Starting phenix.real_space_refine on Mon Mar 25 04:45:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uti_20880/03_2024/6uti_20880.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uti_20880/03_2024/6uti_20880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uti_20880/03_2024/6uti_20880.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uti_20880/03_2024/6uti_20880.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uti_20880/03_2024/6uti_20880.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uti_20880/03_2024/6uti_20880.pdb" } resolution = 3.4 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= 0.001 sd= 0.255 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 196 5.16 5 C 29407 2.51 5 N 7840 2.21 5 O 8953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46396 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain: "B" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain: "C" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain: "D" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain: "F" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain: "G" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain: "O" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1766 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "P" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1766 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "Q" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1766 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "R" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1766 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "S" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1766 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "T" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1766 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "U" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1766 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "H" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "I" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "J" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "K" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "L" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "M" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "N" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "V" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "W" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "X" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "Y" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "Z" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "a" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "b" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Residues with excluded nonbonded symmetry interactions: 57 residue: pdb=" N VAL O 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 77 " occ=0.50 residue: pdb=" N VAL P 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL P 77 " occ=0.50 residue: pdb=" N VAL Q 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL Q 77 " occ=0.50 residue: pdb=" N VAL R 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL R 77 " occ=0.50 residue: pdb=" N VAL S 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL S 77 " occ=0.50 residue: pdb=" N ASN H 24 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN H 24 " occ=0.50 residue: pdb=" N TYR H 58 " occ=0.50 ... (10 atoms not shown) pdb=" OH TYR H 58 " occ=0.50 residue: pdb=" N GLN H 89 " occ=0.50 ... (7 atoms not shown) pdb=" NE2 GLN H 89 " occ=0.50 residue: pdb=" N MET H 96 " occ=0.50 ... (6 atoms not shown) pdb=" CE MET H 96 " occ=0.50 residue: pdb=" N ASN I 24 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN I 24 " occ=0.50 residue: pdb=" N TYR I 58 " occ=0.50 ... (10 atoms not shown) pdb=" OH TYR I 58 " occ=0.50 residue: pdb=" N MET I 96 " occ=0.50 ... (6 atoms not shown) pdb=" CE MET I 96 " occ=0.50 ... (remaining 45 not shown) Time building chain proxies: 23.12, per 1000 atoms: 0.50 Number of scatterers: 46396 At special positions: 0 Unit cell: (135, 136.08, 176.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 196 16.00 O 8953 8.00 N 7840 7.00 C 29407 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: 17.02 Conformation dependent library (CDL) restraints added in 6.9 seconds 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11060 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 56 sheets defined 40.8% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.89 Creating SS restraints... Processing helix chain 'A' and resid 21 through 32 Processing helix chain 'A' and resid 81 through 104 Processing helix chain 'A' and resid 108 through 126 removed outlier: 3.887A pdb=" N LEU A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 180 Processing helix chain 'A' and resid 185 through 202 removed outlier: 3.570A pdb=" N SER A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.784A pdb=" N VAL A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS A 230 " --> pdb=" O GLN A 226 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 32 Processing helix chain 'B' and resid 81 through 104 Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.924A pdb=" N LEU B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 180 Processing helix chain 'B' and resid 185 through 202 removed outlier: 3.607A pdb=" N SER B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 233 removed outlier: 3.806A pdb=" N VAL B 229 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS B 230 " --> pdb=" O GLN B 226 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 32 Processing helix chain 'C' and resid 81 through 104 Processing helix chain 'C' and resid 108 through 126 removed outlier: 3.929A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR C 123 " --> pdb=" O GLN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 180 Processing helix chain 'C' and resid 185 through 202 removed outlier: 3.581A pdb=" N SER C 200 " --> pdb=" O ALA C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.806A pdb=" N VAL C 229 " --> pdb=" O ASP C 225 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS C 230 " --> pdb=" O GLN C 226 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 32 Processing helix chain 'D' and resid 81 through 104 Processing helix chain 'D' and resid 108 through 126 removed outlier: 3.895A pdb=" N LEU D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR D 123 " --> pdb=" O GLN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 180 Processing helix chain 'D' and resid 185 through 202 removed outlier: 3.569A pdb=" N SER D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 233 removed outlier: 3.778A pdb=" N VAL D 229 " --> pdb=" O ASP D 225 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS D 230 " --> pdb=" O GLN D 226 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 32 Processing helix chain 'E' and resid 81 through 104 Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.922A pdb=" N LEU E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR E 123 " --> pdb=" O GLN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 180 Processing helix chain 'E' and resid 185 through 202 removed outlier: 3.576A pdb=" N SER E 200 " --> pdb=" O ALA E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 233 removed outlier: 3.792A pdb=" N VAL E 229 " --> pdb=" O ASP E 225 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS E 230 " --> pdb=" O GLN E 226 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 32 Processing helix chain 'F' and resid 81 through 103 Processing helix chain 'F' and resid 108 through 126 removed outlier: 3.880A pdb=" N LEU F 112 " --> pdb=" O ASN F 108 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR F 123 " --> pdb=" O GLN F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 180 Processing helix chain 'F' and resid 185 through 202 removed outlier: 3.573A pdb=" N SER F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 233 removed outlier: 3.790A pdb=" N VAL F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS F 230 " --> pdb=" O GLN F 226 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 32 Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 126 removed outlier: 3.885A pdb=" N LEU G 112 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL G 116 " --> pdb=" O LEU G 112 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 180 Processing helix chain 'G' and resid 185 through 202 removed outlier: 3.567A pdb=" N SER G 200 " --> pdb=" O ALA G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 233 removed outlier: 3.788A pdb=" N VAL G 229 " --> pdb=" O ASP G 225 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS G 230 " --> pdb=" O GLN G 226 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS G 231 " --> pdb=" O GLU G 227 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 32 removed outlier: 3.547A pdb=" N LYS O 32 " --> pdb=" O LEU O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 64 removed outlier: 3.739A pdb=" N ILE O 64 " --> pdb=" O GLN O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 104 Processing helix chain 'O' and resid 108 through 123 removed outlier: 4.297A pdb=" N LEU O 112 " --> pdb=" O ASN O 108 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR O 123 " --> pdb=" O GLN O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 180 removed outlier: 3.559A pdb=" N ARG O 178 " --> pdb=" O SER O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 185 through 199 Processing helix chain 'O' and resid 225 through 231 removed outlier: 3.619A pdb=" N LYS O 231 " --> pdb=" O GLU O 227 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 32 removed outlier: 3.601A pdb=" N LYS P 32 " --> pdb=" O LEU P 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 64 removed outlier: 3.751A pdb=" N ILE P 64 " --> pdb=" O GLN P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 104 Processing helix chain 'P' and resid 108 through 123 removed outlier: 4.260A pdb=" N LEU P 112 " --> pdb=" O ASN P 108 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR P 123 " --> pdb=" O GLN P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 180 removed outlier: 3.558A pdb=" N ARG P 178 " --> pdb=" O SER P 174 " (cutoff:3.500A) Processing helix chain 'P' and resid 185 through 199 Processing helix chain 'P' and resid 225 through 231 removed outlier: 3.629A pdb=" N LYS P 231 " --> pdb=" O GLU P 227 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 32 removed outlier: 3.556A pdb=" N LYS Q 32 " --> pdb=" O LEU Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 