444 average time/residue: 0.3058 time to fit residues: 206.0853 Evaluate side-chains 401 residues out of total 2023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 371 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 100 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 123 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 185 optimal weight: 0.9980 chunk 151 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 221 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 124 GLN H 42 ASN L 42 ASN L 160 GLN M 42 ASN M 124 GLN D 129 ASN F 129 ASN G 136 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19614 Z= 0.231 Angle : 0.515 8.008 26509 Z= 0.262 Chirality : 0.041 0.281 3080 Planarity : 0.004 0.044 3444 Dihedral : 4.374 21.743 2737 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.22 % Allowed : 10.58 % Favored : 87.20 % 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: 1.92 (0.16), residues: 2485 helix: 2.12 (0.13), residues: 1400 sheet: 1.92 (0.36), residues: 182 loop : -0.19 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 174 HIS 0.006 0.001 HIS M 123 PHE 0.015 0.002 PHE E 83 TYR 0.009 0.001 TYR A 197 ARG 0.005 0.000 ARG E 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 388 time to evaluate : 2.146 Fit side-chains REVERT: N 111 LYS cc_start: 0.8305 (mtpp) cc_final: 0.8047 (mtpt) REVERT: N 168 ASP cc_start: 0.8754 (m-30) cc_final: 0.8350 (m-30) REVERT: H 168 ASP cc_start: 0.8726 (m-30) cc_final: 0.8155 (m-30) REVERT: I 55 ASP cc_start: 0.8431 (t0) cc_final: 0.8174 (t0) REVERT: I 111 LYS cc_start: 0.8313 (mttt) cc_final: 0.8035 (mtpp) REVERT: J 26 SER cc_start: 0.8497 (m) cc_final: 0.8281 (t) REVERT: L 183 TYR cc_start: 0.8654 (t80) cc_final: 0.8432 (t80) REVERT: M 156 GLU cc_start: 0.8436 (tt0) cc_final: 0.8223 (tt0) REVERT: A 38 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7649 (mt-10) REVERT: A 39 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7996 (tp30) REVERT: A 60 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7671 (mm) REVERT: A 61 LEU cc_start: 0.7995 (mt) cc_final: 0.7677 (mp) REVERT: A 71 ASP cc_start: 0.7570 (t70) cc_final: 0.7093 (m-30) REVERT: B 38 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7604 (mt-10) REVERT: B 86 LEU cc_start: 0.8501 (tp) cc_final: 0.8287 (tp) REVERT: C 146 GLN cc_start: 0.8256 (mt0) cc_final: 0.8042 (mt0) REVERT: D 93 MET cc_start: 0.9186 (mtp) cc_final: 0.8910 (mtm) REVERT: D 136 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8170 (pt0) REVERT: E 37 PHE cc_start: 0.8257 (t80) cc_final: 0.7960 (t80) REVERT: E 99 ASP cc_start: 0.8005 (m-30) cc_final: 0.7784 (m-30) REVERT: G 57 MET cc_start: 0.8267 (mtm) cc_final: 0.7856 (mtm) outliers start: 45 outliers final: 31 residues processed: 411 average time/residue: 0.2799 time to fit residues: 180.1097 Evaluate side-chains 401 residues out of total 2023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 368 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 193 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 220 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 223 optimal weight: 0.9980 chunk 236 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 42 ASN N 124 GLN I 42 ASN J 42 ASN K 42 ASN L 124 GLN D 129 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19614 Z= 0.217 Angle : 0.488 7.048 26509 Z= 0.248 Chirality : 0.040 0.154 3080 Planarity : 0.003 0.038 3444 Dihedral : 4.269 22.207 2737 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.57 % Allowed : 12.21 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.87 (0.16), residues: 2485 helix: 2.09 (0.14), residues: 1407 sheet: 1.77 (0.36), residues: 182 loop : -0.22 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 174 HIS 0.004 0.001 HIS M 123 PHE 0.018 0.002 PHE G 83 TYR 0.012 0.001 TYR K 91 ARG 0.003 0.000 ARG E 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 387 time to evaluate : 2.408 Fit side-chains REVERT: N 111 LYS cc_start: 