Starting phenix.real_space_refine on Mon Mar 25 05:44:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utf_20877/03_2024/6utf_20877.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utf_20877/03_2024/6utf_20877.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/6utf_20877/03_2024/6utf_20877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utf_20877/03_2024/6utf_20877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utf_20877/03_2024/6utf_20877.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utf_20877/03_2024/6utf_20877.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= -0.000 sd= 0.062 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 29470 2.51 5 N 7847 2.21 5 O 8981 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "O ARG 10": "NH1" <-> "NH2" Residue "P ARG 10": "NH1" <-> "NH2" Residue "Q ARG 10": "NH1" <-> "NH2" Residue "R ARG 10": "NH1" <-> "NH2" Residue "S ARG 10": "NH1" <-> "NH2" Residue "T ARG 10": "NH1" <-> "NH2" Residue "U ARG 10": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46494 Number of models: 1 Model: "" Number of chains: 28 Chain: "Z" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "M" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "1" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "N" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "2" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "H" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "V" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "I" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "W" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "J" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "X" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "K" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "Y" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "L" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "A" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "B" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "C" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "D" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "E" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "F" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "G" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "O" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1761 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "P" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1761 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "Q" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1761 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "R" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1761 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "S" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1761 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "T" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1761 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "U" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1761 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ARG A 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG A 28 " occ=0.50 residue: pdb=" N VAL A 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL A 77 " occ=0.50 residue: pdb=" N ARG B 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG B 28 " occ=0.50 residue: pdb=" N VAL B 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL B 77 " occ=0.50 residue: pdb=" N ARG C 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG C 28 " occ=0.50 residue: pdb=" N VAL C 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL C 77 " occ=0.50 residue: pdb=" N ARG D 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG D 28 " occ=0.50 residue: pdb=" N VAL D 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL D 77 " occ=0.50 residue: pdb=" N ARG E 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG E 28 " occ=0.50 residue: pdb=" N VAL E 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL E 77 " occ=0.50 residue: pdb=" N ARG F 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG F 28 " occ=0.50 residue: pdb=" N ARG G 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG G 28 " occ=0.50 Time building chain proxies: 23.06, per 1000 atoms: 0.50 Number of scatterers: 46494 At special positions: 0 Unit cell: (132.98, 132.98, 173.24, 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 8981 8.00 N 7847 7.00 C 29470 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: 15.70 Conformation dependent library (CDL) restraints added in 7.8 seconds 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11074 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 56 sheets defined 41.3% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.67 Creating SS restraints... Processing helix chain 'Z' and resid 48 through 71 Processing helix chain 'Z' and resid 75 through 90 removed outlier: 3.918A pdb=" N VAL Z 90 " --> pdb=" O MET Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 142 removed outlier: 4.037A pdb=" N VAL Z 134 " --> pdb=" O GLY Z 130 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 165 Processing helix chain 'Z' and