64 removed outlier: 3.710A pdb=" N ILE Q 64 " --> pdb=" O GLN Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 104 Processing helix chain 'Q' and resid 108 through 123 removed outlier: 4.283A pdb=" N LEU Q 112 " --> pdb=" O ASN Q 108 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR Q 123 " --> pdb=" O GLN Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 180 removed outlier: 3.551A pdb=" N ARG Q 178 " --> pdb=" O SER Q 174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 199 Processing helix chain 'Q' and resid 225 through 231 removed outlier: 3.615A pdb=" N LYS Q 231 " --> pdb=" O GLU Q 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 32 removed outlier: 3.568A pdb=" N LYS R 32 " --> pdb=" O LEU R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 64 removed outlier: 3.755A pdb=" N ILE R 64 " --> pdb=" O GLN R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 104 Processing helix chain 'R' and resid 108 through 123 removed outlier: 4.272A pdb=" N LEU R 112 " --> pdb=" O ASN R 108 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR R 123 " --> pdb=" O GLN R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 180 removed outlier: 3.570A pdb=" N ARG R 178 " --> pdb=" O SER R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 199 Processing helix chain 'R' and resid 225 through 231 removed outlier: 3.623A pdb=" N LYS R 231 " --> pdb=" O GLU R 227 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 32 Processing helix chain 'S' and resid 60 through 64 removed outlier: 3.718A pdb=" N ILE S 64 " --> pdb=" O GLN S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 104 Processing helix chain 'S' and resid 108 through 123 removed outlier: 4.296A pdb=" N LEU S 112 " --> pdb=" O ASN S 108 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR S 123 " --> pdb=" O GLN S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 180 removed outlier: 3.559A pdb=" N ARG S 178 " --> pdb=" O SER S 174 " (cutoff:3.500A) Processing helix chain 'S' and resid 185 through 199 Processing helix chain 'S' and resid 225 through 230 Processing helix chain 'S' and resid 231 through 233 No H-bonds generated for 'chain 'S' and resid 231 through 233' Processing helix chain 'T' and resid 21 through 32 Processing helix chain 'T' and resid 60 through 64 removed outlier: 3.738A pdb=" N ILE T 64 " --> pdb=" O GLN T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 81 through 104 Processing helix chain 'T' and resid 108 through 123 removed outlier: 4.236A pdb=" N LEU T 112 " --> pdb=" O ASN T 108 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR T 123 " --> pdb=" O GLN T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 180 removed outlier: 3.575A pdb=" N ARG T 178 " --> pdb=" O SER T 174 " (cutoff:3.500A) Processing helix chain 'T' and resid 185 through 199 Processing helix chain 'T' and resid 225 through 231 removed outlier: 3.611A pdb=" N LYS T 231 " --> pdb=" O GLU T 227 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 32 Processing helix chain 'U' and resid 60 through 64 removed outlier: 3.740A pdb=" N ILE U 64 " --> pdb=" O GLN U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 104 Processing helix chain 'U' and resid 108 through 123 removed outlier: 4.262A pdb=" N LEU U 112 " --> pdb=" O ASN U 108 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR U 123 " --> pdb=" O GLN U 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 168 through 180 removed outlier: 3.575A pdb=" N ARG U 178 " --> pdb=" O SER U 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 185 through 199 Processing helix chain 'U' and resid 225 through 231 removed outlier: 3.623A pdb=" N LYS U 231 " --> pdb=" O GLU U 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 89 Processing helix chain 'H' and resid 130 through 142 removed outlier: 4.017A pdb=" N SER H 140 " --> pdb=" O GLY H 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR H 142 " --> pdb=" O LEU H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 163 Processing helix chain 'H' and resid 188 through 200 Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 89 Processing helix chain 'I' and resid 130 through 142 removed outlier: 4.017A pdb=" N SER I 140 " --> pdb=" O GLY I 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR I 142 " --> pdb=" O LEU I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 163 Processing helix chain 'I' and resid 188 through 200 Processing helix chain 'J' and resid 48 through 71 Processing helix chain 'J' and resid 75 through 89 Processing helix chain 'J' and resid 130 through 142 removed outlier: 4.017A pdb=" N SER J 140 " --> pdb=" O GLY J 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR J 142 " --> pdb=" O LEU J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 163 Processing helix chain 'J' and resid 188 through 200 Processing helix chain 'K' and resid 48 through 71 Processing helix chain 'K' and resid 75 through 89 Processing helix chain 'K' and resid 130 through 142 removed outlier: 4.017A pdb=" N SER K 140 " --> pdb=" O GLY K 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 163 Processing helix chain 'K' and resid 188 through 200 Processing helix chain 'L' and resid 48 through 71 Processing helix chain 'L' and resid 75 through 89 Processing helix chain 'L' and resid 130 through 142 removed outlier: 4.017A pdb=" N SER L 140 " --> pdb=" O GLY L 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR L 142 " --> pdb=" O LEU L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 163 Processing helix chain 'L' and resid 188 through 200 Processing helix chain 'M' and resid 48 through 71 Processing helix chain 'M' and resid 75 through 89 Processing helix chain 'M' and resid 130 through 142 removed outlier: 4.017A pdb=" N SER M 140 " --> pdb=" O GLY M 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR M 142 " --> pdb=" O LEU M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 163 Processing helix chain 'M' and resid 188 through 200 Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 89 Processing helix chain 'N' and resid 130 through 142 removed outlier: 4.017A pdb=" N SER N 140 " --> pdb=" O GLY N 136 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR N 142 " --> pdb=" O LEU N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 163 Processing helix chain 'N' and resid 188 through 200 Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 89 Processing helix chain 'V' and resid 130 through 142 removed outlier: 4.017A pdb=" N SER V 140 " --> pdb=" O GLY V 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR V 142 " --> pdb=" O LEU V 138 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 163 Processing helix chain 'V' and resid 188 through 200 Processing helix chain 'W' and resid 48 through 71 Processing helix chain 'W' and resid 75 through 89 Processing helix chain 'W' and resid 130 through 142 removed outlier: 4.018A pdb=" N SER W 140 " --> pdb=" O GLY W 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR W 142 " --> pdb=" O LEU W 138 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 163 Processing helix chain 'W' and resid 188 through 200 Processing helix chain 'X' and resid 48 through 71 Processing helix chain 'X' and resid 75 through 89 Processing helix chain 'X' and resid 130 through 142 removed outlier: 4.018A pdb=" N SER X 140 " --> pdb=" O GLY X 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR X 142 " --> pdb=" O LEU X 138 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 163 Processing helix chain 'X' and resid 188 through 200 Processing helix chain 'Y' and resid 48 through 71 Processing helix chain 'Y' and resid 75 through 89 Processing helix chain 'Y' and resid 130 through 142 removed outlier: 4.017A pdb=" N SER Y 140 " --> pdb=" O GLY Y 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 163 Processing helix chain 'Y' and resid 188 through 200 Processing helix chain 'Z' and resid 48 through 71 Processing helix chain 'Z' and resid 75 through 89 Processing helix chain 'Z' and resid 130 through 142 removed outlier: 4.018A pdb=" N SER Z 140 " --> pdb=" O GLY Z 136 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR Z 142 " --> pdb=" O LEU Z 138 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 163 Processing helix chain 'Z' and resid 188 through 200 Processing helix chain 'a' and resid 48 through 71 Processing helix chain 'a' and resid 75 through 89 Processing helix chain 'a' and resid 130 through 142 removed outlier: 4.018A pdb=" N SER a 140 " --> pdb=" O GLY a 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR a 142 " --> pdb=" O LEU a 138 " (cutoff:3.500A) Processing helix chain 'a' and resid 147 through 163 Processing helix chain 'a' and resid 188 through 200 Processing helix chain 'b' and resid 48 through 71 Processing helix chain 'b' and resid 75 through 89 Processing helix chain 'b' and resid 130 through 142 removed outlier: 4.017A pdb=" N SER b 140 " --> pdb=" O GLY b 136 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR b 142 " --> pdb=" O LEU b 138 " (cutoff:3.500A) Processing helix chain 'b' and resid 147 through 163 Processing helix chain 'b' and resid 188 through 200 Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 165 removed outlier: 3.646A pdb=" N GLY A 45 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 222 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 71 removed outlier: 6.287A pdb=" N VAL A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 136 " --> pdb=" O CYS A 151 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE A 138 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN A 158 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 162 through 165 removed outlier: 3.510A pdb=" N ARG B 222 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 71 removed outlier: 6.274A pdb=" N VAL B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 162 through 165 removed outlier: 3.643A pdb=" N GLY C 45 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG C 222 " --> pdb=" O SER C 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 67 through 71 removed outlier: 6.267A pdb=" N VAL C 74 " --> pdb=" O ILE C 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 162 through 165 removed outlier: 3.632A pdb=" N GLY D 45 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG D 222 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 71 removed outlier: 6.295A pdb=" N VAL D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 162 through 165 removed outlier: 3.629A pdb=" N GLY E 45 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG E 222 " --> pdb=" O SER E 214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.287A pdb=" N VAL E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 162 through 165 removed outlier: 3.650A pdb=" N GLY F 45 " --> pdb=" O PHE F 42 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 67 through 71 removed outlier: 6.270A pdb=" N VAL F 74 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU F 136 " --> pdb=" O CYS F 151 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE F 138 " --> pdb=" O PHE F 149 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN F 158 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.631A pdb=" N GLY G 45 " --> pdb=" O PHE G 42 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG G 222 " --> pdb=" O SER G 214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 67 through 71 removed outlier: 6.278A pdb=" N VAL G 74 " --> pdb=" O ILE G 70 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU G 136 " --> pdb=" O CYS G 151 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE G 138 " --> pdb=" O PHE G 149 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN G 158 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 162 through 165 removed outlier: 3.513A pdb=" N GLY O 45 " --> pdb=" O PHE O 42 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ILE O 212 " --> pdb=" O TYR O 224 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 67 through 69 removed outlier: 3.567A pdb=" N ASN O 158 " --> pdb=" O ASP O 150 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 162 through 165 removed outlier: 3.509A pdb=" N GLY P 45 " --> pdb=" O PHE P 42 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ILE P 212 " --> pdb=" O TYR P 224 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 67 through 69 removed outlier: 3.553A pdb=" N ASN P 158 " --> pdb=" O ASP P 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Q' and resid 162 through 165 removed outlier: 3.507A pdb=" N GLY Q 45 " --> pdb=" O PHE Q 42 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE Q 212 " --> pdb=" O TYR Q 224 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Q' and resid 67 through 69 removed outlier: 3.561A pdb=" N ASN Q 158 " --> pdb=" O ASP Q 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'R' and resid 162 through 165 removed outlier: 3.510A pdb=" N GLY R 45 " --> pdb=" O PHE R 42 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE R 212 " --> pdb=" O TYR R 224 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'R' and resid 67 through 69 removed outlier: 3.545A pdb=" N ASN R 158 " --> pdb=" O ASP R 150 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'S' and resid 162 through 165 removed outlier: 3.521A pdb=" N GLY S 45 " --> pdb=" O PHE S 42 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE S 212 " --> pdb=" O TYR S 224 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'S' and resid 67 through 69 removed outlier: 3.556A pdb=" N ASN S 158 " --> pdb=" O ASP S 150 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'T' and resid 162 through 165 removed outlier: 3.547A pdb=" N GLY T 45 " --> pdb=" O PHE T 42 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE T 212 " --> pdb=" O TYR T 224 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 67 through 69 removed outlier: 3.548A pdb=" N ASN T 158 " --> pdb=" O ASP T 150 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 162 through 165 removed outlier: 3.505A pdb=" N GLY U 45 " --> pdb=" O PHE U 42 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE U 212 " --> pdb=" O TYR U 224 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'U' and resid 67 through 69 removed outlier: 3.566A pdb=" N ASN U 158 " --> pdb=" O ASP U 150 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 8 removed outlier: 4.062A pdb=" N ALA H 11 " --> pdb=" O LEU H 8 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 34 through 38 removed outlier: 6.673A pdb=" N THR H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 3 through 8 removed outlier: 4.063A pdb=" N ALA I 11 " --> pdb=" O LEU I 8 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.673A pdb=" N THR I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 3 through 8 removed outlier: 4.062A pdb=" N ALA J 11 " --> pdb=" O LEU J 8 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 34 through 38 removed outlier: 6.674A pdb=" N THR J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 3 through 8 removed outlier: 4.062A pdb=" N ALA K 11 " --> pdb=" O LEU K 8 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 34 through 38 removed outlier: 6.673A pdb=" N THR K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 3 through 8 removed outlier: 4.063A pdb=" N ALA L 11 " --> pdb=" O LEU L 8 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.672A pdb=" N THR L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 3 through 8 removed outlier: 4.062A pdb=" N ALA M 11 " --> pdb=" O LEU M 8 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 34 through 38 removed outlier: 6.673A pdb=" N THR M 41 " --> pdb=" O ILE M 37 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 3 through 8 removed outlier: 4.062A pdb=" N ALA N 11 " --> pdb=" O LEU N 8 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 34 through 38 removed outlier: 6.673A pdb=" N THR N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 3 through 8 removed outlier: 4.063A pdb=" N ALA V 11 " --> pdb=" O LEU V 8 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'V' and resid 34 through 38 removed outlier: 6.673A pdb=" N THR V 41 " --> pdb=" O ILE V 37 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'W' and resid 3 through 8 removed outlier: 4.062A pdb=" N ALA W 11 " --> pdb=" O LEU W 8 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.673A pdb=" N THR W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 3 through 8 removed outlier: 4.063A pdb=" N ALA X 11 " --> pdb=" O LEU X 8 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'X' and resid 34 through 38 removed outlier: 6.674A pdb=" N THR X 41 " --> pdb=" O ILE X 37 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Y' and resid 3 through 8 removed outlier: 4.062A pdb=" N ALA Y 11 " --> pdb=" O LEU Y 8 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Y' and resid 34 through 38 removed outlier: 6.673A pdb=" N THR Y 41 " --> pdb=" O ILE Y 37 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Z' and resid 3 through 8 removed outlier: 4.062A pdb=" N ALA Z 11 " --> pdb=" O LEU Z 8 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.673A pdb=" N THR Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'a' and resid 3 through 8 removed outlier: 4.063A pdb=" N ALA a 11 " --> pdb=" O LEU a 8 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 34 through 38 removed outlier: 6.673A pdb=" N THR a 41 " --> pdb=" O ILE a 37 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'b' and resid 3 through 8 removed outlier: 4.062A pdb=" N ALA b 11 " --> pdb=" O LEU b 8 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'b' and resid 34 through 38 removed outlier: 6.673A pdb=" N THR b 41 " --> pdb=" O ILE b 37 " (cutoff:3.500A) 2538 hydrogen bonds defined for protein. 7401 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: 16.91 Time building geometry restraints manager: 18.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14685 1.34 - 1.46: 6286 1.46 - 1.57: 25635 1.57 - 1.69: 7 1.69 - 1.81: 378 Bond restraints: 46991 Sorted by residual: bond pdb=" CA LYS B 53 " pdb=" CB LYS B 53 " ideal model delta sigma weight residual 1.525 1.593 -0.068 1.47e-02 4.63e+03 2.15e+01 bond pdb=" CA LYS E 53 " pdb=" CB LYS E 53 " ideal model delta sigma weight residual 1.525 1.591 -0.066 1.47e-02 4.63e+03 2.02e+01 bond pdb=" CA LYS C 53 " pdb=" CB LYS C 53 " ideal model delta sigma weight residual 1.525 1.591 -0.066 1.47e-02 4.63e+03 2.02e+01 bond pdb=" CA LYS D 53 " pdb=" CB LYS D 53 " ideal model delta sigma weight residual 1.525 1.590 -0.065 1.47e-02 4.63e+03 1.97e+01 bond pdb=" CA LYS A 53 " pdb=" CB LYS A 53 " ideal model delta sigma weight residual 1.525 1.590 -0.065 1.47e-02 4.63e+03 1.95e+01 ... (remaining 46986 not shown) Histogram of bond angle deviations from ideal: 96.09 - 104.25: 533 104.25 - 112.41: 23252 112.41 - 120.57: 22451 120.57 - 128.73: 17115 128.73 - 136.89: 83 Bond angle restraints: 63434 Sorted by residual: angle pdb=" C LEU A 207 " pdb=" N LYS A 208 " pdb=" CA LYS A 208 " ideal model delta sigma weight residual 121.54 136.89 -15.35 1.91e+00 2.74e-01 6.46e+01 angle pdb=" C LEU F 207 " pdb=" N LYS F 208 " pdb=" CA LYS F 208 " ideal model delta sigma weight residual 121.54 136.85 -15.31 1.91e+00 2.74e-01 6.42e+01 angle pdb=" C LEU C 207 " pdb=" N LYS C 208 " pdb=" CA LYS C 208 " ideal model delta sigma weight residual 121.54 136.83 -15.29 1.91e+00 2.74e-01 6.41e+01 angle pdb=" C LEU B 207 " pdb=" N LYS B 208 " pdb=" CA LYS B 208 " ideal model delta sigma weight residual 121.54 136.82 -15.28 1.91e+00 2.74e-01 6.40e+01 angle pdb=" C LEU D 207 " pdb=" N LYS D 208 " pdb=" CA LYS D 208 " ideal model delta sigma weight residual 121.54 136.82 -15.28 1.91e+00 2.74e-01 6.40e+01 ... (remaining 63429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 27480 16.18 - 32.36: 939 32.36 - 48.54: 261 48.54 - 64.72: 27 64.72 - 80.90: 49 Dihedral angle restraints: 28756 sinusoidal: 11445 harmonic: 17311 Sorted by residual: dihedral pdb=" CA LEU B 207 " pdb=" C LEU B 207 " pdb=" N LYS B 208 " pdb=" CA LYS B 208 " ideal model delta harmonic sigma weight residual 180.00 144.54 35.46 0 5.00e+00 4.00e-02 5.03e+01 dihedral pdb=" CA LEU D 207 " pdb=" C LEU D 207 " pdb=" N LYS D 208 " pdb=" CA LYS D 208 " ideal model delta harmonic sigma weight residual 180.00 144.65 35.35 0 5.00e+00 4.00e-02 5.00e+01 dihedral pdb=" CA LEU C 207 " pdb=" C LEU C 207 " pdb=" N LYS C 208 " pdb=" CA LYS C 208 " ideal model delta harmonic sigma weight residual 180.00 144.67 35.33 0 5.00e+00 4.00e-02 4.99e+01 ... (remaining 28753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 6616 0.095 - 0.190: 778 0.190 - 0.285: 40 0.285 - 0.380: 0 0.380 - 0.475: 7 Chirality restraints: 7441 Sorted by residual: chirality pdb=" CB ILE G 212 " pdb=" CA ILE G 212 " pdb=" CG1 ILE G 212 " pdb=" CG2 ILE G 212 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" CB ILE A 212 " pdb=" CA ILE A 212 " pdb=" CG1 ILE A 212 " pdb=" CG2 ILE A 212 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" CB ILE F 212 " pdb=" CA ILE F 212 " pdb=" CG1 ILE F 212 " pdb=" CG2 ILE F 212 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.38e+00 ... (remaining 7438 not shown) Planarity restraints: 8134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 49 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C ILE F 49 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE F 49 " -0.021 2.00e-02 2.50e+03 pdb=" N SER F 50 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 49 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C ILE G 49 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE G 49 " -0.021 2.00e-02 2.50e+03 pdb=" N SER G 50 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 152 " 0.053 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO G 153 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO G 153 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO G 153 " 0.044 5.00e-02 4.00e+02 ... (remaining 8131 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 7315 2.77 - 3.30: 40567 3.30 - 3.83: 72554 3.83 - 4.37: 84541 4.37 - 4.90: 152161 Nonbonded interactions: 357138 Sorted by model distance: nonbonded pdb=" O LYS Q 41 " pdb=" OH TYR Q 180 " model vdw 2.232 2.440 nonbonded pdb=" O LYS O 41 " pdb=" OH TYR O 180 " model vdw 2.233 2.440 nonbonded pdb=" O LYS P 41 " pdb=" OH TYR P 180 " model vdw 2.233 2.440 nonbonded pdb=" O LYS R 41 " pdb=" OH TYR R 180 " model vdw 2.238 2.440 nonbonded pdb=" O LYS S 41 " pdb=" OH TYR S 180 " model vdw 2.244 2.440 ... (remaining 357133 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' and (resid 9 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'B' and (resid 9 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'C' and (resid 9 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'D' and (resid 9 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'E' and (resid 9 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'F' and (resid 9 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'G' and (resid 9 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'O' and (resid 9 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'P' and (resid 9 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'Q' and (resid 9 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'R' and (resid 9 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'S' and (resid 9 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'T' and (resid 9 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'U' and (resid 9 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } 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=0.50 max=1.00 mean=0.99 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: 2.540 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: 0.040 Extract box with map and model: 14.730 Check model and map are aligned: 0.710 Set scattering table: 0.430 Process input model: 111.720 Find NCS groups from input model: 3.510 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.007 0.091 46991 Z= 0.446 Angle : 1.115 15.346 63434 Z= 0.651 Chirality : 0.060 0.475 7441 Planarity : 0.007 0.080 8134 Dihedral : 10.054 80.902 17696 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.09 % Favored : 94.79 % Rotamer: Outliers : 0.22 % Allowed : 3.88 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.09), residues: 5950 helix: -1.19 (0.09), residues: 2247 sheet: -1.36 (0.14), residues: 1274 loop : -2.86 (0.10), residues: 2429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS J 109 PHE 0.029 0.003 PHE A 42 TYR 0.027 0.003 TYR J 135 ARG 0.021 0.001 ARG U 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1257 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1246 time to evaluate : 5.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9173 (mtp) cc_final: 0.8933 (mtm) REVERT: C 40 MET cc_start: 0.8698 (ptp) cc_final: 0.8348 (ptp) REVERT: D 40 MET cc_start: 0.8836 (ptp) cc_final: 0.8605 (ptp) REVERT: E 173 VAL cc_start: 0.8324 (t) cc_final: 0.8044 (t) REVERT: F 120 MET cc_start: 0.9042 (mtp) cc_final: 0.8747 (mtp) REVERT: G 40 MET cc_start: 0.8947 (ptp) cc_final: 0.8683 (ptp) REVERT: G 120 MET cc_start: 0.9041 (mtp) cc_final: 0.8822 (mtp) REVERT: O 135 SER cc_start: 0.8923 (m) cc_final: 0.8614 (t) REVERT: P 12 ILE cc_start: 0.8530 (tp) cc_final: 0.8165 (tp) REVERT: P 40 MET cc_start: 0.7595 (pmt) cc_final: 0.7283 (ptp) REVERT: P 67 ILE cc_start: 0.8035 (tt) cc_final: 0.7785 (mt) REVERT: Q 67 ILE cc_start: 0.7815 (tt) cc_final: 0.7535 (mt) REVERT: Q 105 SER cc_start: 0.8836 (p) cc_final: 0.8635 (m) REVERT: R 67 ILE cc_start: 0.7958 (tt) cc_final: 0.7642 (mt) REVERT: S 40 MET cc_start: 0.7758 (pmt) cc_final: 0.7466 (ptp) REVERT: S 67 ILE cc_start: 0.8014 (tt) cc_final: 0.7463 (mt) REVERT: U 12 ILE cc_start: 0.8487 (tp) cc_final: 0.8020 (tp) REVERT: U 67 ILE cc_start: 0.8102 (tt) cc_final: 0.7631 (mt) REVERT: H 172 MET cc_start: 0.7531 (tpt) cc_final: 0.7272 (tpt) REVERT: I 105 ASP cc_start: 0.8497 (p0) cc_final: 0.8257 (p0) REVERT: I 172 MET cc_start: 0.7510 (tpt) cc_final: 0.7190 (tpt) REVERT: J 195 ARG cc_start: 0.7175 (mmt180) cc_final: 0.6921 (mmt180) REVERT: Y 67 ARG cc_start: 0.7684 (tmm-80) cc_final: 0.7169 (ttm170) REVERT: Z 18 ARG cc_start: 0.8200 (ptp-170) cc_final: 0.8000 (ptm160) REVERT: b 67 ARG cc_start: 0.7742 (tmm-80) cc_final: 0.7403 (ttp80) outliers start: 11 outliers final: 2 residues processed: 1250 average time/residue: 0.6364 time to fit residues: 1243.6775 Evaluate side-chains 717 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 715 time to evaluate : 6.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain G residue 212 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 496 optimal weight: 0.8980 chunk 445 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 300 optimal weight: 1.9990 chunk 238 optimal weight: 0.6980 chunk 460 optimal weight: 4.9990 chunk 178 optimal weight: 0.8980 chunk 280 optimal weight: 0.9990 chunk 343 optimal weight: 1.9990 chunk 533 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN C 121 GLN D 23 GLN D 121 GLN E 121 GLN F 121 GLN F 122 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN O 219 ASN P 68 GLN P 219 ASN Q 68 GLN Q 219 ASN R 219 ASN S 68 GLN U 68 GLN U 219 ASN I 30 ASN I 88 ASN J 30 ASN K 30 ASN K 88 ASN L 30 ASN M 30 ASN M 88 ASN N 88 ASN V 30 ASN W 30 ASN X 30 ASN Y 30 ASN Z 30 ASN Z 88 ASN a 30 ASN a 89 GLN b 30 ASN b 89 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 46991 Z= 0.182 Angle : 0.574 9.075 63434 Z= 0.313 Chirality : 0.044 0.180 7441 Planarity : 0.005 0.060 8134 Dihedral : 5.110 42.740 6584 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.54 % Favored : 97.34 % Rotamer: Outliers : 2.38 % Allowed : 8.50 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.10), residues: 5950 helix: 0.91 (0.10), residues: 2282 sheet: -0.85 (0.14), residues: 1295 loop : -2.49 (0.10), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS Z 109 PHE 0.013 0.002 PHE C 42 TYR 0.013 0.001 TYR E 221 ARG 0.006 0.001 ARG W 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 839 time to evaluate : 5.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 GLN cc_start: 0.7483 (tt0) cc_final: 0.7270 (mt0) REVERT: B 120 MET cc_start: 0.9101 (mtp) cc_final: 0.8865 (mtp) REVERT: C 98 GLN cc_start: 0.7350 (tt0) cc_final: 0.7149 (tt0) REVERT: D 59 ILE cc_start: 0.8257 (mm) cc_final: 0.8048 (mm) REVERT: E 70 ILE cc_start: 0.9123 (mm) cc_final: 0.8831 (mt) REVERT: O 70 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8724 (mt) REVERT: P 67 ILE cc_start: 0.8209 (tt) cc_final: 0.7818 (mt) REVERT: Q 67 ILE cc_start: 0.7926 (tt) cc_final: 0.7597 (mt) REVERT: Q 70 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8736 (mt) REVERT: R 67 ILE cc_start: 0.8118 (tt) cc_final: 0.7789 (mt) REVERT: R 70 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8743 (mt) REVERT: S 20 ARG cc_start: 0.8357 (mtp180) cc_final: 0.7999 (mtp180) REVERT: S 67 ILE cc_start: 0.8328 (tt) cc_final: 0.7788 (mt) REVERT: S 70 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8799 (mt) REVERT: S 106 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8332 (tp) REVERT: T 20 ARG cc_start: 0.8275 (mtp180) cc_final: 0.7982 (mtm180) REVERT: T 70 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8600 (mt) REVERT: U 20 ARG cc_start: 0.8314 (mtm180) cc_final: 0.8060 (mtp180) REVERT: U 67 ILE cc_start: 0.8268 (tt) cc_final: 0.7831 (mt) REVERT: U 70 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8725 (mt) REVERT: H 172 MET cc_start: 0.7533 (tpt) cc_final: 0.7213 (tpt) REVERT: I 105 ASP cc_start: 0.8447 (p0) cc_final: 0.8228 (p0) REVERT: K 18 ARG cc_start: 0.8223 (ptp-170) cc_final: 0.7852 (ptm160) REVERT: M 45 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8902 (pp) REVERT: M 62 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6922 (mt-10) REVERT: V 71 ARG cc_start: 0.7892 (mtt90) cc_final: 0.7526 (mtm110) REVERT: V 88 ASN cc_start: 0.8944 (t0) cc_final: 0.8696 (t0) REVERT: V 146 MET cc_start: 0.8981 (mtp) cc_final: 0.8719 (mtm) REVERT: W 18 ARG cc_start: 0.8159 (ptp-170) cc_final: 0.7918 (ptm160) REVERT: W 27 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7865 (mmm) REVERT: W 67 ARG cc_start: 0.7371 (ttp80) cc_final: 0.7129 (ttp-170) REVERT: X 88 ASN cc_start: 0.8960 (t0) cc_final: 0.8722 (t0) REVERT: Y 67 ARG cc_start: 0.7824 (tmm-80) cc_final: 0.7348 (ttp80) REVERT: a 70 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.4937 (mpt180) REVERT: a 88 ASN cc_start: 0.8821 (t0) cc_final: 0.8585 (t0) REVERT: b 67 ARG cc_start: 0.7926 (tmm-80) cc_final: 0.7484 (ttp80) outliers start: 119 outliers final: 55 residues processed: 903 average time/residue: 0.6461 time to fit residues: 949.8603 Evaluate side-chains 756 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 690 time to evaluate : 5.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 194 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 194 ILE Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 62 GLU Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain W residue 27 MET Chi-restraints excluded: chain Y residue 30 ASN Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain a residue 30 ASN Chi-restraints excluded: chain a residue 70 ARG Chi-restraints excluded: chain b residue 30 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 296 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 chunk 444 optimal weight: 5.9990 chunk 363 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 534 optimal weight: 3.9990 chunk 577 optimal weight: 4.9990 chunk 476 optimal weight: 2.9990 chunk 530 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 chunk 429 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 121 GLN G 108 ASN G 121 GLN Q 122 GLN U 226 GLN H 30 ASN J 141 GLN K 30 ASN M 30 ASN N 30 ASN W 30 ASN a 89 GLN b 89 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 46991 Z= 0.221 Angle : 0.579 11.190 63434 Z= 0.311 Chirality : 0.044 0.154 7441 Planarity : 0.004 0.046 8134 Dihedral : 4.892 40.718 6582 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.18 % Favored : 96.71 % Rotamer: Outliers : 3.34 % Allowed : 10.82 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.11), residues: 5950 helix: 1.78 (0.11), residues: 2282 sheet: -0.28 (0.14), residues: 1281 loop : -2.18 (0.10), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS J 28 PHE 0.016 0.002 PHE W 25 TYR 0.016 0.001 TYR R 8 ARG 0.005 0.000 ARG J 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 738 time to evaluate : 5.