0.8264 (mtpp) cc_final: 0.8023 (mtpt) REVERT: N 168 ASP cc_start: 0.8748 (m-30) cc_final: 0.8387 (m-30) REVERT: H 168 ASP cc_start: 0.8732 (m-30) cc_final: 0.8356 (m-30) REVERT: J 57 SER cc_start: 0.8025 (m) cc_final: 0.7817 (m) REVERT: K 23 ARG cc_start: 0.8405 (mmm-85) cc_final: 0.8091 (mtp180) REVERT: A 38 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7831 (mt-10) REVERT: A 57 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.6628 (mpp) REVERT: A 60 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7771 (mm) REVERT: A 71 ASP cc_start: 0.7696 (t70) cc_final: 0.7318 (m-30) REVERT: B 38 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7782 (mt-10) REVERT: C 129 ASN cc_start: 0.8621 (m-40) cc_final: 0.8207 (m110) REVERT: C 136 GLN cc_start: 0.8736 (pt0) cc_final: 0.8486 (pt0) REVERT: C 146 GLN cc_start: 0.8290 (mt0) cc_final: 0.7946 (mt0) REVERT: D 136 GLN cc_start: 0.8473 (pm20) cc_final: 0.8219 (pt0) REVERT: D 206 TYR cc_start: 0.8814 (m-80) cc_final: 0.8596 (m-10) REVERT: E 37 PHE cc_start: 0.8340 (t80) cc_final: 0.8020 (t80) REVERT: E 99 ASP cc_start: 0.8044 (m-30) cc_final: 0.7773 (m-30) REVERT: F 164 MET cc_start: 0.7771 (ttp) cc_final: 0.7494 (ttp) REVERT: G 57 MET cc_start: 0.8461 (mtm) cc_final: 0.8076 (mtm) REVERT: G 201 ASP cc_start: 0.8650 (m-30) cc_final: 0.8397 (m-30) outliers start: 52 outliers final: 34 residues processed: 422 average time/residue: 0.2800 time to fit residues: 185.4883 Evaluate side-chains 403 residues out of total 2023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 367 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 193 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 197 optimal weight: 7.9990 chunk 134 optimal weight: 0.0980 chunk 3 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 202 optimal weight: 6.9990 chunk 163 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 124 GLN K 188 HIS ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 GLN E 94 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19614 Z= 0.128 Angle : 0.439 7.797 26509 Z= 0.223 Chirality : 0.039 0.138 3080 Planarity : 0.003 0.031 3444 Dihedral : 3.946 20.001 2737 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.78 % Allowed : 14.09 % Favored : 84.13 % 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: 2.05 (0.16), residues: 2485 helix: 2.25 (0.14), residues: 1407 sheet: 1.26 (0.34), residues: 217 loop : -0.08 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 174 HIS 0.003 0.001 HIS H 123 PHE 0.016 0.001 PHE G 83 TYR 0.011 0.001 TYR K 91 ARG 0.003 0.000 ARG E 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 374 time to evaluate : 2.122 Fit side-chains REVERT: N 168 ASP cc_start: 0.8754 (m-30) cc_final: 0.8382 (m-30) REVERT: H 168 ASP cc_start: 0.8659 (m-30) cc_final: 0.8286 (m-30) REVERT: J 168 ASP cc_start: 0.8669 (m-30) cc_final: 0.8315 (m-30) REVERT: K 23 ARG cc_start: 0.8393 (mmm-85) cc_final: 0.8060 (mtp180) REVERT: L 150 MET cc_start: 0.8244 (mmt) cc_final: 0.8032 (mmt) REVERT: M 156 GLU cc_start: 0.8429 (tt0) cc_final: 0.8189 (tt0) REVERT: M 182 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8334 (tm-30) REVERT: A 38 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7920 (mt-10) REVERT: A 57 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.6491 (mpp) REVERT: A 71 ASP cc_start: 0.7803 (t70) cc_final: 0.7416 (m-30) REVERT: B 38 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7786 (mt-10) REVERT: B 164 MET cc_start: 0.7356 (ttp) cc_final: 0.7129 (ttp) REVERT: D 136 GLN cc_start: 0.8474 (pm20) cc_final: 0.8206 (pt0) REVERT: E 37 PHE cc_start: 0.8279 (t80) cc_final: 0.8021 (t80) REVERT: E 99 ASP cc_start: 0.7996 (m-30) cc_final: 0.7770 (m-30) REVERT: F 37 PHE cc_start: 0.7930 (t80) cc_final: 0.7649 (t80) REVERT: F 164 MET cc_start: 0.7591 (ttp) cc_final: 0.7364 (ttp) outliers start: 36 outliers final: 20 residues processed: 394 average time/residue: 0.2924 time to fit residues: 178.9369 Evaluate