Starting phenix.real_space_refine on Mon Apr 15 04:35:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnp_27576/04_2024/8dnp_27576.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnp_27576/04_2024/8dnp_27576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnp_27576/04_2024/8dnp_27576.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnp_27576/04_2024/8dnp_27576.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnp_27576/04_2024/8dnp_27576.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnp_27576/04_2024/8dnp_27576.pdb" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.071 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: 5 Type Number sf(0) Gaussians Fe 24 7.16 5 S 168 5.16 5 C 21264 2.51 5 N 5952 2.21 5 O 6528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 64": "NH1" <-> "NH2" Residue "B ARG 64": "NH1" <-> "NH2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "F ARG 64": "NH1" <-> "NH2" Residue "G ARG 64": "NH1" <-> "NH2" Residue "H ARG 64": "NH1" <-> "NH2" Residue "I ARG 64": "NH1" <-> "NH2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "M ARG 64": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "P ARG 64": "NH1" <-> "NH2" Residue "Q ARG 64": "NH1" <-> "NH2" Residue "R ARG 64": "NH1" <-> "NH2" Residue "S ARG 64": "NH1" <-> "NH2" Residue "T ARG 64": "NH1" <-> "NH2" Residue "U ARG 64": "NH1" <-> "NH2" Residue "V ARG 64": "NH1" <-> "NH2" Residue "W ARG 64": "NH1" <-> "NH2" Residue "X ARG 64": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 33936 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "B" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "C" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "D" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "E" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "F" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "G" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "H" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "I" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "J" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "K" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "L" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "M" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "N" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "O" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "P" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Q" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "R" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "S" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "T" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "U" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "V" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "W" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "X" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.87, per 1000 atoms: 0.50 Number of scatterers: 33936 At special positions: 0 Unit cell: (135.89, 135.89, 135.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 24 26.01 S 168 16.00 O 6528 8.00 N 5952 7.00 C 21264 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=0, symmetry=0 Time building additional restraints: 14.10 Conformation dependent library (CDL) restraints added in 5.7 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 14 through 42 Processing helix chain 'A' and resid 49 through 77 Processing helix chain 'A' and resid 96 through 125 Processing helix chain 'A' and resid 127 through 138 Processing helix chain 'A' and resid 138 through 160 Processing helix chain 'A' and resid 164 through 175 Processing helix chain 'B' and resid 14 through 42 Processing helix chain 'B' and resid 49 through 77 Processing helix chain 'B' and resid 96 through 125 Processing helix chain 'B' and resid 127 through 138 Processing helix chain 'B' and resid 138 through 160 Processing helix chain 'B' and resid 164 through 175 Processing helix chain 'C' and resid 14 through 42 Processing helix chain 'C' and resid 49 through 77 Processing helix chain 'C' and resid 96 through 125 Processing helix chain 'C' and resid 127 through 138 Processing helix chain 'C' and resid 138 through 160 Processing helix chain 'C' and resid 164 through 175 Processing helix chain 'D' and resid 14 through 42 Processing helix chain 'D' and resid 49 through 77 Processing helix chain 'D' and resid 96 through 125 Processing helix chain 'D' and resid 127 through 138 Processing helix chain 'D' and resid 138 through 160 Processing helix chain 'D' and resid 164 through 175 Processing helix chain 'E' and resid 14 through 42 Processing helix chain 'E' and resid 49 through 77 Processing helix chain 'E' and resid 96 through 125 Processing helix chain 'E' and resid 127 through 138 Processing helix chain 'E' and resid 138 through 160 Processing helix chain 'E' and resid 164 through 175 Processing helix chain 'F' and resid 14 through 42 Processing helix chain 'F' and resid 49 through 77 Processing helix chain 'F' and resid 96 through 125 Processing helix chain 'F' and resid 127 through 138 Processing helix chain 'F' and resid 138 through 160 Processing helix chain 'F' and resid 164 through 175 Processing helix chain 'G' and resid 14 through 42 Processing helix chain 'G' and resid 49 through 77 Processing helix chain 'G' and resid 96 through 125 Processing helix chain 'G' and resid 127 through 138 Processing helix chain 'G' and resid 138 through 160 Processing helix chain 'G' and resid 164 through 175 Processing helix chain 'H' and resid 14 through 42 Processing helix chain 'H' and resid 49 through 77 Processing helix chain 'H' and resid 96 through 125 Processing helix chain 'H' and resid 127 through 138 Processing helix chain 'H' and resid 138 through 160 Processing helix chain 'H' and resid 164 through 175 Processing helix chain 'I' and resid 14 through 42 Processing helix chain 'I' and resid 49 through 77 Processing helix chain 'I' and resid 96 through 125 Processing helix chain 'I' and resid 127 through 138 Processing helix chain 'I' and resid 138 through 160 Processing helix chain 'I' and resid 164 through 175 Processing helix chain 'J' and resid 14 through 42 Processing helix chain 'J' and resid 49 through 77 Processing helix chain 'J' and resid 96 through 125 Processing helix chain 'J' and resid 127 through 138 Processing helix chain 'J' and resid 138 through 160 Processing helix chain 'J' and resid 164 through 175 Processing helix chain 'K' and resid 14 through 42 Processing helix chain 'K' and resid 49 through 77 Processing helix chain 'K' and resid 96 through 125 Processing helix chain 'K' and resid 127 through 138 Processing helix chain 'K' and resid 138 through 160 Processing helix chain 'K' and resid 164 through 175 Processing helix chain 'L' and resid 14 through 42 Processing helix chain 'L' and resid 49 through 77 Processing helix chain 'L' and resid 96 through 125 Processing helix chain 'L' and resid 127 through 138 Processing helix chain 'L' and resid 138 through 160 Processing helix chain 'L' and resid 164 through 175 Processing helix chain 'M' and resid 14 through 42 Processing helix chain 'M' and resid 49 through 77 Processing helix chain 'M' and resid 96 through 125 Processing helix chain 'M' and resid 127 through 138 Processing helix chain 'M' and resid 138 through 160 Processing helix chain 'M' and resid 164 through 175 Processing helix chain 'N' and resid 14 through 42 Processing helix chain 'N' and resid 49 through 77 Processing helix chain 'N' and resid 96 through 125 Processing helix chain 'N' and resid 127 through 138 Processing helix chain 'N' and resid 138 through 160 Processing helix chain 'N' and resid 164 through 175 Processing helix chain 'O' and resid 14 through 42 Processing helix chain 'O' and resid 49 through 77 Processing helix chain 'O' and resid 96 through 125 Processing helix chain 'O' and resid 127 through 138 Processing helix chain 'O' and resid 138 through 160 Processing helix chain 'O' and resid 164 through 175 Processing helix chain 'P' and resid 14 through 42 Processing helix chain 'P' and resid 49 through 77 Processing helix chain 'P' and resid 96 through 125 Processing helix chain 'P' and resid 127 through 138 Processing helix chain 'P' and resid 138 through 160 Processing helix chain 'P' and resid 164 through 175 Processing helix chain 'Q' and resid 14 through 42 Processing helix chain 'Q' and resid 49 through 77 Processing helix chain 'Q' and resid 96 through 125 Processing helix chain 'Q' and resid 127 through 138 Processing helix chain 'Q' and resid 138 through 160 Processing helix chain 'Q' and resid 164 through 175 Processing helix chain 'R' and resid 14 through 42 Processing helix chain 'R' and resid 49 through 77 Processing helix chain 'R' and resid 96 through 125 Processing helix chain 'R' and resid 127 through 138 Processing helix chain 'R' and resid 138 through 160 Processing helix chain 'R' and resid 164 through 175 Processing helix chain 'S' and resid 14 through 42 Processing helix chain 'S' and resid 49 through 77 Processing helix chain 'S' and resid 96 through 125 Processing helix chain 'S' and resid 127 through 138 Processing helix chain 'S' and resid 138 through 160 Processing helix chain 'S' and resid 164 through 175 Processing helix chain 'T' and resid 14 through 42 Processing helix chain 'T' and resid 49 through 77 Processing helix chain 'T' and resid 96 through 125 Processing helix chain 'T' and resid 127 through 138 Processing helix chain 'T' and resid 138 through 160 Processing helix chain 'T' and resid 164 through 175 Processing helix chain 'U' and resid 14 through 42 Processing helix chain 'U' and resid 49 through 77 Processing helix chain 'U' and resid 96 through 125 Processing helix chain 'U' and resid 127 through 138 Processing helix chain 'U' and resid 138 through 160 Processing helix chain 'U' and resid 164 through 175 Processing helix chain 'V' and resid 14 through 42 Processing helix chain 'V' and resid 49 through 77 Processing helix chain 'V' and resid 96 through 125 Processing helix chain 'V' and resid 127 through 138 Processing helix chain 'V' and resid 138 through 160 Processing helix chain 'V' and resid 164 through 175 Processing helix chain 'W' and resid 14 through 42 Processing helix chain 'W' and resid 49 through 77 Processing helix chain 'W' and resid 96 through 125 Processing helix chain 'W' and resid 127 through 138 Processing helix chain 'W' and resid 138 through 160 Processing helix chain 'W' and resid 164 through 175 Processing helix chain 'X' and resid 14 through 42 Processing helix chain 'X' and resid 49 through 77 Processing helix chain 'X' and resid 96 through 125 Processing helix chain 'X' and resid 127 through 138 Processing helix chain 'X' and resid 138 through 160 Processing helix chain 'X' and resid 164 through 175 2664 hydrogen bonds defined for protein. 7992 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: 10.85 Time building geometry restraints manager: 15.