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.7327 (tt0) cc_final: 0.7050 (mt0) REVERT: A 120 MET cc_start: 0.9111 (mtp) cc_final: 0.8535 (mtm) REVERT: E 70 ILE cc_start: 0.9151 (mm) cc_final: 0.8829 (mt) REVERT: O 70 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8709 (mt) REVERT: P 122 GLN cc_start: 0.8298 (tt0) cc_final: 0.7961 (tt0) REVERT: Q 67 ILE cc_start: 0.8281 (tt) cc_final: 0.8068 (mt) REVERT: Q 70 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8684 (mt) REVERT: R 67 ILE cc_start: 0.8456 (tt) cc_final: 0.8215 (mt) REVERT: R 70 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8722 (mt) REVERT: R 182 GLU cc_start: 0.8381 (pm20) cc_final: 0.8004 (pm20) REVERT: S 70 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8754 (mt) REVERT: T 70 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8763 (mt) REVERT: T 160 TYR cc_start: 0.8651 (m-10) cc_final: 0.8361 (m-80) REVERT: U 20 ARG cc_start: 0.8818 (mtm180) cc_final: 0.8441 (mtp180) REVERT: U 40 MET cc_start: 0.8272 (ptp) cc_final: 0.8034 (ptt) REVERT: U 67 ILE cc_start: 0.8481 (tt) cc_final: 0.8256 (mt) REVERT: U 70 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8639 (mt) REVERT: U 182 GLU cc_start: 0.8282 (pm20) cc_final: 0.8081 (pm20) REVERT: H 172 MET cc_start: 0.7473 (tpt) cc_final: 0.7192 (tpt) REVERT: I 64 GLU cc_start: 0.7720 (tt0) cc_final: 0.7460 (tt0) REVERT: J 30 ASN cc_start: 0.8434 (t0) cc_final: 0.8203 (t0) REVERT: J 62 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7139 (mt-10) REVERT: K 64 GLU cc_start: 0.7843 (tt0) cc_final: 0.7480 (tt0) REVERT: M 27 MET cc_start: 0.7618 (tpt) cc_final: 0.7278 (mtt) REVERT: V 71 ARG cc_start: 0.8109 (mtt90) cc_final: 0.7682 (mtm110) REVERT: V 88 ASN cc_start: 0.8918 (t0) cc_final: 0.8696 (t0) REVERT: V 98 GLN cc_start: 0.8289 (tt0) cc_final: 0.8051 (tt0) REVERT: V 195 ARG cc_start: 0.7151 (mmt-90) cc_final: 0.6706 (mmt-90) REVERT: Y 67 ARG cc_start: 0.8153 (tmm-80) cc_final: 0.7890 (ttp80) REVERT: Y 98 GLN cc_start: 0.8386 (tt0) cc_final: 0.8085 (pt0) REVERT: Z 62 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7045 (mt-10) REVERT: a 70 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.5211 (mpt180) REVERT: a 88 ASN cc_start: 0.8816 (t0) cc_final: 0.8593 (t0) REVERT: a 98 GLN cc_start: 0.8340 (tt0) cc_final: 0.8097 (pt0) REVERT: b 67 ARG cc_start: 0.8051 (tmm-80) cc_final: 0.7578 (ttp80) REVERT: b 195 ARG cc_start: 0.7414 (mmt180) cc_final: 0.7185 (mmt180) outliers start: 167 outliers final: 78 residues processed: 861 average time/residue: 0.6148 time to fit residues: 845.6545 Evaluate side-chains 755 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 668 time to evaluate : 5.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 108 ASN Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain P residue 12 ILE Chi-restraints excluded: chain P residue 70 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain Q residue 229 VAL Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain a residue 70 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 528 optimal weight: 4.9990 chunk 402 optimal weight: 6.9990 chunk 277 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 255 optimal weight: 3.9990 chunk 359 optimal weight: 3.9990 chunk 536 optimal weight: 0.9980 chunk 568 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 chunk 508 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN E 23 GLN H 30 ASN K 30 ASN M 141 GLN N 30 ASN N 141 GLN V 191 GLN W 30 ASN ** Y 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN b 89 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 46991 Z= 0.440 Angle : 0.692 8.736 63434 Z= 0.370 Chirality : 0.048 0.151 7441 Planarity : 0.005 0.046 8134 Dihedral : 5.465 53.549 6580 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.92 % Favored : 95.97 % Rotamer: Outliers : 3.62 % Allowed : 11.92 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.30 (0.10), residues: 5950 helix: 1.67 (0.11), residues: 2247 sheet: -0.13 (0.14), residues: 1302 loop : -2.14 (0.10), residues: 2401 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS M 28 PHE 0.025 0.003 PHE M 25 TYR 0.022 0.002 TYR T 8 ARG 0.006 0.001 ARG T 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 650 time to evaluate : 5.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.7311 (tt0) cc_final: 0.7036 (mt0) REVERT: A 120 MET cc_start: 0.9078 (mtp) cc_final: 0.8575 (mtm) REVERT: A 221 TYR cc_start: 0.9102 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: B 49 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8566 (mt) REVERT: C 176 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7719 (mp) REVERT: C 221 TYR cc_start: 0.9219 (OUTLIER) cc_final: 0.8299 (m-80) REVERT: D 232 PHE cc_start: 0.8003 (m-80) cc_final: 0.7745 (m-80) REVERT: E 49 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8631 (mt) REVERT: E 221 TYR cc_start: 0.9267 (OUTLIER) cc_final: 0.8599 (m-80) REVERT: F 98 GLN cc_start: 0.7602 (tt0) cc_final: 0.7340 (tt0) REVERT: G 98 GLN cc_start: 0.7478 (tt0) cc_final: 0.7152 (mt0) REVERT: O 70 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8930 (mt) REVERT: O 143 GLN cc_start: 0.7514 (pt0) cc_final: 0.7282 (pt0) REVERT: P 20 ARG cc_start: 0.8897 (mtm180) cc_final: 0.8695 (mtp180) REVERT: P 122 GLN cc_start: 0.8415 (tt0) cc_final: 0.8058 (tt0) REVERT: P 143 GLN cc_start: 0.7255 (pt0) cc_final: 0.7015 (pt0) REVERT: Q 70 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8879 (mt) REVERT: R 70 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8710 (mt) REVERT: R 222 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7580 (ptt90) REVERT: S 70 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8926 (mt) REVERT: S 114 LYS cc_start: 0.8223 (tppt) cc_final: 0.7711 (tttp) REVERT: S 230 LYS cc_start: 0.7962 (ttmt) cc_final: 0.7636 (mmmt) REVERT: T 70 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8973 (mt) REVERT: T 114 LYS cc_start: 0.8043 (tppt) cc_final: 0.7514 (tttp) REVERT: T 181 LYS cc_start: 0.7891 (mtmt) cc_final: 0.7630 (ttpp) REVERT: U 20 ARG cc_start: 0.8890 (mtm180) cc_final: 0.8552 (mtp180) REVERT: U 40 MET cc_start: 0.8558 (ptp) cc_final: 0.8297 (ptp) REVERT: U 70 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8786 (mt) REVERT: H 195 ARG cc_start: 0.7043 (mmt180) cc_final: 0.6698 (mmt180) REVERT: J 64 GLU cc_start: 0.7858 (tt0) cc_final: 0.7414 (tt0) REVERT: M 195 ARG cc_start: 0.6855 (mmt180) cc_final: 0.6298 (mtt-85) REVERT: V 88 ASN cc_start: 0.9016 (t0) cc_final: 0.8674 (t0) REVERT: W 146 MET cc_start: 0.9218 (mtm) cc_final: 0.8972 (ptp) REVERT: a 70 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.5832 (mpt180) REVERT: a 98 GLN cc_start: 0.8531 (tt0) cc_final: 0.8129 (tt0) REVERT: b 67 ARG cc_start: 0.8357 (tmm-80) cc_final: 0.7975 (ttp80) outliers start: 181 outliers final: 112 residues processed: 782 average time/residue: 0.6306 time to fit residues: 782.8227 Evaluate side-chains 710 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 584 time to evaluate : 5.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 212 ILE Chi-restraints excluded: chain P residue 70 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 194 ILE Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 222 ARG Chi-restraints excluded: chain S residue 50 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 95 SER Chi-restraints excluded: chain S residue 122 GLN Chi-restraints excluded: chain S residue 134 VAL Chi-restraints excluded: chain S residue 173 VAL Chi-restraints excluded: chain S residue 212 ILE Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 174 SER Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 98 GLN Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Z residue 146 MET Chi-restraints excluded: chain Z residue 182 ASP Chi-restraints excluded: chain a residue 22 MET Chi-restraints excluded: chain a residue 70 ARG Chi-restraints excluded: chain b residue 157 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 473 optimal weight: 0.8980 chunk 322 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 423 optimal weight: 0.9990 chunk 234 optimal weight: 0.5980 chunk 485 optimal weight: 0.9990 chunk 392 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 290 optimal weight: 1.9990 chunk 510 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 GLN G 108 ASN ** O 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 98 GLN Q 143 GLN H 30 ASN J 30 ASN K 30 ASN L 30 ASN M 30 ASN X 73 ASN ** Y 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN b 89 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 46991 Z= 0.165 Angle : 0.516 9.936 63434 Z= 0.279 Chirality : 0.043 0.147 7441 Planarity : 0.003 0.044 8134 Dihedral : 4.773 47.449 6580 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.33 % Favored : 96.55 % Rotamer: Outliers : 2.40 % Allowed : 14.15 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.11), residues: 5950 helix: 2.07 (0.11), residues: 2289 sheet: -0.19 (0.14), residues: 1337 loop : -1.94 (0.11), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 28 PHE 0.024 0.001 PHE U 175 TYR 0.012 0.001 TYR N 66 ARG 0.006 0.000 ARG N 157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 651 time to evaluate : 5.