side-chains 379 residues out of total 2023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 358 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 101 GLU Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain F residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 79 optimal weight: 4.9990 chunk 213 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 chunk 196 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 124 GLN L 160 GLN M 124 GLN D 101 GLN D 129 ASN E 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19614 Z= 0.199 Angle : 0.479 8.477 26509 Z= 0.238 Chirality : 0.040 0.143 3080 Planarity : 0.003 0.030 3444 Dihedral : 4.018 20.631 2737 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.93 % Favored : 97.99 % Rotamer: Outliers : 2.13 % Allowed : 13.79 % Favored : 84.08 % 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: 1.98 (0.16), residues: 2485 helix: 2.24 (0.14), residues: 1407 sheet: 1.00 (0.34), residues: 217 loop : -0.13 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 174 HIS 0.004 0.001 HIS H 123 PHE 0.016 0.001 PHE E 83 TYR 0.020 0.001 TYR N 113 ARG 0.003 0.000 ARG E 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 375 time to evaluate : 2.058 Fit side-chains revert: symmetry clash REVERT: N 168 ASP cc_start: 0.8759 (m-30) cc_final: 0.8390 (m-30) REVERT: N 169 SER cc_start: 0.9217 (p) cc_final: 0.9005 (t) REVERT: H 168 ASP cc_start: 0.8633 (m-30) cc_final: 0.8081 (m-30) REVERT: J 168 ASP cc_start: 0.8711 (m-30) cc_final: 0.8295 (m-30) REVERT: K 23 ARG cc_start: 0.8429 (mmm-85) cc_final: 0.8094 (mtp180) REVERT: L 15 SER cc_start: 0.5954 (m) cc_final: 0.5624 (t) REVERT: M 150 MET cc_start: 0.8375 (mmt) cc_final: 0.8143 (mmt) REVERT: M 156 GLU cc_start: 0.8458 (tt0) cc_final: 0.8214 (tt0) REVERT: M 182 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8345 (tm-30) REVERT: A 38 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7954 (mt-10) REVERT: A 57 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.6619 (mpp) REVERT: A 71 ASP cc_start: 0.7836 (t70) cc_final: 0.7538 (m-30) REVERT: B 55 ASP cc_start: 0.7878 (m-30) cc_final: 0.7623 (m-30) REVERT: C 146 GLN cc_start: 0.8362 (mt0) cc_final: 0.7995 (mt0) REVERT: D 136 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8266 (pt0) REVERT: E 37 PHE cc_start: 0.8314 (t80) cc_final: 0.8034 (t80) REVERT: E 99 ASP cc_start: 0.8029 (m-30) cc_final: 0.7795 (m-30) REVERT: F 164 MET cc_start: 0.7657 (ttp) cc_final: 0.7379 (ttp) REVERT: F 183 THR cc_start: 0.9029 (p) cc_final: 0.8689 (t) outliers start: 43 outliers final: 25 residues processed: 401 average time/residue: 0.2833 time to fit residues: 178.3928 Evaluate side-chains 394 residues out of total 2023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 367 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain G residue 42 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 228 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 236 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 143 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 124 GLN B 129 ASN C 136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19614 Z= 0.196 Angle : 0.475 7.835 26509 Z= 0.238 Chirality : 0.040 0.141 3080 Planarity : 0.003 0.031 3444 Dihedral : 4.022 20.609 2737 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.61 % Favored : 98.11 % Rotamer: Outliers : 1.93 % Allowed : 14.58 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.93 (0.16), residues: 2485 helix: 2.22 (0.13), residues: 1407 sheet: 0.86 (0.33), residues: 217 loop : -0.16 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 174 HIS 0.003 0.001 HIS H 123 PHE 0.019 0.001 PHE E 83 TYR 0.014 0.001 TYR I 113 ARG 0.002 0.000 ARG E 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 375 time to evaluate : 2.149 Fit side-chains REVERT: N 168 ASP cc_start: 0.8753 (m-30) cc_final: 0.8381 (m-30) REVERT: N 169 SER cc_start: 0.9217 (p) cc_final: 0.9002 (t) REVERT: H 168 ASP cc_start: 0.8652 (m-30) cc_final: 0.8118 (m-30) REVERT: H 182 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8242 (tm-30) REVERT: I 168 ASP cc_start: 0.8781 (m-30) cc_final: 0.8010 (m-30) REVERT: I 182 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8639 (tm-30) REVERT: J 168 ASP cc_start: 0.8708 (m-30) cc_final: 0.8233 (m-30) REVERT: K 23 ARG cc_start: 0.8301 (mmm-85) cc_final: 0.7969 (mtp180) REVERT: L 15 SER cc_start: 0.5961 (m) cc_final: 0.5636 (t) REVERT: M 156 GLU cc_start: 0.8472 (tt0) cc_final: 0.8220 (tt0) REVERT: M 182 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8365 (tm-30) REVERT: A 38 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7990 (mt-10) REVERT: A 57 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.6678 (mtp) REVERT: A 71 ASP cc_start: 0.7953 (t70) cc_final: 0.7710 (m-30) REVERT: B 153 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6880 (mp10) REVERT: D 136 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8290 (pt0) REVERT: E 37 PHE cc_start: 0.8357 (t80) cc_final: 0.8071 (t80) REVERT: E 99 ASP cc_start: 0.8005 (m-30) cc_final: 0.7760 (m-30) REVERT: F 164 MET cc_start: 0.7678 (ttp) cc_final: 0.7426 (ttp) REVERT: F 183 THR cc_start: 0.9077 (p) cc_final: 0.8759 (t) REVERT: G 57 MET cc_start: 0.8445 (mtm) cc_final: 0.7990 (mtm) outliers start: 39 outliers final: 28 residues processed: 397 average time/residue: 0.2803 time to fit residues: 175.4525 Evaluate side-chains 402 residues out of total 2023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 371 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 101 GLU Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain G residue 42 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 146 optimal weight: 0.3980 chunk 94 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 124 GLN L 124 GLN B 129 ASN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19614 Z= 0.150 Angle : 0.459 7.630 26509 Z= 0.229 Chirality : 0.039 0.135 3080 Planarity : 0.003 0.032 3444 Dihedral : 3.875 19.583 2737 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.37 % Favored : 98.35 % Rotamer: Outliers : 1.73 % Allowed : 14.63 % Favored : 83.64 % 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: 2.01 (0.16), residues: 2485 helix: 2.30 (0.14), residues: 1407 sheet: 0.87 (0.33), residues: 217 loop : -0.15 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 174 HIS 0.003 0.001 HIS H 123 PHE 0.012 0.001 PHE G 83 TYR 0.020 0.001 TYR K 63 ARG 0.002 0.000 ARG E 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 380 time to evaluate : 2.262 Fit side-chains REVERT: N 168 ASP cc_start: 0.8752 (m-30) cc_final: 0.8402 (m-30) REVERT: H 156 GLU cc_start: 0.8277 (tt0) cc_final: 0.8074 (tt0) REVERT: H 168 ASP cc_start: 0.8642 (m-30) cc_final: 0.8109 (m-30) REVERT: I 168 ASP cc_start: 0.8768 (m-30) cc_final: 0.8037 (m-30) REVERT: J 168 ASP cc_start: 0.8688 (m-30) cc_final: 0.8234 (m-30) REVERT: K 23 ARG cc_start: 0.8417 (mmm-85) cc_final: 0.8068 (mtp180) REVERT: M 75 MET cc_start: 0.8966 (tpt) cc_final: 0.8567 (tpt) REVERT: M 156 GLU cc_start: 0.8395 (tt0) cc_final: 0.8170 (tt0) REVERT: M 179 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7730 (mt-10) REVERT: M 182 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8338 (tm-30) REVERT: A 57 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.6636 (mtp) REVERT: B 55 ASP cc_start: 0.8117 (m-30) cc_final: 0.7843 (m-30) REVERT: B 153 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.6929 (mp10) REVERT: D 136 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8283 (pt0) REVERT: E 37 PHE cc_start: 0.8338 (t80) cc_final: 0.8073 (t80) REVERT: E 99 ASP cc_start: 0.7991 (m-30) cc_final: 0.7758 (m-30) REVERT: F 87 MET cc_start: 0.7826 (mmm) cc_final: 0.7519 (mmm) REVERT: F 164 MET cc_start: 0.7602 (ttp) cc_final: 0.7391 (ttp) REVERT: F 183 THR cc_start: 0.9058 (p) cc_final: 0.8756 (t) REVERT: G 57 MET cc_start: 0.8331 (mtm) cc_final: 