resid 188 through 200 Processing helix chain 'M' and resid 48 through 71 Processing helix chain 'M' and resid 75 through 90 removed outlier: 3.918A pdb=" N VAL M 90 " --> pdb=" O MET M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 142 removed outlier: 4.036A pdb=" N VAL M 134 " --> pdb=" O GLY M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 165 Processing helix chain 'M' and resid 188 through 200 Processing helix chain '1' and resid 48 through 71 Processing helix chain '1' and resid 75 through 90 removed outlier: 3.918A pdb=" N VAL 1 90 " --> pdb=" O MET 1 86 " (cutoff:3.500A) Processing helix chain '1' and resid 130 through 142 removed outlier: 4.036A pdb=" N VAL 1 134 " --> pdb=" O GLY 1 130 " (cutoff:3.500A) Processing helix chain '1' and resid 147 through 165 Processing helix chain '1' and resid 188 through 200 Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 90 removed outlier: 3.919A pdb=" N VAL N 90 " --> pdb=" O MET N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 142 removed outlier: 4.036A pdb=" N VAL N 134 " --> pdb=" O GLY N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 165 Processing helix chain 'N' and resid 188 through 200 Processing helix chain '2' and resid 48 through 71 Processing helix chain '2' and resid 75 through 90 removed outlier: 3.918A pdb=" N VAL 2 90 " --> pdb=" O MET 2 86 " (cutoff:3.500A) Processing helix chain '2' and resid 130 through 142 removed outlier: 4.036A pdb=" N VAL 2 134 " --> pdb=" O GLY 2 130 " (cutoff:3.500A) Processing helix chain '2' and resid 147 through 165 Processing helix chain '2' and resid 188 through 200 Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.917A pdb=" N VAL H 90 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 142 removed outlier: 4.036A pdb=" N VAL H 134 " --> pdb=" O GLY H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 165 Processing helix chain 'H' and resid 188 through 200 Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 90 removed outlier: 3.918A pdb=" N VAL V 90 " --> pdb=" O MET V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 142 removed outlier: 4.036A pdb=" N VAL V 134 " --> pdb=" O GLY V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 165 Processing helix chain 'V' and resid 188 through 200 Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 90 removed outlier: 3.918A pdb=" N VAL I 90 " --> pdb=" O MET I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 removed outlier: 4.035A pdb=" N VAL I 134 " --> pdb=" O GLY I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 165 Processing helix chain 'I' and resid 188 through 200 Processing helix chain 'W' and resid 48 through 71 Processing helix chain 'W' and resid 75 through 90 removed outlier: 3.918A pdb=" N VAL W 90 " --> pdb=" O MET W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 142 removed outlier: 4.036A pdb=" N VAL W 134 " --> pdb=" O GLY W 130 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 165 Processing helix chain 'W' and resid 188 through 200 Processing helix chain 'J' and resid 48 through 71 Processing helix chain 'J' and resid 75 through 90 removed outlier: 3.918A pdb=" N VAL J 90 " --> pdb=" O MET J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 142 removed outlier: 4.037A pdb=" N VAL J 134 " --> pdb=" O GLY J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 165 Processing helix chain 'J' and resid 188 through 200 Processing helix chain 'X' and resid 48 through 71 Processing helix chain 'X' and resid 75 through 90 removed outlier: 3.917A pdb=" N VAL X 90 " --> pdb=" O MET X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 142 removed outlier: 4.035A pdb=" N VAL X 134 " --> pdb=" O GLY X 130 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 165 Processing helix chain 'X' and resid 188 through 200 Processing helix chain 'K' and resid 48 through 71 Processing helix chain 'K' and resid 75 through 90 removed outlier: 3.918A pdb=" N VAL K 90 " --> pdb=" O MET K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 142 removed outlier: 4.037A pdb=" N VAL K 134 " --> pdb=" O GLY K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 165 Processing helix chain 'K' and resid 188 through 200 Processing helix chain 'Y' and resid 48 through 71 Processing helix chain 'Y' and resid 75 through 90 removed outlier: 3.918A pdb=" N VAL Y 90 " --> pdb=" O MET Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 142 removed outlier: 4.037A pdb=" N VAL Y 134 " --> pdb=" O GLY Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 165 Processing helix chain 'Y' and resid 188 through 200 Processing helix chain 'L' and resid 48 through 71 Processing helix chain 'L' and resid 75 through 90 removed outlier: 3.917A pdb=" N VAL L 90 " --> pdb=" O MET L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 142 removed outlier: 4.036A pdb=" N VAL L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 165 Processing helix chain 'L' and resid 188 through 200 Processing helix chain 'A' and resid 21 through 33 removed outlier: 3.660A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.613A pdb=" N ILE A 64 " --> pdb=" O GLN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 