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.7218 (tt0) cc_final: 0.6983 (mt0) REVERT: C 221 TYR cc_start: 0.9047 (OUTLIER) cc_final: 0.7817 (m-80) REVERT: E 221 TYR cc_start: 0.9070 (OUTLIER) cc_final: 0.8152 (m-80) REVERT: F 98 GLN cc_start: 0.7333 (tt0) cc_final: 0.7088 (mt0) REVERT: G 98 GLN cc_start: 0.7387 (tt0) cc_final: 0.7050 (mt0) REVERT: O 18 ASP cc_start: 0.8293 (m-30) cc_final: 0.7909 (m-30) REVERT: O 70 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8743 (mt) REVERT: O 143 GLN cc_start: 0.7427 (pt0) cc_final: 0.7190 (pt0) REVERT: P 122 GLN cc_start: 0.8306 (tt0) cc_final: 0.7944 (tt0) REVERT: P 143 GLN cc_start: 0.7119 (pt0) cc_final: 0.6871 (pt0) REVERT: Q 67 ILE cc_start: 0.8272 (tt) cc_final: 0.7913 (mt) REVERT: Q 70 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8714 (mt) REVERT: Q 72 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8085 (t0) REVERT: R 67 ILE cc_start: 0.8579 (tt) cc_final: 0.8152 (mt) REVERT: R 70 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8646 (mt) REVERT: S 70 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8706 (mt) REVERT: S 230 LYS cc_start: 0.7904 (ttmt) cc_final: 0.7575 (mmmt) REVERT: T 40 MET cc_start: 0.8666 (ptp) cc_final: 0.8326 (ptm) REVERT: T 67 ILE cc_start: 0.8557 (tt) cc_final: 0.8322 (mt) REVERT: T 70 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8802 (mp) REVERT: U 18 ASP cc_start: 0.8421 (m-30) cc_final: 0.8103 (m-30) REVERT: U 20 ARG cc_start: 0.8820 (mtm180) cc_final: 0.8455 (mtp180) REVERT: U 70 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8606 (mp) REVERT: U 122 GLN cc_start: 0.8149 (tt0) cc_final: 0.7909 (tt0) REVERT: U 227 GLU cc_start: 0.7644 (mp0) cc_final: 0.7433 (mt-10) REVERT: H 14 MET cc_start: 0.8812 (mtp) cc_final: 0.8567 (mtt) REVERT: I 64 GLU cc_start: 0.7756 (tt0) cc_final: 0.7439 (tt0) REVERT: J 62 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7028 (mm-30) REVERT: K 18 ARG cc_start: 0.8355 (ptp-170) cc_final: 0.8125 (ptm160) REVERT: V 18 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8310 (ptm160) REVERT: V 88 ASN cc_start: 0.8941 (t0) cc_final: 0.8677 (t0) REVERT: W 98 GLN cc_start: 0.8233 (tt0) cc_final: 0.7971 (pt0) REVERT: Y 64 GLU cc_start: 0.7502 (tt0) cc_final: 0.6912 (tt0) REVERT: Y 67 ARG cc_start: 0.8355 (tmm-80) cc_final: 0.8035 (ttp80) REVERT: Y 98 GLN cc_start: 0.8340 (tt0) cc_final: 0.8058 (pt0) REVERT: Y 146 MET cc_start: 0.9104 (mtm) cc_final: 0.8853 (mtp) REVERT: Z 139 GLU cc_start: 0.7799 (tp30) cc_final: 0.7537 (tp30) REVERT: a 70 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.5464 (mpt180) REVERT: a 98 GLN cc_start: 0.8343 (tt0) cc_final: 0.8039 (pt0) REVERT: a 139 GLU cc_start: 0.7579 (tp30) cc_final: 0.7282 (tp30) REVERT: b 67 ARG cc_start: 0.8273 (tmm-80) cc_final: 0.8004 (ttp80) outliers start: 120 outliers final: 82 residues processed: 735 average time/residue: 0.6204 time to fit residues: 725.7661 Evaluate side-chains 716 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 622 time to evaluate : 5.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 108 ASN Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 212 ILE Chi-restraints excluded: chain P residue 70 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 194 ILE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 194 ILE Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain U residue 182 GLU Chi-restraints excluded: chain H residue 30 ASN Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 141 GLN Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 98 GLN Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain a residue 70 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 191 optimal weight: 0.7980 chunk 511 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 333 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 568 optimal weight: 4.9990 chunk 472 optimal weight: 3.9990 chunk 263 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN E 98 GLN G 108 ASN ** O 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 GLN Q 98 GLN Q 122 GLN R 23 GLN S 143 GLN T 23 GLN H 30 ASN J 30 ASN K 30 ASN K 73 ASN X 30 ASN ** Y 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 46991 Z= 0.165 Angle : 0.508 10.701 63434 Z= 0.273 Chirality : 0.042 0.140 7441 Planarity : 0.003 0.046 8134 Dihedral : 4.589 41.825 6580 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.13 % Favored : 96.76 % Rotamer: Outliers : 2.76 % Allowed : 14.11 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.11), residues: 5950 helix: 2.29 (0.11), residues: 2282 sheet: -0.09 (0.14), residues: 1323 loop : -1.84 (0.11), residues: 2345 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 28 PHE 0.026 0.001 PHE U 175 TYR 0.011 0.001 TYR N 66 ARG 0.006 0.000 ARG E 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 650 time to evaluate : 5.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.7280 (tt0) cc_final: 0.7030 (mt0) REVERT: A 221 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.8647 (m-80) REVERT: B 49 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8618 (mt) REVERT: C 98 GLN cc_start: 0.7501 (tt0) cc_final: 0.7299 (tt0) REVERT: E 49 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8634 (mt) REVERT: F 98 GLN cc_start: 0.7440 (tt0) cc_final: 0.7113 (mt0) REVERT: G 98 GLN cc_start: 0.7489 (tt0) cc_final: 0.7171 (mt0) REVERT: O 18 ASP cc_start: 0.8269 (m-30) cc_final: 0.7862 (m-30) REVERT: O 70 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8707 (mt) REVERT: O 143 GLN cc_start: 0.7438 (pt0) cc_final: 0.7129 (pt0) REVERT: P 20 ARG cc_start: 0.8867 (mtm180) cc_final: 0.8571 (mtp180) REVERT: P 122 GLN cc_start: 0.8188 (tt0) cc_final: 0.7802 (tt0) REVERT: Q 67 ILE cc_start: 0.8260 (tt) cc_final: 0.7930 (mt) REVERT: Q 70 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8706 (mt) REVERT: R 70 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8632 (mt) REVERT: S 70 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8677 (mt) REVERT: S 221 TYR cc_start: 0.9041 (OUTLIER) cc_final: 0.8746 (m-80) REVERT: S 230 LYS cc_start: 0.7933 (ttmt) cc_final: 0.7609 (mmmt) REVERT: T 40 MET cc_start: 0.8690 (ptp) cc_final: 0.8345 (ptm) REVERT: T 67 ILE cc_start: 0.8530 (tt) cc_final: 0.8288 (mt) REVERT: T 70 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8855 (mp) REVERT: T 222 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7322 (ttt90) REVERT: U 18 ASP cc_start: 0.8376 (m-30) cc_final: 0.8065 (m-30) REVERT: U 20 ARG cc_start: 0.8826 (mtm180) cc_final: 0.8464 (mtp180) REVERT: U 70 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8573 (mp) REVERT: U 122 GLN cc_start: 0.8167 (tt0) cc_final: 0.7915 (tt0) REVERT: H 14 MET cc_start: 0.8821 (mtp) cc_final: 0.8566 (mtt) REVERT: I 139 GLU cc_start: 0.8375 (tp30) cc_final: 0.7917 (tp30) REVERT: J 62 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6996 (mm-30) REVERT: J 67 ARG cc_start: 0.8136 (ttp80) cc_final: 0.7810 (ttp-170) REVERT: V 18 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8321 (ptm160) REVERT: V 88 ASN cc_start: 0.8940 (t0) cc_final: 0.8645 (t0) REVERT: W 195 ARG cc_start: 0.7339 (mmt180) cc_final: 0.7133 (mmt180) REVERT: Y 64 GLU cc_start: 0.7520 (tt0) cc_final: 0.6909 (tt0) REVERT: Y 67 ARG cc_start: 0.8316 (tmm-80) cc_final: 0.8015 (ttp80) REVERT: Y 139 GLU cc_start: 0.7636 (tp30) cc_final: 0.7278 (tp30) REVERT: Z 98 GLN cc_start: 0.8298 (tt0) cc_final: 0.8052 (pt0) REVERT: Z 139 GLU cc_start: 0.7819 (tp30) cc_final: 0.7534 (tp30) REVERT: Z 141 GLN cc_start: 0.8590 (mt0) cc_final: 0.8345 (mt0) REVERT: a 98 GLN cc_start: 0.8318 (tt0) cc_final: 0.8088 (pt0) REVERT: a 198 LYS cc_start: 0.8555 (ttmm) cc_final: 0.8305 (ttpt) REVERT: b 67 ARG cc_start: 0.8231 (tmm-80) cc_final: 0.7982 (ttp80) REVERT: b 70 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7532 (mpt180) outliers start: 138 outliers final: 104 residues processed: 747 average time/residue: 0.6201 time to fit residues: 737.3342 Evaluate side-chains 748 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 630 time to evaluate : 5.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 108 ASN Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 212 ILE Chi-restraints excluded: chain P residue 70 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 194 ILE Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain Q residue 194 ILE Chi-restraints excluded: chain Q residue 206 GLU Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 122 GLN Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 222 ARG Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 182 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 141 GLN Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 98 GLN Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain a residue 70 ARG Chi-restraints excluded: chain b residue 70 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 548 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 324 optimal weight: 5.9990 chunk 415 optimal weight: 7.9990 chunk 321 optimal weight: 2.9990 chunk 478 optimal weight: 0.9980 chunk 317 optimal weight: 2.9990 chunk 566 optimal weight: 0.8980 chunk 354 optimal weight: 2.9990 chunk 345 optimal weight: 0.9980 chunk 261 optimal weight: 9.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN E 98 GLN O 23 GLN ** O 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 23 GLN U 23 GLN H 30 ASN J 30 ASN K 30 ASN L 30 ASN M 30 ASN N 30 ASN ** Y 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 69 GLN b 89 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 46991 Z= 0.277 Angle : 0.568 10.024 63434 Z= 0.304 Chirality : 0.044 0.135 7441 Planarity : 0.004 0.043 8134 Dihedral : 4.827 41.193 6580 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.82 % Favored : 96.07 % Rotamer: Outliers : 3.26 % Allowed : 14.07 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.11), residues: 5950 helix: 2.14 (0.11), residues: 2275 sheet: 0.02 (0.14), residues: 1281 loop : -1.84 (0.11), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS M 109 PHE 0.024 0.002 PHE U 175 TYR 0.015 0.001 TYR Q 123 ARG 0.008 0.000 ARG Y 195 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 610 time to evaluate : 5.706 Fit side-chains revert: symmetry clash REVERT: A 98 GLN cc_start: 0.7260 (tt0) cc_final: 0.6985 (mt0) REVERT: A 221 TYR cc_start: 0.9143 (OUTLIER) cc_final: 0.8534 (m-80) REVERT: B 49 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8567 (mt) REVERT: C 18 ASP cc_start: 0.8546 (t70) cc_final: 0.8343 (t0) REVERT: C 98 GLN cc_start: 0.7546 (tt0) cc_final: 0.7321 (tt0) REVERT: C 221 TYR cc_start: 0.9095 (OUTLIER) cc_final: 0.7911 (m-80) REVERT: E 49 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8619 (mt) REVERT: E 221 TYR cc_start: 0.9188 (OUTLIER) cc_final: 0.8290 (m-80) REVERT: F 98 GLN cc_start: 0.7568 (tt0) cc_final: 0.7175 (mt0) REVERT: G 98 GLN cc_start: 0.7518 (tt0) cc_final: 0.7194 (mt0) REVERT: O 70 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8799 (mt) REVERT: O 143 GLN cc_start: 0.7449 (pt0) cc_final: 