0.7897 (mtm) REVERT: G 164 MET cc_start: 0.7501 (ttp) cc_final: 0.7254 (ttp) outliers start: 35 outliers final: 25 residues processed: 400 average time/residue: 0.2927 time to fit residues: 183.0872 Evaluate side-chains 398 residues out of total 2023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 370 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 101 GLU Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain E residue 71 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 214 optimal weight: 7.9990 chunk 226 optimal weight: 10.0000 chunk 206 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 95 optimal weight: 0.0970 chunk 172 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 198 optimal weight: 9.9990 chunk 208 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 overall best weight: 4.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 124 GLN M 124 GLN A 101 GLN A 129 ASN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.5883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 19614 Z= 0.399 Angle : 0.611 8.586 26509 Z= 0.306 Chirality : 0.043 0.154 3080 Planarity : 0.004 0.039 3444 Dihedral : 4.505 23.311 2737 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.74 % Favored : 96.98 % Rotamer: Outliers : 2.08 % Allowed : 14.14 % Favored : 83.79 % 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: 1.43 (0.16), residues: 2485 helix: 1.94 (0.13), residues: 1393 sheet: 0.19 (0.31), residues: 238 loop : -0.44 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP M 174 HIS 0.005 0.001 HIS K 123 PHE 0.018 0.002 PHE D 83 TYR 0.016 0.002 TYR J 113 ARG 0.003 0.000 ARG K 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 406 time to evaluate : 2.255 Fit side-chains REVERT: N 57 SER cc_start: 0.8681 (m) cc_final: 0.8376 (m) REVERT: N 168 ASP cc_start: 0.8737 (m-30) cc_final: 0.8430 (m-30) REVERT: H 168 ASP cc_start: 0.8652 (m-30) cc_final: 0.8145 (m-30) REVERT: H 182 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8208 (tm-30) REVERT: J 15 SER cc_start: 0.5830 (m) cc_final: 0.5478 (t) REVERT: J 26 SER cc_start: 0.8572 (m) cc_final: 0.8372 (t) REVERT: J 168 ASP cc_start: 0.8745 (m-30) cc_final: 0.8269 (m-30) REVERT: K 172 ASP cc_start: 0.8352 (m-30) cc_final: 0.8134 (m-30) REVERT: L 15 SER cc_start: 0.6107 (m) cc_final: 0.5761 (t) REVERT: L 23 ARG cc_start: 0.8485 (mmm-85) cc_final: 0.8106 (mtp180) REVERT: L 169 SER cc_start: 0.9239 (p) cc_final: 0.9015 (t) REVERT: M 156 GLU cc_start: 0.8468 (tt0) cc_final: 0.8239 (tt0) REVERT: M 169 SER cc_start: 0.9284 (p) cc_final: 0.9008 (t) REVERT: M 182 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8492 (tm-30) REVERT: A 38 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7794 (mt-10) REVERT: A 57 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8032 (mtm) REVERT: A 183 THR cc_start: 0.9151 (p) cc_final: 0.8933 (t) REVERT: B 153 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.6967 (mp10) REVERT: E 160 MET cc_start: 0.7654 (ttm) cc_final: 0.7343 (ttp) REVERT: E 183 THR cc_start: 0.9164 (p) cc_final: 0.8887 (t) REVERT: F 87 MET cc_start: 0.8228 (mmm) cc_final: 0.7927 (mmm) REVERT: F 183 THR cc_start: 0.9153 (p) cc_final: 0.8922 (t) REVERT: G 57 MET cc_start: 0.8631 (mtm) cc_final: 0.8283 (mtm) REVERT: G 201 ASP cc_start: 0.8623 (m-30) cc_final: 0.8318 (m-30) outliers start: 42 outliers final: 34 residues processed: 432 average time/residue: 0.2803 time to fit residues: 190.2072 Evaluate side-chains 421 residues out of total 2023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 385 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 42 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 144 optimal weight: 1.9990 chunk 232 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 161 optimal weight: 0.6980 chunk 244 optimal weight: 0.0770 chunk 224 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 124 GLN J 124 GLN B 129 ASN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 