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11176 1.33 - 1.45: 6003 1.45 - 1.57: 17165 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 34608 Sorted by residual: bond pdb=" CA LYS X 125 " pdb=" C LYS X 125 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.34e-02 5.57e+03 8.60e+00 bond pdb=" CA LYS T 125 " pdb=" C LYS T 125 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.34e-02 5.57e+03 8.45e+00 bond pdb=" CA LYS N 125 " pdb=" C LYS N 125 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.34e-02 5.57e+03 8.45e+00 bond pdb=" CA LYS G 125 " pdb=" C LYS G 125 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.34e-02 5.57e+03 8.41e+00 bond pdb=" CA LYS C 125 " pdb=" C LYS C 125 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.34e-02 5.57e+03 8.34e+00 ... (remaining 34603 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.14: 952 107.14 - 113.86: 18640 113.86 - 120.58: 14808 120.58 - 127.30: 11896 127.30 - 134.02: 312 Bond angle restraints: 46608 Sorted by residual: angle pdb=" N HIS S 58 " pdb=" CA HIS S 58 " pdb=" C HIS S 58 " ideal model delta sigma weight residual 112.23 104.11 8.12 1.26e+00 6.30e-01 4.15e+01 angle pdb=" N HIS X 58 " pdb=" CA HIS X 58 " pdb=" C HIS X 58 " ideal model delta sigma weight residual 112.23 104.12 8.11 1.26e+00 6.30e-01 4.14e+01 angle pdb=" N HIS U 58 " pdb=" CA HIS U 58 " pdb=" C HIS U 58 " ideal model delta sigma weight residual 112.23 104.13 8.10 1.26e+00 6.30e-01 4.13e+01 angle pdb=" N HIS Q 58 " pdb=" CA HIS Q 58 " pdb=" C HIS Q 58 " ideal model delta sigma weight residual 112.23 104.13 8.10 1.26e+00 6.30e-01 4.13e+01 angle pdb=" N HIS K 58 " pdb=" CA HIS K 58 " pdb=" C HIS K 58 " ideal model delta sigma weight residual 112.23 104.13 8.10 1.26e+00 6.30e-01 4.13e+01 ... (remaining 46603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.85: 18035 12.85 - 25.71: 2077 25.71 - 38.56: 552 38.56 - 51.41: 144 51.41 - 64.27: 120 Dihedral angle restraints: 20928 sinusoidal: 8688 harmonic: 12240 Sorted by residual: dihedral pdb=" CA ALA T 161 " pdb=" C ALA T 161 " pdb=" N PRO T 162 " pdb=" CA PRO T 162 " ideal model delta harmonic sigma weight residual 0.00 28.57 -28.57 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ALA B 161 " pdb=" C ALA B 161 " pdb=" N PRO B 162 " pdb=" CA PRO B 162 " ideal model delta harmonic sigma weight residual 0.00 28.56 -28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ALA H 161 " pdb=" C ALA H 161 " pdb=" N PRO H 162 " pdb=" CA PRO H 162 " ideal model delta harmonic sigma weight residual 0.00 28.54 -28.54 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 20925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3541 0.073 - 0.146: 982 0.146 - 0.218: 301 0.218 - 0.291: 48 0.291 - 0.364: 24 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CA TYR D 40 " pdb=" N TYR D 40 " pdb=" C TYR D 40 " pdb=" CB TYR D 40 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA TYR E 40 " pdb=" N TYR E 40 " pdb=" C TYR E 40 " pdb=" CB TYR E 40 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA TYR C 40 " pdb=" N TYR C 40 " pdb=" C TYR C 40 " pdb=" CB TYR C 40 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 4893 not shown) Planarity restraints: 6144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU Q 57 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C LEU Q 57 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU Q 57 " -0.011 2.00e-02 2.50e+03 pdb=" N HIS Q 58 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 57 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C LEU F 57 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU F 57 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS F 58 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU P 57 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.74e+00 pdb=" C LEU P 57 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU P 57 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS P 58 " 0.010 2.00e-02 2.50e+03 ... (remaining 6141 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 92 2.39 - 3.02: 20017 3.02 - 3.65: 56090 3.65 - 4.27: 93571 4.27 - 4.90: 144378 Nonbonded interactions: 314148 Sorted by model distance: nonbonded pdb=" OE1 GLU A 28 " pdb="FE FE A 201 " model vdw 1.768 2.260 nonbonded pdb=" OE1 GLU B 28 " pdb="FE FE B 201 " model vdw 1.789 2.260 nonbonded pdb=" OE1 GLU V 28 " pdb="FE FE V 201 " model vdw 1.962 2.260 nonbonded pdb=" OE1 GLU J 28 " pdb="FE FE J 201 " model vdw 1.962 2.260 nonbonded pdb=" OE1 GLU D 28 " pdb="FE FE D 201 " model vdw 1.962 2.260 ... (remaining 314143 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' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.870 Check model and map are aligned: 0.450 Set scattering table: 0.290 Process input model: 85.690 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.520 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: 0.020 Load rotamer database and sin/cos tables:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 0.010 0.039 34608 Z= 0.666 Angle : 1.160 8.744 46608 Z= 0.818 Chirality : 0.078 0.364 4896 Planarity : 0.004 0.018 6144 Dihedral : 12.976 64.268 13008 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.31 % Allowed : 3.27 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 0.44 (0.12), residues: 4080 helix: 0.66 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : -0.74 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.002 TRP V 94 HIS 0.005 0.002 HIS M 174 PHE 0.007 0.002 PHE Q 42 TYR 0.018 0.002 TYR L 40 ARG 0.005 0.001 ARG W 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1654 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1606 time to evaluate : 4.030 Fit side-chains revert: symmetry clash REVERT: A 63 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7970 (mm-30) REVERT: B 63 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8016 (mm-30) REVERT: B 102 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7386 (mt-10) REVERT: C 63 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7603 (mm-30) REVERT: C 88 LYS cc_start: 0.8138 (pttt) cc_final: 0.7855 (pttt) REVERT: C 102 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7347 (mt-10) REVERT: D 63 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7835 (mm-30) REVERT: E 63 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7559 (mm-30) REVERT: F 63 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7712 (mm-30) REVERT: F 71 MET cc_start: 0.8380 (mtp) cc_final: 0.8105 (mtp) REVERT: G 63 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7622 (mm-30) REVERT: H 63 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7537 (mm-30) REVERT: H 88 LYS cc_start: 0.7860 (pttt) cc_final: 0.7604 (pttt) REVERT: I 33 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.6538 (t80) REVERT: I 63 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7619 (mm-30) REVERT: J 63 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7851 (mm-30) REVERT: K 63 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7519 (mm-30) REVERT: K 76 GLN cc_start: 0.8068 (mt0) cc_final: 0.7782 (mt0) REVERT: L 63 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7717 (mm-30) REVERT: L 71 MET cc_start: 0.8350 (mtp) cc_final: 0.8135 (mtp) REVERT: L 168 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7622 (mt-10) REVERT: M 63 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7569 (mm-30) REVERT: N 63 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7561 (mm-30) REVERT: O 33 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.6396 (t80) REVERT: O 63 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7617 (mm-30) REVERT: P 63 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7834 (mm-30) REVERT: Q 63 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7605 (mm-30) REVERT: R 63 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7703 (mm-30) REVERT: S 63 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7636 (mm-30) REVERT: T 63 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7524 (mm-30) REVERT: U 63 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7645 (mm-30) REVERT: U 140 ASN cc_start: 0.8121 (t0) cc_final: 0.7906 (t0) REVERT: V 63 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7879 (mm-30) REVERT: V 151 ASP cc_start: 0.7940 (m-30) cc_final: 0.7674 (m-30) REVERT: W 63 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7607 (mm-30) REVERT: W 76 GLN cc_start: 0.8005 (mt0) cc_final: 0.7747 (mt0) REVERT: X 63 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7708 (mm-30) REVERT: X 71 MET cc_start: 0.8348 (mtp) cc_final: 0.8126 (mtp) outliers start: 48 outliers final: 25 residues processed: 1651 average time/residue: 1.6617 time to fit residues: 3209.7550 Evaluate side-chains 1290 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1263 time to evaluate : 3.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain G residue 103 CYS Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain I residue 33 TYR Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain K residue 103 CYS Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain M residue 103 CYS Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain O residue 33 TYR Chi-restraints excluded: chain O residue 103 CYS Chi-restraints excluded: chain P residue 103 CYS Chi-restraints excluded: chain Q residue 103 CYS Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain S residue 103 CYS Chi-restraints excluded: chain T residue 103 CYS Chi-restraints excluded: chain U residue 103 CYS Chi-restraints excluded: chain V residue 103 CYS Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain W residue 103 CYS Chi-restraints excluded: chain X residue 103 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 0.8980 chunk 309 optimal weight: 0.6980 chunk 171 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 208 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 319 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 194 optimal weight: 0.6980 chunk 238 optimal weight: 1.9990 chunk 370 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 99 ASN A 174 HIS B 99 ASN B 174 HIS C 84 GLN C 99 ASN C 113 GLN C 174 HIS ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 174 HIS E 99 ASN E 174 HIS F 61 HIS F 84 GLN F 99 ASN F 174 HIS G 99 ASN G 174 HIS H 61 HIS H 84 GLN H 99 ASN H 113 GLN H 174 HIS I 76 GLN I 99 ASN I 113 GLN I 174 HIS J 99 ASN J 174 HIS K 99 ASN K 174 HIS L 84 GLN L 99 ASN L 174 HIS M 61 HIS M 99 ASN M 174 HIS N 84 GLN N 99 ASN N 174 HIS O 84 GLN O 99 ASN O 174 HIS ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 GLN P 99 ASN P 174 HIS ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 GLN Q 99 ASN Q 174 HIS R 84 GLN R 99 ASN R 174 HIS S 76 GLN S 99 ASN S 174 HIS T 61 HIS T 84 GLN T 99 ASN T 113 GLN T 174 HIS U 99 ASN U 174 HIS V 84 GLN V 99 ASN V 174 HIS W 14 HIS W 99 ASN W 174 HIS X 84 GLN X 174 HIS Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 34608 Z= 0.144 Angle : 0.486 6.901 46608 Z= 0.261 Chirality : 0.037 0.138 4896 Planarity : 0.003 0.031 6144 Dihedral : 4.511 57.388 4519 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 3.57 % Allowed : 13.89 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.88 (0.13), residues: 4080 helix: 3.01 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : 0.65 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 94 HIS 0.004 0.001 HIS P 14 PHE 0.009 0.001 PHE M 42 TYR 0.018 0.002 TYR N 138 ARG 0.008 0.001 ARG H 157 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1458 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1327 time to evaluate : 4.