104 Processing helix chain 'A' and resid 108 through 123 removed outlier: 4.072A pdb=" N LEU A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 180 removed outlier: 3.568A pdb=" N ARG A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 199 Processing helix chain 'A' and resid 225 through 231 removed outlier: 3.533A pdb=" N LYS A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 32 Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.622A pdb=" N ILE B 64 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 104 Processing helix chain 'B' and resid 108 through 123 removed outlier: 4.049A pdb=" N LEU B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 180 removed outlier: 3.522A pdb=" N ARG B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 199 Processing helix chain 'B' and resid 225 through 231 removed outlier: 3.543A pdb=" N LYS B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 32 Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.612A pdb=" N ILE C 64 " --> pdb=" O GLN C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 104 Processing helix chain 'C' and resid 108 through 123 removed outlier: 4.069A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR C 123 " --> pdb=" O GLN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 removed outlier: 3.534A pdb=" N ARG C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 199 Processing helix chain 'C' and resid 225 through 231 removed outlier: 3.534A pdb=" N LYS C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 32 Processing helix chain 'D' and resid 60 through 64 removed outlier: 3.625A pdb=" N ILE D 64 " --> pdb=" O GLN D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 104 Processing helix chain 'D' and resid 108 through 123 removed outlier: 4.060A pdb=" N LEU D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR D 123 " --> pdb=" O GLN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 180 removed outlier: 3.543A pdb=" N ARG D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 199 Processing helix chain 'D' and resid 225 through 231 removed outlier: 3.512A pdb=" N LYS D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 32 Processing helix chain 'E' and resid 60 through 65 removed outlier: 3.664A pdb=" N ILE E 64 " --> pdb=" O GLN E 61 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU E 65 " --> pdb=" O ASN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 103 Processing helix chain 'E' and resid 108 through 123 removed outlier: 4.097A pdb=" N LEU E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR E 123 " --> pdb=" O GLN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 180 removed outlier: 3.524A pdb=" N ARG E 178 " --> pdb=" O SER E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 199 Processing helix chain 'E' and resid 225 through 231 removed outlier: 3.554A pdb=" N LYS E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 32 Processing helix chain 'F' and resid 60 through 64 removed outlier: 3.626A pdb=" N ILE F 64 " --> pdb=" O GLN F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 104 Processing helix chain 'F' and resid 108 through 123 removed outlier: 4.034A pdb=" N LEU F 112 " --> pdb=" O ASN F 108 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR F 123 " --> pdb=" O GLN F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 180 removed outlier: 3.531A pdb=" N ARG F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 199 Processing helix chain 'F' and resid 225 through 231 removed outlier: 3.507A pdb=" N LYS F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 32 Processing helix chain 'G' and resid 60 through 65 removed outlier: 3.650A pdb=" N ILE G 64 " --> pdb=" O GLN G 61 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU G 65 " --> pdb=" O ASN G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 123 removed outlier: 4.058A pdb=" N LEU G 112 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 180 removed outlier: 3.541A pdb=" N ARG G 178 " --> pdb=" O SER G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 199 Processing helix chain 'G' and resid 225 through 231 removed outlier: 3.571A pdb=" N LYS G 231 " --> pdb=" O GLU G 227 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 28 Processing helix chain 'O' and resid 30 through 34 removed outlier: 3.525A pdb=" N GLY O 34 " --> pdb=" O VAL O 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 103 Processing helix chain 'O' and resid 108 through 126 removed outlier: 4.097A pdb=" N LEU O 112 " --> pdb=" O ASN O 108 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR O 123 " --> pdb=" O GLN O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 169 through 180 removed outlier: 3.658A pdb=" N TYR O 180 " --> pdb=" O LEU O 176 " (cutoff:3.500A) Processing helix chain 'O' and resid 185 through 201 Processing helix chain 'O' and resid 225 through 233 removed outlier: 3.710A pdb=" N VAL O 229 " --> pdb=" O ASP O 225 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS O 230 " --> pdb=" O GLN O 226 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS O 231 " --> pdb=" O GLU O 227 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE O 232 " --> pdb=" O GLU O 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 32 Processing helix chain 'P' and resid 81 through 103 Processing helix chain 'P' and resid 108 through 126 removed outlier: 4.176A pdb=" N LEU P 112 " --> pdb=" O ASN P 108 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR P 123 " --> pdb=" O GLN P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 169 through 180 removed outlier: 3.656A pdb=" N TYR P 180 " --> pdb=" O LEU P 176 " (cutoff:3.500A) Processing helix chain 'P' and resid 185 through 201 Processing helix chain 'P' and resid 225 through 233 removed outlier: 3.709A pdb=" N VAL P 229 " --> pdb=" O ASP P 225 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS P 230 " --> pdb=" O GLN P 226 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS P 231 " --> pdb=" O GLU P 227 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE P 232 " --> pdb=" O GLU P 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 28 Processing helix chain 'Q' and resid 30 through 34 removed outlier: 3.507A pdb=" N GLY Q 34 " --> pdb=" O VAL Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 103 Processing helix chain 'Q' and resid 108 through 126 removed outlier: 4.171A pdb=" N LEU Q 112 " --> pdb=" O ASN Q 108 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR Q 123 " --> pdb=" O GLN Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 169 through 180 removed outlier: 3.621A pdb=" N TYR Q 180 " --> pdb=" O LEU Q 176 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 201 Processing helix chain 'Q' and resid 225 through 233 removed outlier: 3.709A pdb=" N VAL Q 229 " --> pdb=" O ASP Q 225 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS Q 230 " --> pdb=" O GLN Q 226 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS Q 231 " --> pdb=" O GLU Q 227 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE Q 232 " --> pdb=" O GLU Q 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 32 Processing helix chain 'R' and resid 81 through 103 Processing helix chain 'R' and resid 108 through 126 removed outlier: 4.069A pdb=" N LEU R 112 " --> pdb=" O ASN R 108 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR R 123 " --> pdb=" O GLN R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 180 removed outlier: 3.649A pdb=" N TYR R 180 " --> pdb=" O LEU R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 201 Processing helix chain 'R' and resid 225 through 233 removed outlier: 3.717A pdb=" N VAL R 229 " --> pdb=" O ASP R 225 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS R 230 " --> pdb=" O GLN R 226 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS R 231 " --> pdb=" O GLU R 227 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE R 232 " --> pdb=" O GLU R 228 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 28 Processing helix chain 'S' and resid 30 through 34 Processing helix chain 'S' and resid 81 through 103 Processing helix chain 'S' and resid 108 through 126 removed outlier: 4.145A pdb=" N LEU S 112 " --> pdb=" O ASN S 108 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR S 123 " --> pdb=" O GLN S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 169 through 180 removed outlier: 3.673A pdb=" N TYR S 180 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing helix chain 'S' and resid 185 through 201 Processing helix chain 'S' and resid 225 through 233 removed outlier: 3.701A pdb=" N VAL S 229 " --> pdb=" O ASP S 225 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS S 230 " --> pdb=" O GLN S 226 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS S 231 " --> pdb=" O GLU S 227 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE S 232 " --> pdb=" O GLU S 228 " (cutoff:3.500A) Processing helix chain 'T' and resid 21 through 28 Processing helix chain 'T' and resid 30 through 34 Processing helix chain 'T' and resid 81 through 103 Processing helix chain 'T' and resid 108 through 126 removed outlier: 4.161A pdb=" N LEU T 112 " --> pdb=" O ASN T 108 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR T 123 " --> pdb=" O GLN T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 169 through 180 removed outlier: 3.653A pdb=" N TYR T 180 " --> pdb=" O LEU T 176 " (cutoff:3.500A) Processing helix chain 'T' and resid 185 through 201 Processing helix chain 'T' and resid 225 through 233 removed outlier: 3.706A pdb=" N VAL T 229 " --> pdb=" O ASP T 225 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS T 230 " --> pdb=" O GLN T 226 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS T 231 " --> pdb=" O GLU T 227 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE T 232 " --> pdb=" O GLU T 228 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 28 Processing helix chain 'U' and resid 30 through 34 removed outlier: 3.513A pdb=" N GLY U 34 " --> pdb=" O VAL U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 103 Processing helix chain 'U' and resid 108 through 126 removed outlier: 4.175A pdb=" N LEU U 112 " --> pdb=" O ASN U 108 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR U 123 " --> pdb=" O GLN U 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 