GLN D 136 GLN G 129 ASN G 136 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.6045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19614 Z= 0.147 Angle : 0.501 11.401 26509 Z= 0.247 Chirality : 0.040 0.158 3080 Planarity : 0.003 0.033 3444 Dihedral : 4.058 19.427 2737 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.37 % Favored : 98.35 % Rotamer: Outliers : 1.43 % Allowed : 15.67 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.67 (0.16), residues: 2485 helix: 2.06 (0.13), residues: 1407 sheet: 0.62 (0.33), residues: 217 loop : -0.35 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 174 HIS 0.004 0.001 HIS H 123 PHE 0.013 0.001 PHE D 83 TYR 0.015 0.001 TYR K 63 ARG 0.002 0.000 ARG C 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 380 time to evaluate : 2.054 Fit side-chains REVERT: N 57 SER cc_start: 0.8585 (m) cc_final: 0.8302 (m) REVERT: N 168 ASP cc_start: 0.8723 (m-30) cc_final: 0.8410 (m-30) REVERT: H 168 ASP cc_start: 0.8623 (m-30) cc_final: 0.8108 (m-30) REVERT: H 182 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8174 (tm-30) REVERT: I 168 ASP cc_start: 0.8823 (m-30) cc_final: 0.7925 (m-30) REVERT: I 182 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8549 (tm-30) REVERT: J 168 ASP cc_start: 0.8746 (m-30) cc_final: 0.8370 (m-30) REVERT: K 169 SER cc_start: 0.9193 (p) cc_final: 0.8927 (t) REVERT: L 15 SER cc_start: 0.6177 (m) cc_final: 0.5823 (t) REVERT: L 23 ARG cc_start: 0.8433 (mmm-85) cc_final: 0.8070 (mtp180) REVERT: M 75 MET cc_start: 0.8993 (tpt) cc_final: 0.8622 (tpt) REVERT: M 156 GLU cc_start: 0.8384 (tt0) cc_final: 0.8164 (tt0) REVERT: M 169 SER cc_start: 0.9190 (p) cc_final: 0.8967 (t) REVERT: M 182 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8492 (tm-30) REVERT: A 60 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7642 (mm) REVERT: A 164 MET cc_start: 0.7547 (ttp) cc_final: 0.7321 (ttp) REVERT: A 183 THR cc_start: 0.9093 (p) cc_final: 0.8889 (t) REVERT: B 153 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.6934 (mp10) REVERT: E 37 PHE cc_start: 0.8368 (t80) cc_final: 0.8083 (t80) REVERT: F 87 MET cc_start: 0.7779 (mmm) cc_final: 0.7544 (mmm) REVERT: G 57 MET cc_start: 0.8510 (mtm) cc_final: 0.8086 (mtm) REVERT: G 164 MET cc_start: 0.7525 (ttp) cc_final: 0.7318 (ttp) outliers start: 29 outliers final: 23 residues processed: 398 average time/residue: 0.2809 time to fit residues: 174.8653 Evaluate side-chains 390 residues out of total 2023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 365 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 154 optimal weight: 0.6980 chunk 207 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 0.0050 overall best weight: 1.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 124 GLN J 124 GLN L 124 GLN L 188 HIS D 129 ASN G 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.140386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.125499 restraints weight = 24138.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.129919 restraints weight = 12024.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.132853 restraints weight = 7091.706| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.6097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19614 Z= 0.200 Angle : 0.522 11.767 26509 Z= 0.257 Chirality : 0.040 0.156 3080 Planarity : 0.003 0.034 3444 Dihedral : 4.078 20.514 2737 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.93 % Favored : 97.79 % Rotamer: Outliers : 1.58 % Allowed : 15.32 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.67 (0.16), residues: 2485 helix: 2.07 (0.14), residues: 1407 sheet: 0.61 (0.33), residues: 217 loop : -0.36 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 174 HIS 0.003 0.001 HIS J 117 PHE 0.017 0.001 PHE E 83 TYR 0.021 0.001 TYR N 113 ARG 0.002 0.000 ARG C 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3853.09 seconds wall clock time: 70 minutes 48.83 seconds (4248.83 seconds total)