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8167 (m-80) cc_final: 0.7816 (m-80) REVERT: A 84 GLN cc_start: 0.8289 (mm-40) cc_final: 0.8077 (mm-40) REVERT: A 120 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7263 (tmtp) REVERT: B 40 TYR cc_start: 0.8188 (m-80) cc_final: 0.7769 (m-80) REVERT: C 23 ARG cc_start: 0.7847 (mtm110) cc_final: 0.7629 (mtm110) REVERT: C 40 TYR cc_start: 0.8139 (m-80) cc_final: 0.7766 (m-80) REVERT: C 84 GLN cc_start: 0.8312 (mm-40) cc_final: 0.8084 (mm-40) REVERT: C 88 LYS cc_start: 0.8047 (pttt) cc_final: 0.7748 (pttt) REVERT: D 40 TYR cc_start: 0.8107 (m-80) cc_final: 0.7522 (m-80) REVERT: D 63 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8034 (mm-30) REVERT: D 68 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7502 (mt-10) REVERT: D 126 ASN cc_start: 0.7821 (OUTLIER) cc_final: 0.7569 (m-40) REVERT: E 40 TYR cc_start: 0.8136 (m-80) cc_final: 0.7619 (m-80) REVERT: E 64 ARG cc_start: 0.7648 (ttp-170) cc_final: 0.7436 (ttm110) REVERT: E 96 SER cc_start: 0.8086 (OUTLIER) cc_final: 0.7766 (p) REVERT: F 40 TYR cc_start: 0.8093 (m-80) cc_final: 0.7585 (m-80) REVERT: F 68 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7668 (mt-10) REVERT: G 40 TYR cc_start: 0.8147 (m-80) cc_final: 0.7736 (m-80) REVERT: G 68 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7689 (mt-10) REVERT: G 120 LYS cc_start: 0.7540 (tttt) cc_final: 0.7266 (tmtp) REVERT: H 40 TYR cc_start: 0.8145 (m-80) cc_final: 0.7587 (m-80) REVERT: H 96 SER cc_start: 0.8026 (OUTLIER) cc_final: 0.7746 (p) REVERT: H 110 ASN cc_start: 0.7637 (m-40) cc_final: 0.7404 (m110) REVERT: I 40 TYR cc_start: 0.8119 (m-80) cc_final: 0.7665 (m-80) REVERT: I 96 SER cc_start: 0.8118 (OUTLIER) cc_final: 0.7775 (p) REVERT: J 23 ARG cc_start: 0.7856 (mtm110) cc_final: 0.7651 (mtm110) REVERT: J 40 TYR cc_start: 0.8125 (m-80) cc_final: 0.7534 (m-80) REVERT: J 68 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7598 (mt-10) REVERT: K 40 TYR cc_start: 0.8108 (m-80) cc_final: 0.7569 (m-80) REVERT: K 96 SER cc_start: 0.8080 (OUTLIER) cc_final: 0.7740 (p) REVERT: L 40 TYR cc_start: 0.8124 (m-80) cc_final: 0.7573 (m-80) REVERT: L 64 ARG cc_start: 0.7616 (ttp-170) cc_final: 0.7347 (ttp-110) REVERT: L 68 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7698 (mt-10) REVERT: L 84 GLN cc_start: 0.8265 (mm-40) cc_final: 0.8047 (mm-40) REVERT: M 40 TYR cc_start: 0.8157 (m-80) cc_final: 0.7711 (m-80) REVERT: M 59 GLN cc_start: 0.8466 (mp10) cc_final: 0.8255 (mm110) REVERT: M 68 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7722 (mt-10) REVERT: M 96 SER cc_start: 0.8080 (OUTLIER) cc_final: 0.7745 (p) REVERT: M 120 LYS cc_start: 0.7494 (tmtp) cc_final: 0.7235 (tmtp) REVERT: N 40 TYR cc_start: 0.8125 (m-80) cc_final: 0.7577 (m-80) REVERT: N 102 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7246 (mt-10) REVERT: N 120 LYS cc_start: 0.7492 (tmtp) cc_final: 0.7256 (tmtp) REVERT: N 157 ARG cc_start: 0.7491 (mtt-85) cc_final: 0.7244 (mtt-85) REVERT: O 40 TYR cc_start: 0.8109 (m-80) cc_final: 0.7688 (m-80) REVERT: O 64 ARG cc_start: 0.7516 (ttp-170) cc_final: 0.7275 (ttm110) REVERT: O 84 GLN cc_start: 0.8287 (mm-40) cc_final: 0.8056 (mm-40) REVERT: O 96 SER cc_start: 0.8113 (OUTLIER) cc_final: 0.7788 (p) REVERT: O 120 LYS cc_start: 0.7633 (tmtt) cc_final: 0.7399 (tmtp) REVERT: P 40 TYR cc_start: 0.8134 (m-80) cc_final: 0.7532 (m-80) REVERT: P 126 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7536 (m-40) REVERT: Q 40 TYR cc_start: 0.8124 (m-80) cc_final: 0.7634 (m-80) REVERT: Q 58 HIS cc_start: 0.8289 (t-90) cc_final: 0.8029 (t-90) REVERT: Q 96 SER cc_start: 0.8105 (OUTLIER) cc_final: 0.7759 (p) REVERT: R 40 TYR cc_start: 0.8106 (m-80) cc_final: 0.7573 (m-80) REVERT: R 54 LYS cc_start: 0.7831 (tmtt) cc_final: 0.7598 (tptt) REVERT: R 68 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7704 (mt-10) REVERT: R 85 ASP cc_start: 0.8200 (m-30) cc_final: 0.7996 (m-30) REVERT: S 40 TYR cc_start: 0.8171 (m-80) cc_final: 0.7739 (m-80) REVERT: S 68 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7582 (mt-10) REVERT: S 96 SER cc_start: 0.8141 (OUTLIER) cc_final: 0.7787 (p) REVERT: T 40 TYR cc_start: 0.8123 (m-80) cc_final: 0.7569 (m-80) REVERT: U 40 TYR cc_start: 0.8134 (m-80) cc_final: 0.7688 (m-80) REVERT: U 120 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7252 (tmtp) REVERT: V 40 TYR cc_start: 0.8113 (m-80) cc_final: 0.7516 (m-80) REVERT: V 63 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8010 (mm-30) REVERT: V 96 SER cc_start: 0.8067 (OUTLIER) cc_final: 0.7766 (p) REVERT: V 126 ASN cc_start: 0.7723 (OUTLIER) cc_final: 0.7498 (m-40) REVERT: W 40 TYR cc_start: 0.8165 (m-80) cc_final: 0.7659 (m-80) REVERT: W 58 HIS cc_start: 0.8228 (t-90) cc_final: 0.8020 (t-90) REVERT: W 120 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7199 (tmtp) REVERT: X 40 TYR cc_start: 0.8099 (m-80) cc_final: 0.7579 (m-80) REVERT: X 68 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7700 (mt-10) outliers start: 131 outliers final: 38 residues processed: 1363 average time/residue: 1.7141 time to fit residues: 2728.4578 Evaluate side-chains 1230 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1177 time to evaluate : 4.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 173 LYS Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 168 GLU Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 173 LYS Chi-restraints excluded: chain P residue 126 ASN Chi-restraints excluded: chain P residue 168 GLU Chi-restraints excluded: chain Q residue 46 ASP Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 168 GLU Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 90 ASP Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 120 LYS Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 96 SER Chi-restraints excluded: chain V residue 126 ASN Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain W residue 120 LYS Chi-restraints excluded: chain W residue 168 GLU Chi-restraints excluded: chain X residue 46 ASP Chi-restraints excluded: chain X residue 168 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 308 optimal weight: 0.6980 chunk 252 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 371 optimal weight: 0.9990 chunk 400 optimal weight: 6.9990 chunk 330 optimal weight: 4.9990 chunk 368 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 chunk 297 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 113 GLN A 140 ASN B 84 GLN B 110 ASN B 140 ASN C 110 ASN C 113 GLN C 140 ASN D 14 HIS D 110 ASN D 140 ASN E 84 GLN E 110 ASN E 113 GLN E 140 ASN F 84 GLN F 110 ASN F 113 GLN F 140 ASN G 59 GLN G 76 GLN G 110 ASN G 140 ASN H 84 GLN H 113 GLN H 140 ASN I 110 ASN I 140 ASN J 84 GLN J 110 ASN J 140 ASN K 84 GLN K 110 ASN K 113 GLN K 140 ASN L 110 ASN L 113 GLN L 140 ASN M 140 ASN N 140 ASN O 110 ASN O 140 ASN ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 ASN R 110 ASN R 140 ASN S 59 GLN T 84 GLN T 110 ASN T 113 GLN T 140 ASN U 110 ASN U 140 ASN V 84 GLN V 110 ASN V 113 GLN V 140 ASN W 110 ASN W 113 GLN X 84 GLN X 110 ASN X 140 ASN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 34608 Z= 0.137 Angle : 0.457 6.068 46608 Z= 0.247 Chirality : 0.036 0.126 4896 Planarity : 0.003 0.026 6144 Dihedral : 3.971 56.468 4491 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 4.49 % Allowed : 17.02 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.81 (0.13), residues: 4080 helix: 3.60 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.21 (0.25), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 94 HIS 0.004 0.001 HIS M 66 PHE 0.009 0.001 PHE L 42 TYR 0.015 0.002 TYR H 138 ARG 0.009 0.001 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1435 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1270 time to evaluate : 4.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8187 (m-80) cc_final: 0.7664 (m-80) REVERT: A 84 GLN cc_start: 0.8271 (mm-40) cc_final: 0.8016 (mm110) REVERT: A 102 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7071 (mt-10) REVERT: B 40 TYR cc_start: 0.8191 (m-80) cc_final: 0.7654 (m-80) REVERT: B 63 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8027 (mm-30) REVERT: B 68 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7604 (mt-10) REVERT: C 40 TYR cc_start: 0.8149 (m-80) cc_final: 0.7650 (m-80) REVERT: C 68 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7611 (mt-10) REVERT: C 84 GLN cc_start: 0.8252 (mm-40) cc_final: 0.8036 (mm-40) REVERT: C 88 LYS cc_start: 0.7979 (pttt) cc_final: 0.7750 (pttt) REVERT: C 96 SER cc_start: 0.8100 (OUTLIER) cc_final: 0.7817 (p) REVERT: D 40 TYR cc_start: 0.8111 (m-80) cc_final: 0.7500 (m-80) REVERT: D 54 LYS cc_start: 0.8007 (tmtt) cc_final: 0.7728 (tptt) REVERT: D 63 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8172 (mm-30) REVERT: D 68 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7503 (mt-10) REVERT: E 40 TYR cc_start: 0.8086 (m-80) cc_final: 0.7522 (m-80) REVERT: E 64 ARG cc_start: 0.7638 (ttp-170) cc_final: 0.7407 (ttm110) REVERT: E 84 GLN cc_start: 0.8282 (mm-40) cc_final: 0.8048 (mm-40) REVERT: E 96 SER cc_start: 0.8027 (OUTLIER) cc_final: 0.7810 (p) REVERT: F 40 TYR cc_start: 0.8065 (m-80) cc_final: 0.7530 (m-80) REVERT: F 84 GLN cc_start: 0.8260 (mm-40) cc_final: 0.8044 (mm-40) REVERT: G 23 ARG cc_start: 0.7908 (mtm110) cc_final: 0.7646 (mtm110) REVERT: G 40 TYR cc_start: 0.8109 (m-80) cc_final: 0.7589 (m-80) REVERT: H 23 ARG cc_start: 0.7856 (mtm110) cc_final: 0.7606 (mtm110) REVERT: H 40 TYR cc_start: 0.8079 (m-80) cc_final: 0.7493 (m-80) REVERT: H 68 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7551 (mt-10) REVERT: H 84 GLN cc_start: 0.8266 (mm-40) cc_final: 0.8064 (mm-40) REVERT: H 96 SER cc_start: 0.8023 (OUTLIER) cc_final: 0.7802 (p) REVERT: H 110 ASN cc_start: 0.7576 (m-40) cc_final: 0.7319 (m110) REVERT: I 40 TYR cc_start: 0.8102 (m-80) cc_final: 0.7591 (m-80) REVERT: I 96 SER cc_start: 0.8049 (OUTLIER) cc_final: 0.7809 (p) REVERT: J 40 TYR cc_start: 0.8131 (m-80) cc_final: 0.7524 (m-80) REVERT: J 63 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8074 (mm-30) REVERT: K 40 TYR cc_start: 0.8069 (m-80) cc_final: 0.7543 (m-80) REVERT: K 96 SER cc_start: 0.8003 (OUTLIER) cc_final: 0.7790 (p) REVERT: L 23 ARG cc_start: 0.7912 (mtm110) cc_final: 0.7649 (mtm110) REVERT: L 40 TYR cc_start: 0.8102 (m-80) cc_final: 0.7545 (m-80) REVERT: L 64 ARG cc_start: 0.7596 (ttp-170) cc_final: 0.7323 (ttp-110) REVERT: L 68 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7506 (mt-10) REVERT: M 40 TYR cc_start: 0.8105 (m-80) cc_final: 0.7542 (m-80) REVERT: M 92 ASP cc_start: 0.6595 (OUTLIER) cc_final: 0.6216 (p0) REVERT: M 96 SER cc_start: 0.8004 (OUTLIER) cc_final: 0.7792 (p) REVERT: M 125 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7410 (mptp) REVERT: N 40 TYR cc_start: 0.8076 (m-80) cc_final: 0.7515 (m-80) REVERT: O 40 TYR cc_start: 0.8122 (m-80) cc_final: 0.7630 (m-80) REVERT: O 68 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7571 (mt-10) REVERT: O 84 GLN cc_start: 0.8280 (mm-40) cc_final: 0.8064 (mm-40) REVERT: O 96 SER cc_start: 0.8051 (OUTLIER) cc_final: 0.7820 (p) REVERT: P 40 TYR cc_start: 0.8130 (m-80) cc_final: 0.7493 (m-80) REVERT: P 63 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8033 (mm-30) REVERT: P 68 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7663 (mt-10) REVERT: P 102 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7141 (mt-10) REVERT: Q 40 TYR cc_start: 0.8090 (m-80) cc_final: 0.7530 (m-80) REVERT: Q 96 SER cc_start: 0.8037 (OUTLIER) cc_final: 0.7799 (p) REVERT: R 23 ARG cc_start: 0.7904 (mtm110) cc_final: 0.7661 (mtm110) REVERT: R 40 TYR cc_start: 0.8075 (m-80) cc_final: 0.7521 (m-80) REVERT: S 40 TYR cc_start: 0.8135 (m-80) cc_final: 0.7616 (m-80) REVERT: S 96 SER cc_start: 0.8063 (OUTLIER) cc_final: 0.7813 (p) REVERT: T 40 TYR cc_start: 0.8062 (m-80) cc_final: 0.7528 (m-80) REVERT: T 120 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7356 (tptp) REVERT: U 23 ARG cc_start: 0.7899 (mtm110) cc_final: 0.7649 (mtm110) REVERT: U 40 TYR cc_start: 0.8179 (m-80) cc_final: 0.7656 (m-80) REVERT: U 68 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7508 (mt-10) REVERT: V 40 TYR cc_start: 0.8115 (m-80) cc_final: 0.7518 (m-80) REVERT: V 63 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8031 (mm-30) REVERT: W 23 ARG cc_start: 0.7902 (mtm110) cc_final: 0.7624 (mtm110) REVERT: W 40 TYR cc_start: 0.8118 (m-80) cc_final: 0.7582 (m-80) REVERT: W 68 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7727 (mt-10) REVERT: W 92 ASP cc_start: 0.6516 (OUTLIER) cc_final: 0.6076 (p0) REVERT: X 23 ARG cc_start: 0.7911 (mtm110) cc_final: 0.7657 (mtm110) REVERT: X 40 TYR cc_start: 0.8057 (m-80) cc_final: 0.7564 (m-80) REVERT: X 68 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7632 (mt-10) outliers start: 165 outliers final: 64 residues processed: 1314 average time/residue: 1.6990 time to fit residues: 2607.5197 Evaluate side-chains 1249 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1172 time to evaluate : 4.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain M residue 46 ASP Chi-restraints excluded: chain M residue 62 GLU Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 168 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 158 LYS Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 90 ASP Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain P residue 168 GLU Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 168 GLU Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain T residue 103 CYS Chi-restraints excluded: chain T residue 120 LYS Chi-restraints excluded: chain T residue 158 LYS Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 158 LYS Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain W residue 92 ASP Chi-restraints excluded: chain W residue 125 LYS Chi-restraints excluded: chain W residue 168 GLU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 103 CYS Chi-restraints excluded: chain X residue 168 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 7.9990 chunk 279 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 177 optimal weight: 0.0050 chunk 249 optimal weight: 2.9990 chunk 372 optimal weight: 2.9990 chunk 394 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 353 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 113 GLN A 140 ASN B 110 ASN B 140 ASN C 110 ASN C 113 GLN C 140 ASN D 110 ASN D 140 ASN E 110 ASN E 113 GLN E 140 ASN F 110 ASN F 113 GLN F 140 ASN F 155 ASN G 110 ASN G 140 ASN H 113 GLN H 140 ASN H 155 ASN I 66 HIS I 110 ASN I 140 ASN J 110 ASN K 84 GLN K 110 ASN K 113 GLN K 140 ASN L 110 ASN L 113 GLN L 155 ASN M 66 HIS M 140 ASN N 84 GLN N 140 ASN N 155 ASN O 110 ASN O 140 ASN ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 GLN P 110 ASN P 140 ASN Q 66 HIS Q 84 GLN Q 126 ASN Q 140 ASN R 84 GLN R 110 ASN R 140 ASN R 155 ASN S 15 GLN S 66 HIS S 84 GLN S 140 ASN T 84 GLN T 110 ASN T 113 GLN T 140 ASN T 155 ASN U 110 ASN U 140 ASN V 110 ASN V 113 GLN V 126 ASN V 140 ASN W 66 HIS W 84 GLN W 110 ASN W 113 GLN W 140 ASN X 110 ASN X 155 ASN Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 34608 Z= 0.153 Angle : 0.472 5.960 46608 Z= 0.252 Chirality : 0.036 0.128 4896 Planarity : 0.003 0.029 6144 Dihedral : 3.959 55.672 4491 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 4.19 % Allowed : 18.14 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.11 (0.13), residues: 4080 helix: 3.87 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.12 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 94 HIS 0.006 0.001 HIS R 66 PHE 0.010 0.001 PHE D 42 TYR 0.015 0.002 TYR O 40 ARG 0.009 0.001 ARG T 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1409 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1255 time to evaluate : 4.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.7286 (mm-40) cc_final: 0.7044 (mm-40) REVERT: A 40 TYR cc_start: 0.8244 (m-80) cc_final: 0.7652 (m-80) REVERT: A 84 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7992 (mm-40) REVERT: A 92 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.5532 (m-30) REVERT: B 15 GLN cc_start: 0.7265 (mm-40) cc_final: 0.7037 (mm-40) REVERT: B 40 TYR cc_start: 0.8239 (m-80) cc_final: 0.7619 (m-80) REVERT: B 68 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7649 (mt-10) REVERT: B 157 ARG cc_start: 0.7724 (mtt-85) cc_final: 0.7264 (mtt-85) REVERT: C 40 TYR cc_start: 0.8209 (m-80) cc_final: 0.7645 (m-80) REVERT: C 64 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7431 (ttm110) REVERT: C 96 SER cc_start: 0.8111 (OUTLIER) cc_final: 0.7838 (p) REVERT: C 157 ARG cc_start: 0.7701 (mtt-85) cc_final: 0.7488 (mtt-85) REVERT: D 40 TYR cc_start: 0.8177 (m-80) cc_final: 0.7564 (m-80) REVERT: D 68 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7534 (mt-10) REVERT: D 92 ASP cc_start: 0.6859 (OUTLIER) cc_final: 0.6563 (p0) REVERT: E 40 TYR cc_start: 0.8161 (m-80) cc_final: 0.7540 (m-80) REVERT: E 84 GLN cc_start: 0.8269 (mm-40) cc_final: 0.8016 (mm-40) REVERT: E 96 SER cc_start: 0.8040 (OUTLIER) cc_final: 0.7813 (p) REVERT: F 40 TYR cc_start: 0.8139 (m-80) cc_final: 0.7559 (m-80) REVERT: G 40 TYR cc_start: 0.8161 (m-80) cc_final: 0.7566 (m-80) REVERT: G 92 ASP cc_start: 0.6755 (OUTLIER) cc_final: 0.6471 (p0) REVERT: H 40 TYR cc_start: 0.8171 (m-80) cc_final: 0.7573 (m-80) REVERT: H 96 SER cc_start: 0.8028 (OUTLIER) cc_final: 0.7752 (p) REVERT: H 110 ASN cc_start: 0.7635 (m-40) cc_final: 0.7393 (m110) REVERT: I 40 TYR cc_start: 0.8212 (m-80) cc_final: 0.7629 (m-80) REVERT: I 96 SER cc_start: 0.8049 (OUTLIER) cc_final: 0.7813 (p) REVERT: J 23 ARG cc_start: 0.7914 (mtm110) cc_final: 0.7678 (mtm110) REVERT: J 40 TYR cc_start: 0.8178 (m-80) cc_final: 0.7555 (m-80) REVERT: K 40 TYR cc_start: 0.8152 (m-80) cc_final: 0.7559 (m-80) REVERT: K 96 SER cc_start: 0.8020 (OUTLIER) cc_final: 0.7775 (p) REVERT: L 40 TYR cc_start: 0.8183 (m-80) cc_final: 0.7545 (m-80) REVERT: L 64 ARG cc_start: 0.7608 (ttp-170) cc_final: 0.7388 (ttm170) REVERT: L 92 ASP cc_start: 0.6514 (p0) cc_final: 0.6179 (p0) REVERT: L 125 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7399 (mptp) REVERT: M 40 TYR cc_start: 0.8177 (m-80) cc_final: 0.7601 (m-80) REVERT: M 96 SER cc_start: 0.8016 (OUTLIER) cc_final: 0.7786 (p) REVERT: N 40 TYR cc_start: 0.8175 (m-80) cc_final: 0.7580 (m-80) REVERT: O 40 TYR cc_start: 0.8220 (m-80) cc_final: 0.7617 (m-80) REVERT: O 84 GLN cc_start: 0.8270 (mm-40) cc_final: 0.8039 (mm-40) REVERT: O 96 SER cc_start: 0.8050 (OUTLIER) cc_final: 0.7814 (p) REVERT: P 40 TYR cc_start: 0.8190 (m-80) cc_final: 0.7551 (m-80) REVERT: P 68 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7715 (mt-10) REVERT: P 157 ARG cc_start: 0.7587 (mtt-85) cc_final: 0.7381 (mtt-85) REVERT: Q 40 TYR cc_start: 0.8159 (m-80) cc_final: 0.7593 (m-80) REVERT: Q 96 SER cc_start: 0.8060 (OUTLIER) cc_final: 0.7805 (p) REVERT: R 15 GLN cc_start: 0.7372 (mm-40) cc_final: 0.7148 (mm-40) REVERT: R 40 TYR cc_start: 0.8163 (m-80) cc_final: 0.7569 (m-80) REVERT: R 92 ASP cc_start: 0.6837 (OUTLIER) cc_final: 0.6572 (p0) REVERT: S 40 TYR cc_start: 0.8182 (m-80) cc_final: 0.7598 (m-80) REVERT: S 96 SER cc_start: 0.8068 (OUTLIER) cc_final: 0.7809 (p) REVERT: T 40 TYR cc_start: 0.8157 (m-80) cc_final: 0.7536 (m-80) REVERT: T 68 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7789 (mt-10) REVERT: U 40 TYR cc_start: 0.8230 (m-80) cc_final: 0.7575 (m-80) REVERT: U 68 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7482 (mt-10) REVERT: V 40 TYR cc_start: 0.8183 (m-80) cc_final: 0.7562 (m-80) REVERT: W 40 TYR cc_start: 0.8155 (m-80) cc_final: 0.7570 (m-80) REVERT: X 40 TYR cc_start: 0.8144 (m-80) cc_final: 0.7570 (m-80) outliers start: 154 outliers final: 61 residues processed: 1310 average time/residue: 1.7411 time to fit residues: 2655.3465 Evaluate side-chains 1241 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1165 time to evaluate : 3.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 64 ARG Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 125 LYS Chi-restraints excluded: chain M residue 46 ASP Chi-restraints excluded: chain M residue 62 GLU Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 168 GLU Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 158 LYS Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 92 ASP Chi-restraints excluded: chain P residue 168 GLU Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 168 GLU Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 103 CYS Chi-restraints excluded: chain T residue 158 LYS Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 158 LYS Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 168 GLU Chi-restraints excluded: chain X residue 103 CYS Chi-restraints excluded: chain X residue 168 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 293 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 336 optimal weight: 0.9990 chunk 272 optimal weight: 0.0050 chunk 0 optimal weight: 7.9990 chunk 201 optimal weight: 0.8980 chunk 353 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 113 GLN A 140 ASN B 84 GLN B 110 ASN B 140 ASN C 110 ASN C 113 GLN C 140 ASN D 110 ASN ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 ASN E 113 GLN E 140 ASN F 84 GLN F 110 ASN F 113 GLN F 140 ASN G 110 ASN G 140 ASN H 84 GLN H 113 GLN H 140 ASN I 66 HIS I 110 ASN I 140 ASN J 84 GLN J 110 ASN J 140 ASN K 84 GLN K 110 ASN K 113 GLN K 140 ASN L 110 ASN L 113 GLN L 140 ASN M 66 HIS M 84 GLN M 140 ASN N 140 ASN O 66 HIS O 110 ASN O 140 ASN ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 ASN P 140 ASN Q 66 HIS Q 140 ASN R 84 GLN R 110 ASN R 140 ASN S 66 HIS S 140 ASN T 84 GLN T 110 ASN T 113 GLN T 140 ASN U 110 ASN ** U 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 140 ASN V 84 GLN V 110 ASN V 113 GLN V 140 ASN W 66 HIS W 110 ASN W 113 GLN W 140 ASN X 84 GLN X 110 ASN X 126 ASN X 140 ASN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 34608 Z= 0.152 Angle : 0.470 5.749 46608 Z= 0.251 Chirality : 0.036 0.126 4896 Planarity : 0.003 0.023 6144 Dihedral : 3.923 54.899 4491 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 4.55 % Allowed : 18.76 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.34 (0.13), residues: 4080 helix: 3.99 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.37 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 94 HIS 0.007 0.001 HIS W 66 PHE 0.010 0.001 PHE B 42 TYR 0.015 0.001 TYR O 40 ARG 0.009 0.001 ARG X 157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1403 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1236 time to evaluate : 4.