169 through 180 removed outlier: 3.657A pdb=" N TYR U 180 " --> pdb=" O LEU U 176 " (cutoff:3.500A) Processing helix chain 'U' and resid 185 through 201 Processing helix chain 'U' and resid 225 through 233 removed outlier: 3.704A pdb=" N VAL U 229 " --> pdb=" O ASP U 225 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS U 230 " --> pdb=" O GLN U 226 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS U 231 " --> pdb=" O GLU U 227 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE U 232 " --> pdb=" O GLU U 228 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Z' and resid 124 through 125 removed outlier: 3.613A pdb=" N THR Z 179 " --> pdb=" O GLY Z 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.611A pdb=" N THR Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU Z 100 " --> pdb=" O THR Z 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL Z 110 " --> pdb=" O ASP Z 122 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP Z 122 " --> pdb=" O VAL Z 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER Z 112 " --> pdb=" O VAL Z 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 124 through 125 removed outlier: 3.612A pdb=" N THR M 179 " --> pdb=" O GLY M 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 34 through 38 removed outlier: 6.610A pdb=" N THR M 41 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU M 100 " --> pdb=" O THR M 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL M 110 " --> pdb=" O ASP M 122 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP M 122 " --> pdb=" O VAL M 110 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER M 112 " --> pdb=" O VAL M 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 124 through 125 removed outlier: 3.612A pdb=" N THR 1 179 " --> pdb=" O GLY 1 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 34 through 38 removed outlier: 6.611A pdb=" N THR 1 41 " --> pdb=" O ILE 1 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU 1 100 " --> pdb=" O THR 1 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL 1 110 " --> pdb=" O ASP 1 122 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP 1 122 " --> pdb=" O VAL 1 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER 1 112 " --> pdb=" O VAL 1 120 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 124 through 125 removed outlier: 3.613A pdb=" N THR N 179 " --> pdb=" O GLY N 183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 34 through 38 removed outlier: 6.610A pdb=" N THR N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU N 100 " --> pdb=" O THR N 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL N 110 " --> pdb=" O ASP N 122 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP N 122 " --> pdb=" O VAL N 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER N 112 " --> pdb=" O VAL N 120 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '2' and resid 124 through 125 removed outlier: 3.613A pdb=" N THR 2 179 " --> pdb=" O GLY 2 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '2' and resid 34 through 38 removed outlier: 6.611A pdb=" N THR 2 41 " --> pdb=" O ILE 2 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU 2 100 " --> pdb=" O THR 2 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL 2 110 " --> pdb=" O ASP 2 122 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP 2 122 " --> pdb=" O VAL 2 110 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER 2 112 " --> pdb=" O VAL 2 120 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 124 through 125 removed outlier: 3.613A pdb=" N THR H 179 " --> pdb=" O GLY H 183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 34 through 38 removed outlier: 6.610A pdb=" N THR H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU H 100 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL H 110 " --> pdb=" O ASP H 122 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP H 122 " --> pdb=" O VAL H 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER H 112 " --> pdb=" O VAL H 120 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'V' and resid 124 through 125 removed outlier: 3.613A pdb=" N THR V 179 " --> pdb=" O GLY V 183 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'V' and resid 34 through 38 removed outlier: 6.611A pdb=" N THR V 41 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU V 100 " --> pdb=" O THR V 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL V 110 " --> pdb=" O ASP V 122 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP V 122 " --> pdb=" O VAL V 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER V 112 " --> pdb=" O VAL V 120 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 124 through 125 removed outlier: 3.612A pdb=" N THR I 179 " --> pdb=" O GLY I 183 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.611A pdb=" N THR I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU I 100 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL I 110 " --> pdb=" O ASP I 122 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP I 122 " --> pdb=" O VAL I 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER I 112 " --> pdb=" O VAL I 120 