0.7050 (pt0) REVERT: P 122 GLN cc_start: 0.8307 (tt0) cc_final: 0.7933 (tt0) REVERT: Q 70 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8800 (mt) REVERT: R 70 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8663 (mt) REVERT: R 103 TYR cc_start: 0.8438 (m-80) cc_final: 0.8187 (m-80) REVERT: R 222 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7453 (ptt90) REVERT: S 70 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8774 (mt) REVERT: S 221 TYR cc_start: 0.9132 (OUTLIER) cc_final: 0.8230 (m-80) REVERT: S 230 LYS cc_start: 0.7984 (ttmt) cc_final: 0.7667 (mmmt) REVERT: T 40 MET cc_start: 0.8774 (ptp) cc_final: 0.8438 (ptm) REVERT: T 70 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8957 (mp) REVERT: T 222 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7522 (ttt90) REVERT: T 230 LYS cc_start: 0.8029 (mttt) cc_final: 0.7714 (mmmt) REVERT: U 10 ARG cc_start: 0.8869 (mmt-90) cc_final: 0.8656 (mmt-90) REVERT: U 18 ASP cc_start: 0.8374 (m-30) cc_final: 0.8104 (m-30) REVERT: U 20 ARG cc_start: 0.8857 (mtm180) cc_final: 0.8536 (mtp180) REVERT: U 70 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8679 (mp) REVERT: U 227 GLU cc_start: 0.7746 (mp0) cc_final: 0.7489 (mt-10) REVERT: H 195 ARG cc_start: 0.7067 (mmt180) cc_final: 0.6556 (mtt-85) REVERT: J 62 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.7006 (mm-30) REVERT: V 88 ASN cc_start: 0.8941 (t0) cc_final: 0.8610 (t0) REVERT: Y 67 ARG cc_start: 0.8405 (tmm-80) cc_final: 0.8200 (ttp80) REVERT: Y 98 GLN cc_start: 0.8652 (pt0) cc_final: 0.8386 (pt0) REVERT: Z 198 LYS cc_start: 0.8276 (ttpt) cc_final: 0.7674 (tttm) REVERT: a 98 GLN cc_start: 0.8336 (tt0) cc_final: 0.8107 (pt0) REVERT: a 198 LYS cc_start: 0.8597 (ttmm) cc_final: 0.8328 (ttpt) REVERT: b 67 ARG cc_start: 0.8381 (tmm-80) cc_final: 0.8177 (ttp80) outliers start: 163 outliers final: 112 residues processed: 737 average time/residue: 0.6070 time to fit residues: 712.9827 Evaluate side-chains 721 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 594 time to evaluate : 5.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 212 ILE Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 70 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 194 ILE Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 222 ARG Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 122 GLN Chi-restraints excluded: chain S residue 173 VAL Chi-restraints excluded: chain S residue 212 ILE Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 222 ARG Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 86 MET Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 141 GLN Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 98 GLN Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 194 SER Chi-restraints excluded: chain Z residue 194 SER Chi-restraints excluded: chain a residue 44 THR Chi-restraints excluded: chain a residue 70 ARG Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain b residue 194 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 350 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 338 optimal weight: 0.7980 chunk 170 optimal weight: 0.9980 chunk 111 optimal weight: 0.0370 chunk 109 optimal weight: 7.9990 chunk 360 optimal weight: 3.9990 chunk 386 optimal weight: 0.7980 chunk 280 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 445 optimal weight: 0.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN E 98 GLN ** O 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 GLN H 30 ASN J 30 ASN K 30 ASN M 30 ASN N 30 ASN V 69 GLN ** V 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 69 GLN ** Y 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN a 69 GLN b 89 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 46991 Z= 0.141 Angle : 0.492 10.729 63434 Z= 0.266 Chirality : 0.042 0.143 7441 Planarity : 0.003 0.040 8134 Dihedral : 4.451 35.771 6580 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.21 % Favored : 96.67 % Rotamer: Outliers : 2.44 % Allowed : 15.05 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.11), residues: 5950 helix: 2.41 (0.11), residues: 2282 sheet: -0.24 (0.14), residues: 1421 loop : -1.80 (0.11), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS V 109 PHE 0.020 0.001 PHE U 175 TYR 0.012 0.001 TYR T 160 ARG 0.007 0.000 ARG Y 195 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 646 time to evaluate : 5.521 Fit side-chains revert: symmetry clash REVERT: A 221 TYR cc_start: 0.8960 (OUTLIER) cc_final: 0.8744 (m-80) REVERT: B 49 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8608 (mt) REVERT: C 221 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.7766 (m-80) REVERT: E 49 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8631 (mt) REVERT: E 221 TYR cc_start: 0.9038 (OUTLIER) cc_final: 0.7999 (m-80) REVERT: F 98 GLN cc_start: 0.7358 (tt0) cc_final: 0.7052 (mt0) REVERT: G 98 GLN cc_start: 0.7479 (tt0) cc_final: 0.7218 (tt0) REVERT: G 137 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8387 (pt) REVERT: O 18 ASP cc_start: 0.8250 (m-30) cc_final: 0.7878 (m-30) REVERT: O 70 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8686 (mt) REVERT: O 143 GLN cc_start: 0.7372 (pt0) cc_final: 0.7040 (pt0) REVERT: P 20 ARG cc_start: 0.8767 (mtm180) cc_final: 0.8547 (mtp180) REVERT: P 67 ILE cc_start: 0.8420 (tt) cc_final: 0.8034 (mt) REVERT: P 122 GLN cc_start: 0.8151 (tt0) cc_final: 0.7759 (tt0) REVERT: Q 67 ILE cc_start: 0.8277 (tt) cc_final: 0.7929 (mt) REVERT: Q 70 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8629 (mt) REVERT: R 70 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8621 (mt) REVERT: S 70 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8610 (mt) REVERT: S 230 LYS cc_start: 0.7999 (ttmt) cc_final: 0.7683 (mmmt) REVERT: T 67 ILE cc_start: 0.8574 (tt) cc_final: 0.8293 (mt) REVERT: T 70 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8824 (mp) REVERT: T 222 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7425 (ttt90) REVERT: T 230 LYS cc_start: 0.8038 (mttt) cc_final: 0.7717 (mmmt) REVERT: U 18 ASP cc_start: 0.8325 (m-30) cc_final: 0.8047 (m-30) REVERT: U 20 ARG cc_start: 0.8846 (mtm180) cc_final: 0.8502 (mtp180) REVERT: U 70 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8535 (mp) REVERT: H 14 MET cc_start: 0.8837 (mtp) cc_final: 0.8558 (mtt) REVERT: H 22 MET cc_start: 0.4206 (tmm) cc_final: 0.3991 (tmm) REVERT: I 74 MET cc_start: 0.8485 (mtp) cc_final: 0.8148 (ttm) REVERT: I 139 GLU cc_start: 0.8292 (tp30) cc_final: 0.7847 (tp30) REVERT: J 67 ARG cc_start: 0.8131 (ttp80) cc_final: 0.7823 (ttp-170) REVERT: K 1 THR cc_start: 0.8284 (p) cc_final: 0.7952 (t) REVERT: V 18 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8320 (ptm160) REVERT: V 88 ASN cc_start: 0.8913 (t0) cc_final: 0.8650 (t0) REVERT: X 141 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8286 (mt0) REVERT: Y 64 GLU cc_start: 0.7513 (tt0) cc_final: 0.6989 (tt0) REVERT: Y 67 ARG cc_start: 0.8307 (tmm-80) cc_final: 0.8023 (ttp80) REVERT: Y 98 GLN cc_start: 0.8691 (pt0) cc_final: 0.8463 (pt0) REVERT: Z 62 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6913 (mt-10) REVERT: Z 98 GLN cc_start: 0.8267 (tt0) cc_final: 0.8025 (pt0) REVERT: Z 139 GLU cc_start: 0.7710 (tp30) cc_final: 0.7354 (tp30) REVERT: Z 141 GLN cc_start: 0.8522 (mt0) cc_final: 0.8259 (mt0) REVERT: a 98 GLN cc_start: 0.8260 (tt0) cc_final: 0.8054 (pt0) REVERT: a 198 LYS cc_start: 0.8508 (ttmm) cc_final: 0.8303 (ttpt) REVERT: b 67 ARG cc_start: 0.8207 (tmm-80) cc_final: 0.8001 (ttp80) outliers start: 122 outliers final: 89 residues processed: 735 average time/residue: 0.6156 time to fit residues: 724.5953 Evaluate side-chains 741 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 636 time to evaluate : 5.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 212 ILE Chi-restraints excluded: chain P residue 70 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 194 ILE Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 206 GLU Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 212 ILE Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 222 ARG Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 182 GLU Chi-restraints excluded: chain H residue 30 ASN Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 98 GLN Chi-restraints excluded: chain L residue 141 GLN Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 98 GLN Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain X residue 69 GLN Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 141 GLN Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain a residue 70 ARG Chi-restraints excluded: chain a residue 99 LEU Chi-restraints excluded: chain b residue 194 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 515 optimal weight: 0.0470 chunk 542 optimal weight: 2.9990 chunk 495 optimal weight: 3.9990 chunk 528 optimal weight: 0.9980 chunk 317 optimal weight: 0.9990 chunk 230 optimal weight: 0.9990 chunk 414 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 477 optimal weight: 2.9990 chunk 499 optimal weight: 0.7980 chunk 526 optimal weight: 0.9980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 GLN H 30 ASN J 30 ASN J 73 ASN K 30 ASN M 30 ASN N 30 ASN V 30 ASN V 69 GLN ** V 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 69 GLN Y 69 GLN ** Y 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 69 GLN b 69 GLN b 89 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 46991 Z= 0.148 Angle : 0.496 10.598 63434 Z= 0.266 Chirality : 0.042 0.140 7441 Planarity : 0.003 0.038 8134 Dihedral : 4.377 30.891 6580 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.09 % Favored : 96.79 % Rotamer: Outliers : 2.54 % Allowed : 15.23 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.11), residues: 5950 helix: 2.48 (0.11), residues: 2275 sheet: -0.16 (0.14), residues: 1421 loop : -1.77 (0.11), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS V 109 PHE 0.019 0.001 PHE U 175 TYR 0.011 0.001 TYR N 66 ARG 0.006 0.000 ARG Y 195 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 650 time to evaluate : 5.356 Fit side-chains revert: symmetry clash REVERT: C 221 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.7782 (m-80) REVERT: D 221 TYR cc_start: 0.9294 (OUTLIER) cc_final: 0.8663 (m-80) REVERT: E 221 TYR cc_start: 0.9050 (OUTLIER) cc_final: 0.8126 (m-80) REVERT: F 178 ARG cc_start: 0.7982 (ttp80) cc_final: 0.7513 (ttm170) REVERT: G 98 GLN cc_start: 0.7521 (tt0) cc_final: 0.7255 (tt0) REVERT: G 137 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8406 (pt) REVERT: O 18 ASP