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.7288 (mm-40) cc_final: 0.7038 (mm-40) REVERT: A 40 TYR cc_start: 0.8209 (m-80) cc_final: 0.7591 (m-80) REVERT: A 84 GLN cc_start: 0.8275 (mm-40) cc_final: 0.8026 (mm-40) REVERT: A 92 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.5602 (m-30) REVERT: B 15 GLN cc_start: 0.7252 (mm-40) cc_final: 0.7017 (mm-40) REVERT: B 40 TYR cc_start: 0.8184 (m-80) cc_final: 0.7572 (m-80) REVERT: B 84 GLN cc_start: 0.8317 (mm-40) cc_final: 0.8099 (mm-40) REVERT: B 92 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6589 (m-30) REVERT: C 40 TYR cc_start: 0.8167 (m-80) cc_final: 0.7604 (m-80) REVERT: C 64 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7423 (ttm110) REVERT: D 40 TYR cc_start: 0.8183 (m-80) cc_final: 0.7557 (m-80) REVERT: D 68 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7485 (mt-10) REVERT: D 92 ASP cc_start: 0.6871 (OUTLIER) cc_final: 0.6551 (p0) REVERT: E 40 TYR cc_start: 0.8159 (m-80) cc_final: 0.7508 (m-80) REVERT: E 84 GLN cc_start: 0.8285 (mm-40) cc_final: 0.8041 (mm-40) REVERT: E 96 SER cc_start: 0.8018 (OUTLIER) cc_final: 0.7800 (p) REVERT: F 40 TYR cc_start: 0.8126 (m-80) cc_final: 0.7523 (m-80) REVERT: F 84 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7967 (mm-40) REVERT: G 40 TYR cc_start: 0.8159 (m-80) cc_final: 0.7538 (m-80) REVERT: G 92 ASP cc_start: 0.6815 (OUTLIER) cc_final: 0.6491 (p0) REVERT: H 40 TYR cc_start: 0.8155 (m-80) cc_final: 0.7509 (m-80) REVERT: H 84 GLN cc_start: 0.8257 (mm-40) cc_final: 0.8049 (mm-40) REVERT: H 96 SER cc_start: 0.8032 (OUTLIER) cc_final: 0.7780 (p) REVERT: H 110 ASN cc_start: 0.7625 (m-40) cc_final: 0.7378 (m110) REVERT: I 40 TYR cc_start: 0.8168 (m-80) cc_final: 0.7578 (m-80) REVERT: I 96 SER cc_start: 0.8021 (OUTLIER) cc_final: 0.7790 (p) REVERT: J 40 TYR cc_start: 0.8167 (m-80) cc_final: 0.7564 (m-80) REVERT: K 40 TYR cc_start: 0.8131 (m-80) cc_final: 0.7510 (m-80) REVERT: K 96 SER cc_start: 0.8013 (OUTLIER) cc_final: 0.7767 (p) REVERT: K 120 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.7156 (tptp) REVERT: L 15 GLN cc_start: 0.7282 (mm-40) cc_final: 0.7058 (mm-40) REVERT: L 23 ARG cc_start: 0.7911 (mtm110) cc_final: 0.7683 (mtm110) REVERT: L 40 TYR cc_start: 0.8174 (m-80) cc_final: 0.7542 (m-80) REVERT: L 64 ARG cc_start: 0.7618 (ttp-170) cc_final: 0.7403 (ttm170) REVERT: L 68 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7612 (mt-10) REVERT: L 92 ASP cc_start: 0.6688 (p0) cc_final: 0.6297 (p0) REVERT: L 125 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7548 (mptp) REVERT: M 40 TYR cc_start: 0.8150 (m-80) cc_final: 0.7558 (m-80) REVERT: M 96 SER cc_start: 0.7986 (OUTLIER) cc_final: 0.7773 (p) REVERT: M 125 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7343 (mptp) REVERT: N 40 TYR cc_start: 0.8163 (m-80) cc_final: 0.7548 (m-80) REVERT: N 68 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7694 (mt-10) REVERT: N 92 ASP cc_start: 0.6513 (OUTLIER) cc_final: 0.6151 (p0) REVERT: O 15 GLN cc_start: 0.7249 (mm-40) cc_final: 0.7028 (mm-40) REVERT: O 40 TYR cc_start: 0.8185 (m-80) cc_final: 0.7578 (m-80) REVERT: O 68 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7601 (mt-10) REVERT: O 84 GLN cc_start: 0.8307 (mm-40) cc_final: 0.8070 (mm-40) REVERT: O 96 SER cc_start: 0.8038 (OUTLIER) cc_final: 0.7815 (p) REVERT: P 40 TYR cc_start: 0.8153 (m-80) cc_final: 0.7523 (m-80) REVERT: P 68 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7714 (mt-10) REVERT: Q 40 TYR cc_start: 0.8144 (m-80) cc_final: 0.7556 (m-80) REVERT: Q 96 SER cc_start: 0.8043 (OUTLIER) cc_final: 0.7785 (p) REVERT: R 15 GLN cc_start: 0.7371 (mm-40) cc_final: 0.7144 (mm-40) REVERT: R 40 TYR cc_start: 0.8148 (m-80) cc_final: 0.7546 (m-80) REVERT: R 84 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7970 (mm-40) REVERT: S 40 TYR cc_start: 0.8165 (m-80) cc_final: 0.7587 (m-80) REVERT: S 96 SER cc_start: 0.8040 (OUTLIER) cc_final: 0.7797 (p) REVERT: T 40 TYR cc_start: 0.8154 (m-80) cc_final: 0.7503 (m-80) REVERT: T 68 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7712 (mt-10) REVERT: U 40 TYR cc_start: 0.8184 (m-80) cc_final: 0.7538 (m-80) REVERT: V 40 TYR cc_start: 0.8157 (m-80) cc_final: 0.7530 (m-80) REVERT: V 68 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7712 (mt-10) REVERT: W 23 ARG cc_start: 0.7906 (mtm110) cc_final: 0.7659 (mtm110) REVERT: W 40 TYR cc_start: 0.8150 (m-80) cc_final: 0.7554 (m-80) REVERT: W 92 ASP cc_start: 0.6663 (OUTLIER) cc_final: 0.6179 (p0) REVERT: X 15 GLN cc_start: 0.7301 (mm-40) cc_final: 0.7073 (mm-40) REVERT: X 40 TYR cc_start: 0.8148 (m-80) cc_final: 0.7538 (m-80) REVERT: X 157 ARG cc_start: 0.7606 (mtt-85) cc_final: 0.7345 (mtt-85) outliers start: 167 outliers final: 98 residues processed: 1294 average time/residue: 1.7170 time to fit residues: 2592.5848 Evaluate side-chains 1273 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1157 time to evaluate : 4.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 64 ARG Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 158 LYS Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 120 LYS Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 125 LYS Chi-restraints excluded: chain M residue 46 ASP Chi-restraints excluded: chain M residue 62 GLU Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 168 GLU Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 62 GLU Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 158 LYS Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain P residue 92 ASP Chi-restraints excluded: chain P residue 168 GLU Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 168 GLU Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 87 LYS Chi-restraints excluded: chain S residue 90 ASP Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 62 GLU Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain T residue 103 CYS Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 158 LYS Chi-restraints excluded: chain U residue 62 GLU Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 158 LYS Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 46 ASP Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain V residue 173 LYS Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 87 LYS Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain W residue 92 ASP Chi-restraints excluded: chain W residue 125 LYS Chi-restraints excluded: chain W residue 168 GLU Chi-restraints excluded: chain X residue 62 GLU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 92 ASP Chi-restraints excluded: chain X residue 103 CYS Chi-restraints excluded: chain X residue 168 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 3.9990 chunk 355 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 231 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 394 optimal weight: 2.9990 chunk 327 optimal weight: 0.9990 chunk 182 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 130 optimal weight: 0.4980 chunk 207 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 110 ASN A 113 GLN A 140 ASN B 110 ASN B 140 ASN C 84 GLN C 110 ASN C 113 GLN C 140 ASN D 110 ASN D 140 ASN ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 ASN E 113 GLN E 140 ASN F 113 GLN F 140 ASN G 110 ASN G 140 ASN H 113 GLN H 140 ASN I 66 HIS I 110 ASN I 140 ASN J 110 ASN J 140 ASN K 84 GLN K 110 ASN K 113 GLN K 140 ASN L 110 ASN L 113 GLN L 140 ASN M 66 HIS M 140 ASN N 140 ASN O 66 HIS O 110 ASN O 140 ASN ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 HIS P 84 GLN P 110 ASN P 140 ASN Q 66 HIS Q 84 GLN Q 140 ASN R 110 ASN R 140 ASN S 66 HIS S 140 ASN T 84 GLN T 113 GLN T 140 ASN U 110 ASN ** U 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 140 ASN V 84 GLN V 110 ASN V 113 GLN V 140 ASN W 66 HIS W 84 GLN W 110 ASN W 113 GLN W 140 ASN X 110 ASN X 140 ASN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 34608 Z= 0.138 Angle : 0.458 5.479 46608 Z= 0.245 Chirality : 0.035 0.122 4896 Planarity : 0.003 0.029 6144 Dihedral : 3.687 14.402 4488 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.14 % Allowed : 20.02 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.55 (0.13), residues: 4080 helix: 4.12 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.51 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 94 HIS 0.008 0.001 HIS M 66 PHE 0.010 0.001 PHE X 42 TYR 0.014 0.001 TYR O 40 ARG 0.011 0.001 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1374 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1222 time to evaluate : 3.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.7263 (mm-40) cc_final: 0.7017 (mm-40) REVERT: A 40 TYR cc_start: 0.8103 (m-80) cc_final: 0.7546 (m-80) REVERT: A 84 GLN cc_start: 0.8271 (mm-40) cc_final: 0.8036 (mm-40) REVERT: B 15 GLN cc_start: 0.7239 (mm-40) cc_final: 0.7013 (mm-40) REVERT: B 40 TYR cc_start: 0.8067 (m-80) cc_final: 0.7484 (m-80) REVERT: C 40 TYR cc_start: 0.8070 (m-80) cc_final: 0.7509 (m-80) REVERT: C 64 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7385 (ttm110) REVERT: D 40 TYR cc_start: 0.8088 (m-80) cc_final: 0.7520 (m-80) REVERT: D 68 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7419 (mt-10) REVERT: D 92 ASP cc_start: 0.6857 (OUTLIER) cc_final: 0.6478 (p0) REVERT: D 102 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7157 (mt-10) REVERT: E 40 TYR cc_start: 0.8071 (m-80) cc_final: 0.7509 (m-80) REVERT: E 84 GLN cc_start: 0.8290 (mm-40) cc_final: 0.8048 (mm-40) REVERT: F 40 TYR cc_start: 0.8061 (m-80) cc_final: 0.7490 (m-80) REVERT: G 40 TYR cc_start: 0.8076 (m-80) cc_final: 0.7487 (m-80) REVERT: G 92 ASP cc_start: 0.6873 (OUTLIER) cc_final: 0.6535 (p0) REVERT: G 125 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7490 (mptp) REVERT: G 126 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7641 (m-40) REVERT: H 23 ARG cc_start: 0.7855 (mtm110) cc_final: 0.7617 (mtm110) REVERT: H 40 TYR cc_start: 0.8101 (m-80) cc_final: 0.7506 (m-80) REVERT: H 84 GLN cc_start: 0.8275 (mm-40) cc_final: 0.8061 (mm-40) REVERT: H 110 ASN cc_start: 0.7524 (m-40) cc_final: 0.7283 (m110) REVERT: I 40 TYR cc_start: 0.8034 (m-80) cc_final: 0.7518 (m-80) REVERT: J 40 TYR cc_start: 0.8090 (m-80) cc_final: 0.7509 (m-80) REVERT: K 40 TYR cc_start: 0.8095 (m-80) cc_final: 0.7534 (m-80) REVERT: K 96 SER cc_start: 0.7960 (OUTLIER) cc_final: 0.7711 (p) REVERT: K 120 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.7166 (tptp) REVERT: L 40 TYR cc_start: 0.8105 (m-80) cc_final: 0.7472 (m-80) REVERT: L 64 ARG cc_start: 0.7639 (ttp-170) cc_final: 0.7424 (ttm170) REVERT: L 92 ASP cc_start: 0.6732 (p0) cc_final: 0.6347 (p0) REVERT: M 40 TYR cc_start: 0.8080 (m-80) cc_final: 0.7536 (m-80) REVERT: M 96 SER cc_start: 0.7920 (OUTLIER) cc_final: 0.7706 (p) REVERT: M 125 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7299 (mptp) REVERT: N 40 TYR cc_start: 0.8090 (m-80) cc_final: 0.7500 (m-80) REVERT: N 68 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7662 (mt-10) REVERT: N 92 ASP