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'W' and resid 124 through 125 removed outlier: 3.613A pdb=" N THR W 179 " --> pdb=" O GLY W 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.611A pdb=" N THR W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU W 100 " --> pdb=" O THR W 44 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL W 110 " --> pdb=" O ASP W 122 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP W 122 " --> pdb=" O VAL W 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER W 112 " --> pdb=" O VAL W 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 124 through 125 removed outlier: 3.612A pdb=" N THR J 179 " --> pdb=" O GLY J 183 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 34 through 38 removed outlier: 6.611A pdb=" N THR J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU J 100 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL J 110 " --> pdb=" O ASP J 122 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP J 122 " --> pdb=" O VAL J 110 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER J 112 " --> pdb=" O VAL J 120 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'X' and resid 124 through 125 removed outlier: 3.613A pdb=" N THR X 179 " --> pdb=" O GLY X 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'X' and resid 34 through 38 removed outlier: 6.611A pdb=" N THR X 41 " --> pdb=" O ILE X 37 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU X 100 " --> pdb=" O THR X 44 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL X 110 " --> pdb=" O ASP X 122 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP X 122 " --> pdb=" O VAL X 110 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER X 112 " --> pdb=" O VAL X 120 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 124 through 125 removed outlier: 3.612A pdb=" N THR K 179 " --> pdb=" O GLY K 183 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 34 through 38 removed outlier: 6.611A pdb=" N THR K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU K 100 " --> pdb=" O THR K 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL K 110 " --> pdb=" O ASP K 122 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP K 122 " --> pdb=" O VAL K 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER K 112 " --> pdb=" O VAL K 120 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Y' and resid 124 through 125 removed outlier: 3.613A pdb=" N THR Y 179 " --> pdb=" O GLY Y 183 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Y' and resid 34 through 38 removed outlier: 6.610A pdb=" N THR Y 41 " --> pdb=" O ILE Y 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU Y 100 " --> pdb=" O THR Y 44 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL Y 110 " --> pdb=" O ASP Y 122 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP Y 122 " --> pdb=" O VAL Y 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER Y 112 " --> pdb=" O VAL Y 120 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 124 through 125 removed outlier: 3.613A pdb=" N THR L 179 " --> pdb=" O GLY L 183 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.611A pdb=" N THR L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL L 110 " --> pdb=" O ASP L 122 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP L 122 " --> pdb=" O VAL L 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER L 112 " --> pdb=" O VAL L 120 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 162 through 165 removed outlier: 3.589A pdb=" N GLY A 45 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE A 212 " --> pdb=" O TYR A 224 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 67 through 69 Processing sheet with id=AD4, first strand: chain 'B' and resid 162 through 165 removed outlier: 3.577A pdb=" N GLY B 45 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE B 212 " --> pdb=" O TYR B 224 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AD6, first strand: chain 'C' and resid 162 through 165 removed outlier: 3.565A pdb=" N GLY C 45 " --> pdb=" O PHE C 42 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 67 through 69 Processing sheet with id=AD8, first strand: chain 'D' and resid 162 through 165 removed outlier: 3.597A pdb=" N GLY D 45 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE D 212 " --> pdb=" O TYR D 224 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 67 through 69 Processing sheet with id=AE1, first strand: chain 'E' and resid 162 through 165 removed outlier: 3.571A pdb=" N GLY E 45 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE E 212 " --> pdb=" O TYR E 224 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 67 through 69 Processing sheet with id=AE3, first strand: chain 'F' and resid 162 through 165 removed outlier: 3.610A pdb=" N GLY F 45 " --> pdb=" O PHE F 42 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ILE F 212 " --> pdb=" O TYR F 224 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 67 through 69 Processing sheet with id=AE5, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.565A pdb=" N GLY G 45 " --> pdb=" O PHE G 42 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 67 through 69 