cc_start: 0.8242 (m-30) cc_final: 0.7864 (m-30) REVERT: O 70 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8681 (mt) REVERT: O 143 GLN cc_start: 0.7322 (pt0) cc_final: 0.6970 (pt0) REVERT: P 20 ARG cc_start: 0.8807 (mtm180) cc_final: 0.8573 (mtp180) REVERT: P 122 GLN cc_start: 0.8144 (tt0) cc_final: 0.7752 (tt0) REVERT: Q 67 ILE cc_start: 0.8265 (tt) cc_final: 0.7938 (mt) REVERT: Q 70 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8835 (mt) REVERT: R 70 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8631 (mt) REVERT: S 70 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8632 (mt) REVERT: S 230 LYS cc_start: 0.7992 (ttmt) cc_final: 0.7671 (mmmt) REVERT: T 67 ILE cc_start: 0.8571 (tt) cc_final: 0.8287 (mt) REVERT: T 70 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8818 (mp) REVERT: T 222 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7384 (ttt90) REVERT: T 230 LYS cc_start: 0.8037 (mttt) cc_final: 0.7725 (mmmt) REVERT: U 18 ASP cc_start: 0.8357 (m-30) cc_final: 0.8078 (m-30) REVERT: U 20 ARG cc_start: 0.8832 (mtm180) cc_final: 0.8499 (mtp180) REVERT: U 70 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8552 (mp) REVERT: I 74 MET cc_start: 0.8517 (mtp) cc_final: 0.8193 (ttm) REVERT: I 139 GLU cc_start: 0.8362 (tp30) cc_final: 0.7950 (tp30) REVERT: J 67 ARG cc_start: 0.8149 (ttp80) cc_final: 0.7821 (ttp-170) REVERT: M 139 GLU cc_start: 0.8243 (tp30) cc_final: 0.7826 (tp30) REVERT: V 18 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8211 (ptm160) REVERT: V 88 ASN cc_start: 0.8908 (t0) cc_final: 0.8623 (t0) REVERT: V 195 ARG cc_start: 0.7184 (mmt-90) cc_final: 0.6821 (mmt180) REVERT: X 141 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8267 (mt0) REVERT: Y 64 GLU cc_start: 0.7456 (tt0) cc_final: 0.6795 (tt0) REVERT: Y 67 ARG cc_start: 0.8266 (tmm-80) cc_final: 0.7995 (ttp80) REVERT: Z 139 GLU cc_start: 0.7697 (tp30) cc_final: 0.7349 (tp30) REVERT: Z 141 GLN cc_start: 0.8528 (mt0) cc_final: 0.8257 (mt0) REVERT: a 198 LYS cc_start: 0.8493 (ttmm) cc_final: 0.8279 (ttpt) REVERT: b 67 ARG cc_start: 0.8234 (tmm-80) cc_final: 0.7999 (ttp80) outliers start: 127 outliers final: 99 residues processed: 737 average time/residue: 0.6070 time to fit residues: 712.7759 Evaluate side-chains 746 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 634 time to evaluate : 5.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 212 ILE Chi-restraints excluded: chain P residue 70 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 194 ILE Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain Q residue 40 MET Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 122 GLN Chi-restraints excluded: chain S residue 212 ILE Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 222 ARG Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 182 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 98 GLN Chi-restraints excluded: chain L residue 141 GLN Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 98 GLN Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain X residue 69 GLN Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 141 GLN Chi-restraints excluded: chain Y residue 69 GLN Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 194 SER Chi-restraints excluded: chain Z residue 194 SER Chi-restraints excluded: chain a residue 27 MET Chi-restraints excluded: chain a residue 70 ARG Chi-restraints excluded: chain b residue 194 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 346 optimal weight: 1.9990 chunk 558 optimal weight: 0.0000 chunk 340 optimal weight: 6.9990 chunk 264 optimal weight: 4.9990 chunk 388 optimal weight: 3.9990 chunk 585 optimal weight: 0.9990 chunk 539 optimal weight: 5.9990 chunk 466 optimal weight: 5.9990 chunk 48 optimal weight: 0.0010 chunk 360 optimal weight: 2.9990 chunk 286 optimal weight: 0.0980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 219 ASN H 30 ASN J 30 ASN K 30 ASN L 30 ASN M 30 ASN N 30 ASN V 30 ASN V 69 GLN ** V 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 69 GLN X 69 GLN Y 69 GLN ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 69 GLN b 69 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 46991 Z= 0.132 Angle : 0.484 10.363 63434 Z= 0.260 Chirality : 0.042 0.141 7441 Planarity : 0.003 0.039 8134 Dihedral : 4.244 27.039 6580 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.13 % Favored : 96.76 % Rotamer: Outliers : 2.26 % Allowed : 15.67 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.11), residues: 5950 helix: 2.58 (0.11), residues: 2275 sheet: -0.08 (0.14), residues: 1386 loop : -1.75 (0.11), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS V 109 PHE 0.019 0.001 PHE U 175 TYR 0.011 0.001 TYR N 66 ARG 0.007 0.000 ARG A 178 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 654 time to evaluate : 5.220 Fit side-chains revert: symmetry clash REVERT: C 221 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.7781 (m-80) REVERT: D 221 TYR cc_start: 0.9274 (OUTLIER) cc_final: 0.8657 (m-80) REVERT: E 212 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8382 (mt) REVERT: E 221 TYR cc_start: 0.8997 (OUTLIER) cc_final: 0.8079 (m-80) REVERT: F 178 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7502 (ttm170) REVERT: G 137 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8403 (pt) REVERT: O 18 ASP cc_start: 0.8234 (m-30) cc_final: 0.7871 (m-30) REVERT: O 70 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8642 (mp) REVERT: O 143 GLN cc_start: 0.7315 (pt0) cc_final: 0.6940 (pt0) REVERT: P 20 ARG cc_start: 0.8797 (mtm180) cc_final: 0.8548 (mtp180) REVERT: P 67 ILE cc_start: 0.8356 (tt) cc_final: 0.7969 (mt) REVERT: Q 67 ILE cc_start: 0.8185 (tt) cc_final: 0.7899 (mt) REVERT: Q 70 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8778 (mt) REVERT: R 67 ILE cc_start: 0.8484 (tt) cc_final: 0.7991 (mt) REVERT: R 70 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8592 (mt) REVERT: S 70 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8582 (mt) REVERT: S 230 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7682 (mmmt) REVERT: T 67 ILE cc_start: 0.8520 (tt) cc_final: 0.8227 (mt) REVERT: T 70 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8788 (mt) REVERT: T 222 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7333 (ttt90) REVERT: T 230 LYS cc_start: 0.8064 (mttt) cc_final: 0.7760 (mmmt) REVERT: U 18 ASP cc_start: 0.8333 (m-30) cc_final: 0.8075 (m-30) REVERT: U 20 ARG cc_start: 0.8811 (mtm180) cc_final: 0.8476 (mtp180) REVERT: U 70 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8520 (mp) REVERT: U 122 GLN cc_start: 0.8106 (tt0) cc_final: 0.7851 (tt0) REVERT: I 64 GLU cc_start: 0.7613 (tt0) cc_final: 0.7321 (tt0) REVERT: I 139 GLU cc_start: 0.8320 (tp30) cc_final: 0.7939 (tp30) REVERT: J 67 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7816 (ttp-170) REVERT: M 98 GLN cc_start: 0.8774 (pt0) cc_final: 0.8554 (pt0) REVERT: M 139 GLU cc_start: 0.8244 (tp30) cc_final: 0.7839 (tp30) REVERT: V 18 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8329 (ptm160) REVERT: V 88 ASN cc_start: 0.8928 (t0) cc_final: 0.8661 (t0) REVERT: V 195 ARG cc_start: 0.7143 (mmt-90) cc_final: 0.6824 (mmt180) REVERT: X 141 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8192 (mt0) REVERT: Y 64 GLU cc_start: 0.7472 (tt0) cc_final: 0.6827 (tt0) REVERT: Y 67 ARG cc_start: 0.8263 (tmm-80) cc_final: 0.7940 (ttp80) REVERT: Z 139 GLU cc_start: 0.7674 (tp30) cc_final: 0.7336 (tp30) REVERT: Z 141 GLN cc_start: 0.8455 (mt0) cc_final: 0.8188 (mt0) REVERT: b 67 ARG cc_start: 0.8194 (tmm-80) cc_final: 0.7959 (ttp80) REVERT: b 198 LYS cc_start: 0.8250 (ttmm) cc_final: 0.7617 (tttt) outliers start: 113 outliers final: 94 residues processed: 730 average time/residue: 0.6171 time to fit residues: 717.2944 Evaluate side-chains 744 residues out of total 4998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 636 time to evaluate : 5.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain P residue 70 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 194 ILE Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 212 ILE Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 222 ARG Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain U residue 182 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 98 GLN Chi-restraints excluded: chain L residue 141 GLN Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 98 GLN Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain W residue 69 GLN Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain X residue 69 GLN Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 141 GLN Chi-restraints excluded: chain Y residue 69 GLN Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Z residue 194 SER Chi-restraints excluded: chain a residue 27 MET Chi-restraints excluded: chain a residue 70 ARG Chi-restraints excluded: chain b residue 69 GLN Chi-restraints excluded: chain b residue 194 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 370 optimal weight: 3.9990 chunk 496 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 430 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 129 optimal weight: 0.0870 chunk 467 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 479 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN J 30 ASN K 30 ASN L 30 ASN M 30 ASN N 30 ASN V 30 ASN V 69 GLN ** V 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 69 GLN W 141 GLN X 69 GLN ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 141 GLN ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 69 GLN b 69 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.136025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.107535 restraints weight = 53383.498| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.29 r_work: 0.3060 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.190 46991 Z= 0.224 Angle : 0.825 59.188 63434 Z= 0.527 Chirality : 0.046 0.972 7441 Planarity : 0.005 0.143 8134 Dihedral : 4.365 51.005 6580 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.19 % Favored : 96.67 % Rotamer: Outliers : 2.42 % Allowed : 15.85 % Favored : 81.73 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.53 (0.11), residues: 5950 helix: 2.56 (0.11), residues: 2275 sheet: -0.07 (0.14), residues: 1386 loop : -1.75 (0.11), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS V 109 PHE 0.018 0.001 PHE U 175 TYR 0.011 0.001 TYR R 160 ARG 0.006 0.000 ARG A 178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13441.98 seconds wall clock time: 240 minutes 0.11 seconds (14400.11 seconds total)