cc_start: 0.6580 (OUTLIER) cc_final: 0.6175 (p0) REVERT: O 40 TYR cc_start: 0.8053 (m-80) cc_final: 0.7485 (m-80) REVERT: O 68 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7598 (mt-10) REVERT: O 84 GLN cc_start: 0.8283 (mm-40) cc_final: 0.8038 (mm-40) REVERT: O 92 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.5737 (m-30) REVERT: O 96 SER cc_start: 0.8002 (OUTLIER) cc_final: 0.7791 (p) REVERT: P 40 TYR cc_start: 0.8098 (m-80) cc_final: 0.7515 (m-80) REVERT: P 68 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7637 (mt-10) REVERT: Q 40 TYR cc_start: 0.8075 (m-80) cc_final: 0.7500 (m-80) REVERT: Q 96 SER cc_start: 0.7935 (OUTLIER) cc_final: 0.7689 (p) REVERT: R 15 GLN cc_start: 0.7336 (mm-40) cc_final: 0.7097 (mm-40) REVERT: R 40 TYR cc_start: 0.8083 (m-80) cc_final: 0.7496 (m-80) REVERT: R 84 GLN cc_start: 0.8265 (mm-40) cc_final: 0.8003 (mm-40) REVERT: S 40 TYR cc_start: 0.8080 (m-80) cc_final: 0.7512 (m-80) REVERT: S 96 SER cc_start: 0.7940 (OUTLIER) cc_final: 0.7702 (p) REVERT: T 40 TYR cc_start: 0.8076 (m-80) cc_final: 0.7478 (m-80) REVERT: T 68 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7706 (mt-10) REVERT: U 40 TYR cc_start: 0.8092 (m-80) cc_final: 0.7492 (m-80) REVERT: U 125 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7531 (mptp) REVERT: V 40 TYR cc_start: 0.8095 (m-80) cc_final: 0.7518 (m-80) REVERT: V 68 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7689 (mt-10) REVERT: W 40 TYR cc_start: 0.8063 (m-80) cc_final: 0.7471 (m-80) REVERT: X 15 GLN cc_start: 0.7290 (mm-40) cc_final: 0.7061 (mm-40) REVERT: X 40 TYR cc_start: 0.8057 (m-80) cc_final: 0.7483 (m-80) outliers start: 152 outliers final: 93 residues processed: 1276 average time/residue: 1.7193 time to fit residues: 2554.4681 Evaluate side-chains 1268 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1160 time to evaluate : 4.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 64 ARG Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 158 LYS Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 173 LYS Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain K residue 120 LYS Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain M residue 46 ASP Chi-restraints excluded: chain M residue 62 GLU Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 168 GLU Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 158 LYS Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 173 LYS Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain P residue 168 GLU Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 168 GLU Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 62 GLU Chi-restraints excluded: chain T residue 90 ASP Chi-restraints excluded: chain T residue 103 CYS Chi-restraints excluded: chain T residue 158 LYS Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 62 GLU Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 125 LYS Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 46 ASP Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain V residue 173 LYS Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 87 LYS Chi-restraints excluded: chain W residue 125 LYS Chi-restraints excluded: chain X residue 62 GLU Chi-restraints excluded: chain X residue 92 ASP Chi-restraints excluded: chain X residue 168 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 332 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 393 optimal weight: 4.9990 chunk 246 optimal weight: 0.7980 chunk 239 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 113 GLN A 140 ASN B 84 GLN B 110 ASN B 140 ASN C 110 ASN C 113 GLN C 140 ASN D 110 ASN D 140 ASN ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 ASN E 113 GLN E 140 ASN F 84 GLN F 113 GLN F 140 ASN G 110 ASN G 140 ASN H 113 GLN H 140 ASN I 11 GLN I 66 HIS I 110 ASN I 140 ASN J 84 GLN J 110 ASN J 140 ASN K 84 GLN K 110 ASN K 113 GLN K 140 ASN L 84 GLN L 110 ASN L 113 GLN L 140 ASN M 66 HIS M 140 ASN N 84 GLN N 140 ASN O 66 HIS O 110 ASN O 140 ASN ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 ASN P 140 ASN Q 66 HIS Q 140 ASN R 110 ASN R 140 ASN S 66 HIS S 140 ASN T 84 GLN T 113 GLN T 140 ASN U 110 ASN U 126 ASN U 140 ASN V 84 GLN V 110 ASN V 113 GLN V 126 ASN V 140 ASN W 66 HIS W 110 ASN W 113 GLN W 140 ASN X 110 ASN X 140 ASN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 34608 Z= 0.288 Angle : 0.604 6.990 46608 Z= 0.313 Chirality : 0.041 0.150 4896 Planarity : 0.004 0.032 6144 Dihedral : 3.974 12.866 4488 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.93 % Allowed : 19.50 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.04 (0.13), residues: 4080 helix: 3.69 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.73 (0.28), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 94 HIS 0.010 0.001 HIS M 66 PHE 0.013 0.002 PHE X 42 TYR 0.023 0.002 TYR O 40 ARG 0.010 0.001 ARG J 157 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1395 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1214 time to evaluate : 4.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8083 (mm-40) REVERT: B 15 GLN cc_start: 0.7342 (mm-40) cc_final: 0.7103 (mm-40) REVERT: B 40 TYR cc_start: 0.8379 (m-80) cc_final: 0.7608 (m-80) REVERT: C 40 TYR cc_start: 0.8355 (m-80) cc_final: 0.7592 (m-80) REVERT: C 64 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7454 (ttm110) REVERT: C 120 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7387 (tmtt) REVERT: D 54 LYS cc_start: 0.8075 (tmtt) cc_final: 0.7848 (tptt) REVERT: D 92 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.6499 (p0) REVERT: D 126 ASN cc_start: 0.7835 (OUTLIER) cc_final: 0.7618 (m-40) REVERT: E 84 GLN cc_start: 0.8300 (mm-40) cc_final: 0.8061 (mm-40) REVERT: F 157 ARG cc_start: 0.7593 (mtt-85) cc_final: 0.7388 (mtt-85) REVERT: G 126 ASN cc_start: 0.7892 (OUTLIER) cc_final: 0.7654 (m-40) REVERT: H 110 ASN cc_start: 0.7763 (m-40) cc_final: 0.7458 (m110) REVERT: I 40 TYR cc_start: 0.8373 (m-80) cc_final: 0.7612 (m-80) REVERT: K 96 SER cc_start: 0.8138 (OUTLIER) cc_final: 0.7705 (p) REVERT: K 120 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7299 (tptp) REVERT: L 125 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7493 (mptp) REVERT: M 96 SER cc_start: 0.8121 (OUTLIER) cc_final: 0.7733 (p) REVERT: M 125 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7203 (mptp) REVERT: N 92 ASP cc_start: 0.6774 (OUTLIER) cc_final: 0.6308 (p0) REVERT: O 84 GLN cc_start: 0.8284 (mm-40) cc_final: 0.8056 (mm-40) REVERT: O 96 SER cc_start: 0.8106 (OUTLIER) cc_final: 0.7711 (p) REVERT: P 157 ARG cc_start: 0.7826 (mtt-85) cc_final: 0.7493 (mtt-85) REVERT: Q 96 SER cc_start: 0.8143 (OUTLIER) cc_final: 0.7722 (p) REVERT: R 15 GLN cc_start: 0.7412 (mm-40) cc_final: 0.7171 (mm-40) REVERT: R 120 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7276 (tptp) REVERT: S 96 SER cc_start: 0.8150 (OUTLIER) cc_final: 0.7766 (p) REVERT: U 40 TYR cc_start: 0.8406 (m-80) cc_final: 0.7608 (m-80) REVERT: U 125 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7485 (mptp) REVERT: W 15 GLN cc_start: 0.7413 (mm-40) cc_final: 0.7199 (mm-40) outliers start: 181 outliers final: 119 residues processed: 1276 average time/residue: 1.7024 time to fit residues: 2538.0626 Evaluate side-chains 1265 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1130 time to evaluate : 4.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 64 ARG Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 158 LYS Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain K residue 120 LYS Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 125 LYS Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 62 GLU Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 114 SER Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 168 GLU Chi-restraints excluded: chain N residue 62 GLU Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 96 SER Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 158 LYS Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain O residue 62 GLU Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 117 GLU Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 92 ASP Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 168 GLU Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 114 SER Chi-restraints excluded: chain Q residue 168 GLU Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain T residue 62 GLU Chi-restraints excluded: chain T residue 92 ASP Chi-restraints excluded: chain T residue 103 CYS Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 158 LYS Chi-restraints excluded: chain U residue 62 GLU Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 125 LYS Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 16 ASP Chi-restraints excluded: chain V residue 114 SER Chi-restraints excluded: chain V residue 126 ASN Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain V residue 173 LYS Chi-restraints excluded: chain W residue 87 LYS Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain W residue 114 SER Chi-restraints excluded: chain W residue 125 LYS Chi-restraints excluded: chain W residue 168 GLU Chi-restraints excluded: chain X residue 62 GLU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 92 ASP Chi-restraints excluded: chain X residue 103 CYS Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 158 LYS Chi-restraints excluded: chain X residue 168 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 250 optimal weight: 0.7980 chunk 267 optimal weight: 0.5980 chunk 194 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 309 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 113 GLN A 140 ASN B 110 ASN C 110 ASN C 113 GLN C 140 ASN D 110 ASN D 140 ASN ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 ASN E 113 GLN E 140 ASN F 84 GLN F 113 GLN F 140 ASN G 58 HIS G 110 ASN G 140 ASN H 84 GLN H 113 GLN H 140 ASN I 110 ASN I 140 ASN J 110 ASN J 140 ASN K 84 GLN K 110 ASN K 113 GLN K 140 ASN L 61 HIS L 110 ASN L 113 GLN M 140 ASN N 140 ASN O 110 ASN O 140 ASN ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 ASN P 140 ASN R 84 GLN R 110 ASN R 140 ASN S 140 ASN T 84 GLN T 113 GLN T 140 ASN U 110 ASN ** U 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 140 ASN V 84 GLN V 110 ASN V 113 GLN V 140 ASN W 110 ASN W 113 GLN W 140 ASN X 110 ASN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 34608 Z= 0.238 Angle : 0.570 6.498 46608 Z= 0.298 Chirality : 0.039 0.143 4896 Planarity : 0.003 0.026 6144 Dihedral : 3.934 13.540 4488 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 4.44 % Allowed : 20.15 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.13 (0.13), residues: 4080 helix: 3.73 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.90 (0.29), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP T 94 HIS 0.008 0.001 HIS A 66 PHE 0.012 0.002 PHE J 42 TYR 0.019 0.002 TYR O 40 ARG 0.011 0.001 ARG J 157 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1334 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1171 time to evaluate : 4.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8346 (m-80) cc_final: 0.7385 (m-80) REVERT: A 54 LYS cc_start: 0.8040 (tmtt) cc_final: 0.7832 (tptt) REVERT: B 15 GLN cc_start: 0.7364 (mm-40) cc_final: 0.7120 (mm-40) REVERT: B 40 TYR cc_start: 0.8331 (m-80) cc_final: 0.7367 (m-80) REVERT: B 68 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7609 (mt-10) REVERT: B 92 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6533 (m-30) REVERT: C 40 TYR cc_start: 0.8314 (m-80) cc_final: 0.7403 (m-80) REVERT: C 54 LYS cc_start: 0.8009 (tmtt) cc_final: 0.7787 (tptt) REVERT: C 157 ARG cc_start: 0.7883 (mtt-85) cc_final: 0.7547 (mtt-85) REVERT: D 40 TYR cc_start: 0.8348 (m-80) cc_final: 0.7457 (m-80) REVERT: D 68 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7785 (mt-10) REVERT: D 92 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6555 (p0) REVERT: D 126 ASN cc_start: 0.7856 (OUTLIER) cc_final: 0.7646 (m-40) REVERT: E 40 TYR cc_start: 0.8321 (m-80) cc_final: 0.7466 (m-80) REVERT: E 84 GLN cc_start: 0.8322 (mm-40) cc_final: 0.8038 (mm-40) REVERT: F 40 TYR cc_start: 0.8311 (m-80) cc_final: 0.7481 (m-80) REVERT: F 84 GLN cc_start: 0.8241 (mm-40) cc_final: 0.8008 (mm-40) REVERT: F 102 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7184 (mt-10) REVERT: G 40 TYR cc_start: 0.8343 (m-80) cc_final: 0.7438 (m-80) REVERT: H 40 TYR cc_start: 0.8346 (m-80) cc_final: 0.7497 (m-80) REVERT: H 84 GLN cc_start: 0.8289 (mm-40) cc_final: 0.8069 (mm-40) REVERT: H 110 ASN cc_start: 0.7743 (m-40) cc_final: 0.7445 (m110) REVERT: I 40 TYR cc_start: 0.8311 (m-80) cc_final: 0.7525 (m-80) REVERT: I 68 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7497 (mt-10) REVERT: J 40 TYR cc_start: 0.8334 (m-80) cc_final: 0.7446 (m-80) REVERT: K 40 TYR cc_start: 0.8319 (m-80) cc_final: 0.7449 (m-80) REVERT: K 96 SER cc_start: 0.8216 (OUTLIER) cc_final: 0.7818 (p) REVERT: K 120 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7263 (tptp) REVERT: L 40 TYR cc_start: 0.8350 (m-80) cc_final: 0.7476 (m-80) REVERT: L 125 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7560 (mptp) REVERT: M 40 TYR cc_start: 0.8340 (m-80) cc_final: 0.7470 (m-80) REVERT: M 96 SER cc_start: 0.8111 (OUTLIER) cc_final: 0.7756 (p) REVERT: N 40 TYR cc_start: 0.8333 (m-80) cc_final: 0.7486 (m-80) REVERT: O 40 TYR cc_start: 0.8351 (m-80) cc_final: 0.7533 (m-80) REVERT: O 84 GLN cc_start: 0.8295 (mm-40) cc_final: 0.8094 (mm-40) REVERT: O 96 SER cc_start: 0.8135 (OUTLIER) cc_final: 0.7760 (p) REVERT: O 102 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7204 (mt-10) REVERT: P 40 TYR cc_start: 0.8356 (m-80) cc_final: 0.7454 (m-80) REVERT: P 157 ARG cc_start: 0.7825 (mtt-85) cc_final: 0.7532 (mtt-85) REVERT: Q 40 TYR cc_start: 0.8327 (m-80) cc_final: 0.7564 (m-80) REVERT: Q 96 SER cc_start: 0.8112 (OUTLIER) cc_final: 0.7726 (p) REVERT: R 15 GLN cc_start: 0.7406 (mm-40) cc_final: 0.7161 (mm-40) REVERT: R 40 TYR cc_start: 0.8334 (m-80) cc_final: 0.7480 (m-80) REVERT: R 54 LYS cc_start: 0.8078 (tmtt) cc_final: 0.7869 (tptt) REVERT: R 84 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7998 (mm-40) REVERT: S 40 TYR cc_start: 0.8325 (m-80) cc_final: 0.7436 (m-80) REVERT: S 92 ASP cc_start: 0.6727 (OUTLIER) cc_final: 0.6384 (p0) REVERT: S 96 SER cc_start: 0.8124 (OUTLIER) cc_final: 0.7720 (p) REVERT: S 102 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7261 (mt-10) REVERT: T 40 TYR cc_start: 0.8339 (m-80) cc_final: 0.7484 (m-80) REVERT: T 84 GLN cc_start: 0.8283 (mm-40) cc_final: 0.8034 (mm-40) REVERT: T 92 ASP cc_start: 0.6713 (p0) cc_final: 0.6271 (p0) REVERT: T 120 LYS cc_start: 0.7673 (tmtp) cc_final: 0.7203 (tptp) REVERT: U 40 TYR cc_start: 0.8344 (m-80) cc_final: 0.7492 (m-80) REVERT: U 54 LYS cc_start: 0.8072 (tmtt) cc_final: 0.7858 (tptt) REVERT: U 120 LYS cc_start: 0.7598 (tmtp) cc_final: 0.7291 (tptp) REVERT: V 40 TYR cc_start: 0.8335 (m-80) cc_final: 0.7449 (m-80) REVERT: W 15 GLN cc_start: 0.7413 (mm-40) cc_final: 0.7201 (mm-40) REVERT: W 40 TYR cc_start: 0.8352 (m-80) cc_final: 0.7474 (m-80) REVERT: W 120 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7363 (tptp) REVERT: X 40 TYR cc_start: 0.8333 (m-80) cc_final: 0.7483 (m-80) outliers start: 163 outliers final: 119 residues processed: 1227 average time/residue: 1.7924 time to fit residues: 2553.3083 Evaluate side-chains 1252 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1121 time to evaluate : 3.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 158 LYS Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 173 LYS Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain K residue 120 LYS Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 125 LYS Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 62 GLU Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 168 GLU Chi-restraints excluded: chain N residue 62 GLU Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 96 SER Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 158 LYS Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 62 GLU Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 117 GLU Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 173 LYS Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 92 ASP Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 168 GLU Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 168 GLU Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain S residue 117 GLU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 126 ASN Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain T residue 16 ASP Chi-restraints excluded: chain T residue 62 GLU Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 103 CYS Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 158 LYS Chi-restraints excluded: chain U residue 62 GLU Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 114 SER Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain V residue 173 LYS Chi-restraints excluded: chain W residue 87 LYS Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain W residue 114 SER Chi-restraints excluded: chain W residue 120 LYS Chi-restraints excluded: chain W residue 125 LYS Chi-restraints excluded: chain W residue 168 GLU Chi-restraints excluded: chain X residue 62 GLU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 92 ASP Chi-restraints excluded: chain X residue 103 CYS Chi-restraints excluded: chain X residue 168 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 0.1980 chunk 376 optimal weight: 4.9990 chunk 343 optimal weight: 2.9990 chunk 366 optimal weight: 3.9990 chunk 220 optimal weight: 0.8980 chunk 159 optimal weight: 0.5980 chunk 287 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 331 optimal weight: 4.9990 chunk 346 optimal weight: 0.8980 chunk 365 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 113 GLN A 140 ASN B 84 GLN B 110 ASN C 110 ASN C 113 GLN C 140 ASN D 110 ASN D 140 ASN ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 ASN E 113 GLN E 140 ASN F 113 GLN F 140 ASN G 58 HIS G 110 ASN G 140 ASN H 113 GLN H 140 ASN I 110 ASN I 140 ASN J 84 GLN J 99 ASN J 110 ASN J 126 ASN J 140 ASN K 84 GLN K 110 ASN K 113 GLN K 140 ASN L 84 GLN L 110 ASN L 113 GLN L 140 ASN M 140 ASN N 84 GLN N 140 ASN O 110 ASN O 140 ASN ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 ASN P 140 ASN R 110 ASN R 140 ASN S 140 ASN T 113 GLN T 140 ASN U 110 ASN U 126 ASN U 140 ASN V 14 HIS V 84 GLN V 110 ASN V 113 GLN V 140 ASN W 110 ASN W 113 GLN W 126 ASN W 140 ASN X 110 ASN X 140 ASN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34608 Z= 0.147 Angle : 0.488 7.775 46608 Z= 0.261 Chirality : 0.035 0.125 4896 Planarity : 0.003 0.030 6144 Dihedral : 3.743 14.435 4488 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.43 % Allowed : 21.76 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.58 (0.13), residues: 4080 helix: 4.09 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.78 (0.29), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP T 94 HIS 0.006 0.001 HIS A 66 PHE 0.011 0.001 PHE J 42 TYR 0.014 0.001 TYR O 40 ARG 0.012 0.001 ARG F 157 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1320 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1194 time to evaluate : 4.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8111 (m-80) cc_final: 0.7558 (m-80) REVERT: A 157 ARG cc_start: 0.7700 (mtt-85) cc_final: 0.7244 (mtt-85) REVERT: B 15 GLN cc_start: 0.7295 (mm-40) cc_final: 0.7085 (mm-40) REVERT: B 40 TYR cc_start: 0.8076 (m-80) cc_final: 0.7494 (m-80) REVERT: C 40 TYR cc_start: 0.8095 (m-80) cc_final: 0.7515 (m-80) REVERT: C 157 ARG cc_start: 0.7742 (mtt-85) cc_final: 0.7475 (mtt-85) REVERT: D 40 TYR cc_start: 0.8105 (m-80) cc_final: 0.7552 (m-80) REVERT: D 54 LYS cc_start: 0.7907 (tptt) cc_final: 0.7686 (tptt) REVERT: D 68 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7672 (mt-10) REVERT: D 92 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6543 (p0) REVERT: D 126 ASN cc_start: 0.7852 (OUTLIER) cc_final: 0.7613 (m-40) REVERT: D 157 ARG cc_start: 0.7709 (mtt-85) cc_final: 0.7441 (mtt-85) REVERT: E 40 TYR cc_start: 0.8095 (m-80) cc_final: 0.7535 (m-80) REVERT: E 84 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8088 (mm-40) REVERT: F 40 TYR cc_start: 0.8075 (m-80) cc_final: 0.7574 (m-80) REVERT: F 84 GLN cc_start: 0.8316 (mm-40) cc_final: 0.8103 (mm-40) REVERT: F 158 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7310 (mmmm) REVERT: G 40 TYR cc_start: 0.8090 (m-80) cc_final: 0.7563 (m-80) REVERT: H 40 TYR cc_start: 0.8116 (m-80) cc_final: 0.7583 (m-80) REVERT: H 84 GLN cc_start: 0.8347 (mm-40) cc_final: 0.8127 (mm-40) REVERT: H 110 ASN cc_start: 0.7608 (m-40) cc_final: 0.7363 (m110) REVERT: I 40 TYR cc_start: 0.8105 (m-80) cc_final: 0.7583 (m-80) REVERT: I 113 GLN cc_start: 0.8014 (tp-100) cc_final: 0.7751 (tp-100) REVERT: I 117 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: J 40 TYR cc_start: 0.8075 (m-80) cc_final: 0.7541 (m-80) REVERT: K 40 TYR cc_start: 0.8093 (m-80) cc_final: 0.7559 (m-80) REVERT: K 96 SER cc_start: 0.8037 (OUTLIER) cc_final: 0.7770 (p) REVERT: L 40 TYR cc_start: 0.8111 (m-80) cc_final: 0.7556 (m-80) REVERT: L 68 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7547 (mt-10) REVERT: L 92 ASP cc_start: 0.6766 (OUTLIER) cc_final: 0.6491 (p0) REVERT: L 125 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7605 (mptp) REVERT: M 40 TYR cc_start: 0.8096 (m-80) cc_final: 0.7570 (m-80) REVERT: N 40 TYR cc_start: 0.8099 (m-80) cc_final: 0.7582 (m-80) REVERT: O 40 TYR cc_start: 0.8120 (m-80) cc_final: 0.7583 (m-80) REVERT: O 84 GLN cc_start: 0.8266 (mm-40) cc_final: 0.8019 (mm-40) REVERT: O 96 SER cc_start: 0.8065 (OUTLIER) cc_final: 0.7808 (p) REVERT: O 157 ARG cc_start: 0.7756 (mtt-85) cc_final: 0.7551 (mtt-85) REVERT: P 40 TYR cc_start: 0.8117 (m-80) cc_final: 0.7551 (m-80) REVERT: P 54 LYS cc_start: 0.8078 (tmtt) cc_final: 0.7876 (tptt) REVERT: P 63 GLU cc_start: 0.8430 (mm-30) cc_final: 0.7967 (mm-30) REVERT: P 102 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7233 (mt-10) REVERT: P 157 ARG cc_start: 0.7723 (mtt-85) cc_final: 0.7442 (mtt-85) REVERT: Q 40 TYR cc_start: 0.8088 (m-80) cc_final: 0.7571 (m-80) REVERT: Q 92 ASP cc_start: 0.6620 (OUTLIER) cc_final: 0.6180 (p0) REVERT: Q 96 SER cc_start: 0.8020 (OUTLIER) cc_final: 0.7746 (p) REVERT: R 15 GLN cc_start: 0.7348 (mm-40) cc_final: 0.7118 (mm-40) REVERT: R 40 TYR cc_start: 0.8089 (m-80) cc_final: 0.7570 (m-80) REVERT: R 84 GLN cc_start: 0.8266 (mm-40) cc_final: 0.8009 (mm-40) REVERT: R 120 LYS cc_start: 0.7605 (tmtp) cc_final: 0.7390 (tptp) REVERT: S 40 TYR cc_start: 0.8096 (m-80) cc_final: 0.7584 (m-80) REVERT: T 40 TYR cc_start: 0.8083 (m-80) cc_final: 0.7563 (m-80) REVERT: T 84 GLN cc_start: 0.8333 (mm-40) cc_final: 0.8108 (mm-40) REVERT: T 120 LYS cc_start: 0.7616 (tmtp) cc_final: 0.7379 (tptp) REVERT: T 157 ARG cc_start: 0.7702 (mtt-85) cc_final: 0.7474 (mtt-85) REVERT: U 40 TYR cc_start: 0.8110 (m-80) cc_final: 0.7545 (m-80) REVERT: V 40 TYR cc_start: 0.8107 (m-80) cc_final: 0.7523 (m-80) REVERT: W 40 TYR cc_start: 0.8110 (m-80) cc_final: 0.7588 (m-80) REVERT: W 120 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7263 (tptp) REVERT: X 40 TYR cc_start: 0.8095 (m-80) cc_final: 0.7573 (m-80) REVERT: X 157 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7482 (mtt90) outliers start: 126 outliers final: 76 residues processed: 1243 average time/residue: 1.7409 time to fit residues: 2516.5282 Evaluate side-chains 1230 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1142 time to evaluate : 4.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 125 LYS Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 168 GLU Chi-restraints excluded: chain N residue 62 GLU Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 117 GLU Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain P residue 62 GLU Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 168 GLU Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain S residue 117 GLU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain T residue 62 GLU Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 103 CYS Chi-restraints excluded: chain T residue 158 LYS Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain V residue 173 LYS Chi-restraints excluded: chain W residue 87 LYS Chi-restraints excluded: chain W residue 120 LYS Chi-restraints excluded: chain W residue 126 ASN Chi-restraints excluded: chain W residue 158 LYS Chi-restraints excluded: chain X residue 62 GLU Chi-restraints excluded: chain X residue 92 ASP Chi-restraints excluded: chain X residue 103 CYS Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 157 ARG Chi-restraints excluded: chain X residue 168 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 2.9990 chunk 387 optimal weight: 0.9980 chunk 236 optimal weight: 0.0470 chunk 183 optimal weight: 5.9990 chunk 269 optimal weight: 0.6980 chunk 406 optimal weight: 0.6980 chunk 374 optimal weight: 2.9990 chunk 323 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 250 optimal weight: 0.5980 chunk 198 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 84 GLN A 110 ASN A 140 ASN B 110 ASN B 140 ASN C 110 ASN C 140 ASN D 110 ASN D 140 ASN ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 ASN E 140 ASN F 113 GLN F 126 ASN F 140 ASN G 58 HIS G 110 ASN G 140 ASN H 113 GLN H 140 ASN I 110 ASN I 140 ASN J 110 ASN J 140 ASN K 84 GLN K 110 ASN K 140 ASN L 110 ASN L 113 GLN L 140 ASN M 84 GLN M 140 ASN N 140 ASN O 110 ASN O 140 ASN ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 GLN P 110 ASN P 140 ASN Q 140 ASN R 110 ASN R 140 ASN S 126 ASN S 140 ASN T 113 GLN T 140 ASN U 110 ASN U 126 ASN U 140 ASN V 14 HIS V 84 GLN V 110 ASN V 140 ASN W 110 ASN W 113 GLN W 126 ASN W 140 ASN X 110 ASN X 140 ASN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34608 Z= 0.142 Angle : 0.489 8.244 46608 Z= 0.262 Chirality : 0.035 0.121 4896 Planarity : 0.003 0.035 6144 Dihedral : 3.692 14.393 4488 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.34 % Allowed : 23.31 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.74 (0.13), residues: 4080 helix: 4.21 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.84 (0.29), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP T 94 HIS 0.006 0.001 HIS A 66 PHE 0.011 0.001 PHE J 42 TYR 0.013 0.001 TYR O 40 ARG 0.010 0.001 ARG A 157 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1293 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1207 time to evaluate : 4.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.7978 (m-80) cc_final: 0.7440 (m-80) REVERT: A 68 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7555 (mt-10) REVERT: B 40 TYR cc_start: 0.7962 (m-80) cc_final: 0.7402 (m-80) REVERT: C 40 TYR cc_start: 0.7958 (m-80) cc_final: 0.7397 (m-80) REVERT: C 157 ARG cc_start: 0.7737 (mtt-85) cc_final: 0.7468 (mtt-85) REVERT: D 40 TYR cc_start: 0.7982 (m-80) cc_final: 0.7431 (m-80) REVERT: D 68 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7656 (mt-10) REVERT: D 92 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6747 (p0) REVERT: D 126 ASN cc_start: 0.7832 (OUTLIER) cc_final: 0.7607 (m-40) REVERT: D 157 ARG cc_start: 0.7752 (mtt-85) cc_final: 0.7354 (mtt-85) REVERT: E 40 TYR cc_start: 0.7977 (m-80) cc_final: 0.7456 (m-80) REVERT: E 84 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8073 (mm-40) REVERT: F 40 TYR cc_start: 0.7958 (m-80) cc_final: 0.7453 (m-80) REVERT: G 40 TYR cc_start: 0.7987 (m-80) cc_final: 0.7458 (m-80) REVERT: H 40 TYR cc_start: 0.7994 (m-80) cc_final: 0.7426 (m-80) REVERT: H 63 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8104 (mm-30) REVERT: H 84 GLN cc_start: 0.8351 (mm-40) cc_final: 0.8146 (mm-40) REVERT: H 110 ASN cc_start: 0.7526 (m-40) cc_final: 0.7286 (m110) REVERT: I 40 TYR cc_start: 0.7996 (m-80) cc_final: 0.7520 (m-80) REVERT: J 40 TYR cc_start: 0.7952 (m-80) cc_final: 0.7420 (m-80) REVERT: J 92 ASP cc_start: 0.6946 (OUTLIER) cc_final: 0.6727 (p0) REVERT: K 40 TYR cc_start: 0.7967 (m-80) cc_final: 0.7452 (m-80) REVERT: L 40 TYR cc_start: 0.7995 (m-80) cc_final: 0.7444 (m-80) REVERT: L 68 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7570 (mt-10) REVERT: L 125 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7612 (mptp) REVERT: M 40 TYR cc_start: 0.7961 (m-80) cc_final: 0.7482 (m-80) REVERT: N 40 TYR cc_start: 0.7980 (m-80) cc_final: 0.7472 (m-80) REVERT: O 40 TYR cc_start: 0.7989 (m-80) cc_final: 0.7466 (m-80) REVERT: O 84 GLN cc_start: 0.8258 (mm-40) cc_final: 0.8035 (mm-40) REVERT: P 40 TYR cc_start: 0.7983 (m-80) cc_final: 0.7437 (m-80) REVERT: P 54 LYS cc_start: 0.8061 (tmtt) cc_final: 0.7832 (tptt) REVERT: P 63 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7964 (mm-30) REVERT: P 102 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7170 (mt-10) REVERT: P 157 ARG cc_start: 0.7721 (mtt-85) cc_final: 0.7448 (mtt-85) REVERT: Q 40 TYR cc_start: 0.7957 (m-80) cc_final: 0.7442 (m-80) REVERT: Q 157 ARG cc_start: 0.7788 (mtt-85) cc_final: 0.7528 (mtt-85) REVERT: R 15 GLN cc_start: 0.7305 (mm-40) cc_final: 0.7078 (mm-40) REVERT: R 40 TYR cc_start: 0.7977 (m-80) cc_final: 0.7458 (m-80) REVERT: R 84 GLN cc_start: 0.8275 (mm-40) cc_final: 0.8036 (mm-40) REVERT: S 40 TYR cc_start: 0.7975 (m-80) cc_final: 0.7450 (m-80) REVERT: T 40 TYR cc_start: 0.7958 (m-80) cc_final: 0.7441 (m-80) REVERT: T 120 LYS cc_start: 0.7507 (tmtp) cc_final: 0.7262 (tptp) REVERT: T 157 ARG cc_start: 0.7766 (mtt-85) cc_final: 0.7469 (mtt-85) REVERT: U 40 TYR cc_start: 0.7984 (m-80) cc_final: 0.7390 (m-80) REVERT: U 125 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7515 (mptp) REVERT: V 40 TYR cc_start: 0.7972 (m-80) cc_final: 0.7428 (m-80) REVERT: W 40 TYR cc_start: 0.7988 (m-80) cc_final: 0.7451 (m-80) REVERT: W 120 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.7240 (tptp) REVERT: X 40 TYR cc_start: 0.7978 (m-80) cc_final: 0.7465 (m-80) outliers start: 86 outliers final: 50 residues processed: 1247 average time/residue: 1.6980 time to fit residues: 2469.5379 Evaluate side-chains 1206 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1150 time to evaluate : 4.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 126 ASN Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 168 GLU Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 125 LYS Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 168 GLU Chi-restraints excluded: chain N residue 103 CYS Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 117 GLU Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain Q residue 114 SER Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 126 ASN Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain T residue 62 GLU Chi-restraints excluded: chain T residue 158 LYS Chi-restraints excluded: chain U residue 125 LYS Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain W residue 120 LYS Chi-restraints excluded: chain W residue 126 ASN Chi-restraints excluded: chain W residue 168 GLU Chi-restraints excluded: chain X residue 103 CYS Chi-restraints excluded: chain X residue 114 SER Chi-restraints excluded: chain X residue 168 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 6.9990 chunk 344 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 298 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 324 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 332 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 66 HIS A 84 GLN A 110 ASN A 140 ASN B 110 ASN B 140 ASN C 58 HIS C 110 ASN C 113 GLN C 140 ASN D 58 HIS D 66 HIS D 110 ASN D 140 ASN ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN E 66 HIS E 110 ASN E 126 ASN E 140 ASN ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN G 58 HIS G 110 ASN G 140 ASN H 58 HIS H 140 ASN I 66 HIS I 110 ASN I 140 ASN ** J 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN J 110 ASN J 140 ASN K 58 HIS K 84 GLN K 110 ASN K 113 GLN K 140 ASN ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 110 ASN L 113 GLN L 140 ASN ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 ASN N 66 HIS N 84 GLN N 140 ASN ** O 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 66 HIS O 110 ASN O 140 ASN ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 ASN P 140 ASN ** Q 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 126 ASN Q 140 ASN R 66 HIS R 110 ASN R 140 ASN S 14 HIS S 58 HIS S 140 ASN T 66 HIS T 84 GLN T 140 ASN U 66 HIS U 110 ASN U 126 ASN U 140 ASN ** V 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 84 GLN V 110 ASN V 113 GLN V 140 ASN ** W 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 66 HIS W 110 ASN W 140 ASN ** X 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 84 GLN X 110 ASN X 140 ASN Total number of N/Q/H flips: 74 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.138860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.131535 restraints weight = 34670.296| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 0.73 r_work: 0.3255 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 34608 Z= 0.227 Angle : 0.863 59.156 46608 Z= 0.498 Chirality : 0.042 0.891 4896 Planarity : 0.003 0.077 6144 Dihedral : 3.740 32.328 4488 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.96 % Allowed : 24.65 % Favored : 73.39 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 5.72 (0.13), residues: 4080 helix: 4.20 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.81 (0.29), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP T 94 HIS 0.009 0.001 HIS E 66 PHE 0.011 0.001 PHE J 42 TYR 0.013 0.002 TYR O 40 ARG 0.018 0.001 ARG A 157 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29526.85 seconds wall clock time: 521 minutes 5.98 seconds (31265.98 seconds total)