removed outlier: 3.505A pdb=" N ASN G 158 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 162 through 165 removed outlier: 3.538A pdb=" N GLY O 45 " --> pdb=" O PHE O 42 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER O 214 " --> pdb=" O ARG O 222 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 68 through 69 Processing sheet with id=AE9, first strand: chain 'P' and resid 162 through 165 removed outlier: 3.528A pdb=" N GLY P 45 " --> pdb=" O PHE P 42 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER P 214 " --> pdb=" O ARG P 222 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 68 through 69 Processing sheet with id=AF2, first strand: chain 'Q' and resid 162 through 165 removed outlier: 3.537A pdb=" N GLY Q 45 " --> pdb=" O PHE Q 42 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER Q 214 " --> pdb=" O ARG Q 222 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 68 through 69 Processing sheet with id=AF4, first strand: chain 'R' and resid 162 through 165 removed outlier: 3.531A pdb=" N GLY R 45 " --> pdb=" O PHE R 42 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER R 214 " --> pdb=" O ARG R 222 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 68 through 69 Processing sheet with id=AF6, first strand: chain 'S' and resid 162 through 165 removed outlier: 3.530A pdb=" N GLY S 45 " --> pdb=" O PHE S 42 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER S 214 " --> pdb=" O ARG S 222 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 68 through 69 Processing sheet with id=AF8, first strand: chain 'T' and resid 162 through 165 removed outlier: 3.519A pdb=" N GLY T 45 " --> pdb=" O PHE T 42 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER T 214 " --> pdb=" O ARG T 222 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'T' and resid 68 through 69 Processing sheet with id=AG1, first strand: chain 'U' and resid 162 through 165 removed outlier: 3.517A pdb=" N GLY U 45 " --> pdb=" O PHE U 42 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER U 214 " --> pdb=" O ARG U 222 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 68 through 69 2552 hydrogen bonds defined for protein. 7341 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: 18.49 Time building geometry restraints manager: 17.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 8035 1.31 - 1.43: 11154 1.43 - 1.56: 27505 1.56 - 1.68: 24 1.68 - 1.80: 378 Bond restraints: 47096 Sorted by residual: bond pdb=" CA LEU D 21 " pdb=" CB LEU D 21 " ideal model delta sigma weight residual 1.525 1.453 0.072 1.47e-02 4.63e+03 2.40e+01 bond pdb=" CB MET G 40 " pdb=" CG MET G 40 " ideal model delta sigma weight residual 1.520 1.409 0.111 3.00e-02 1.11e+03 1.38e+01 bond pdb=" CB MET E 40 " pdb=" CG MET E 40 " ideal model delta sigma weight residual 1.520 1.416 0.104 3.00e-02 1.11e+03 1.21e+01 bond pdb=" CB MET A 40 " pdb=" CG MET A 40 " ideal model delta sigma weight residual 1.520 1.418 0.102 3.00e-02 1.11e+03 1.17e+01 bond pdb=" CB MET B 40 " pdb=" CG MET B 40 " ideal model delta sigma weight residual 1.520 1.418 0.102 3.00e-02 1.11e+03 1.15e+01 ... (remaining 47091 not shown) Histogram of bond angle deviations from ideal: 95.09 - 104.08: 551 104.08 - 113.07: 25393 113.07 - 122.05: 28954 122.05 - 131.04: 8628 131.04 - 140.03: 62 Bond angle restraints: 63588 Sorted by residual: angle pdb=" C THR V 21 " pdb=" N MET V 22 " pdb=" CA MET V 22 " ideal model delta sigma weight residual 121.70 140.03 -18.33 1.80e+00 3.09e-01 1.04e+02 angle pdb=" C THR X 21 " pdb=" N MET X 22 " pdb=" CA MET X 22 " ideal model delta sigma weight residual 121.70 140.02 -18.32 1.80e+00 3.09e-01 1.04e+02 angle pdb=" C THR W 21 " pdb=" N MET W 22 " pdb=" CA MET W 22 " ideal model delta sigma weight residual 121.70 140.02 -18.32 1.80e+00 3.09e-01 1.04e+02 angle pdb=" C THR I 21 " pdb=" N MET I 22 " pdb=" CA MET I 22 " ideal model delta sigma weight residual 121.70 140.00 -18.30 1.80e+00 3.09e-01 1.03e+02 angle pdb=" C THR 1 21 " pdb=" N MET 1 22 " pdb=" CA MET 1 22 " ideal model delta sigma weight residual 121.70 139.99 -18.29 1.80e+00 3.09e-01 1.03e+02 ... (remaining 63583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.40: 27195 15.40 - 30.79: 1249 30.79 - 46.19: 300 46.19 - 61.58: 19 61.58 - 76.98: 49 Dihedral angle restraints: 28812 sinusoidal: 11473 harmonic: 17339 Sorted by residual: dihedral pdb=" CA ASP R 9 " pdb=" C ASP R 9 " pdb=" N ARG R 10 " pdb=" CA ARG R 10 " ideal model delta harmonic sigma weight residual 180.00 118.64 61.36 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA ASN K 24 " pdb=" C ASN K 24 " pdb=" N PHE K 25 " pdb=" CA PHE K 25 " ideal model delta harmonic sigma weight residual 180.00 120.64 59.36 0 5.00e+00 4.00e-02 1.41e+02 dihedral pdb=" CA ASN 1 24 " pdb=" C ASN 1 24 " pdb=" N PHE 1 25 " pdb=" CA PHE 1 25 " ideal model delta harmonic sigma weight residual 180.00 120.66 59.34 0 5.00e+00 4.00e-02 1.41e+02 ... (remaining 28809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 5878 0.070 - 0.140: 1204 0.140 - 0.211: 279 0.211 - 0.281: 55 0.281 - 0.351: 32 Chirality restraints: 7448 Sorted by residual: chirality pdb=" CB VAL C 74 " pdb=" CA VAL C 74 " pdb=" CG1 VAL C 74 " pdb=" CG2 VAL C 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CB VAL B 74 " pdb=" CA VAL B 74 " pdb=" CG1 VAL B 74 " pdb=" CG2 VAL B 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CB VAL G 74 " pdb=" CA VAL G 74 " pdb=" CG1 VAL G 74 " pdb=" CG2 VAL G 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 7445 not shown) Planarity restraints: 8162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP Q 9 " -0.029 2.00e-02 2.50e+03 5.71e-02 3.26e+01 pdb=" C ASP Q 9 " 0.099 2.00e-02 2.50e+03 pdb=" O ASP Q 9 " -0.036 2.00e-02 2.50e+03 pdb=" N ARG Q 10 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 10 " -0.098 9.50e-02 1.11e+02 6.15e-02 2.43e+01 pdb=" NE ARG Q 10 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG Q 10 " 0.084 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 10 " -0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 10 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR Q 26 " 0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C TYR Q 26 " -0.068 2.00e-02 2.50e+03 pdb=" O TYR Q 26 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA Q 27 " 0.023 2.00e-02 2.50e+03 ... (remaining 8159 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 530 2.61 - 3.18: 38473 3.18 - 3.75: 73362 3.75 - 4.33: 100779 4.33 - 4.90: 167504 Nonbonded interactions: 380648 Sorted by model distance: nonbonded pdb=" O GLU S 25 " pdb=" O LEU S 28 " model vdw 2.036 3.040 nonbonded pdb=" O GLU U 25 " pdb=" O LEU U 28 " model vdw 2.042 3.040 nonbonded pdb=" O GLU O 25 " pdb=" O LEU O 28 " model vdw 2.044 3.040 nonbonded pdb=" O GLU Q 25 " pdb=" O LEU Q 28 " model vdw 2.048 3.040 nonbonded pdb=" O GLU T 25 " pdb=" O LEU T 28 " model vdw 2.062 3.040 ... (remaining 380643 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 '1' selection = chain '2' selection = 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' } ncs_group { reference = (chain 'A' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'B' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'C' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'D' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'E' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'F' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'G' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'O' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'P' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'Q' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'R' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'S' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'T' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) selection = (chain 'U' and (resid 8 through 27 or resid 29 through 65 or resid 67 through 23 \ 3)) } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 9.550 Check model and map are aligned: 0.690 Set scattering table: 0.410 Process input model: 111.390 Find NCS groups from input model: 3.480 Set up NCS constraints: 0.210 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: 0.030 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 : 0.009 0.117 47096 Z= 0.567 Angle : 1.287 18.330 63588 Z= 0.728 Chirality : 0.066 0.351 7448 Planarity : 0.007 0.068 8162 Dihedral : 10.410 76.979 17738 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.69 % Favored : 93.86 % Rotamer: Outliers : 0.70 % Allowed : 5.57 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.09), residues: 5957 helix: -1.76 (0.08), residues: 2289 sheet: -1.45 (0.14), residues: 1211 loop : -2.85 (0.10), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS Y 28 PHE 0.031 0.004 PHE B 15 TYR 0.040 0.004 TYR T 224 ARG 0.083 0.001 ARG Q 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2600 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 2565 time to evaluate : 5.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 33 LYS cc_start: 0.8685 (mttm) cc_final: 0.8433 (mttt) REVERT: Z 35 PHE cc_start: 0.8399 (m-80) cc_final: 0.7980 (m-80) REVERT: Z 37 ILE cc_start: 0.9261 (tp) cc_final: 0.9034 (tp) REVERT: Z 40 TYR cc_start: 0.8554 (m-80) cc_final: 0.8174 (m-10) REVERT: Z 59 MET cc_start: 0.8523 (mmt) cc_final: 0.8213 (mmp) REVERT: Z 77 GLU cc_start: 0.8448 (tt0) cc_final: 0.8163 (mp0) REVERT: Z 93 MET cc_start: 0.7615 (mmt) cc_final: 0.7341 (mmt) REVERT: Z 98 GLN cc_start: 0.8926 (mt0) cc_final: 0.8312 (tt0) REVERT: Z 139 GLU cc_start: 0.8639 (tp30) cc_final: 0.8195 (tp30) REVERT: Z 141 GLN cc_start: 0.8980 (mt0) cc_final: 0.8748 (mt0) REVERT: M 19 ARG cc_start: 0.8762 (ttm170) cc_final: 0.8231 (ttm170) REVERT: M 33 LYS cc_start: 0.8862 (mttm) cc_final: 0.8551 (mtmm) REVERT: M 43 MET cc_start: 0.8434 (ttm) cc_final: 0.8225 (ttp) REVERT: M 66 TYR cc_start: 0.8250 (t80) cc_final: 0.7675 (t80) REVERT: M 149 ASP cc_start: 0.8425 (m-30) cc_final: 0.8004 (m-30) REVERT: M 153 ASP cc_start: 0.8166 (m-30) cc_final: 0.7945 (m-30) REVERT: M 166 ASP cc_start: 0.8628 (t70) cc_final: 0.8181 (t0) REVERT: 1 16 THR cc_start: 0.9015 (p) cc_final: 0.8805 (p) REVERT: 1 17 GLU cc_start: 0.6705 (pp20) cc_final: 0.6309 (pm20) REVERT: 1 27 MET cc_start: 0.7232 (ttt) cc_final: 0.6892 (ttt) REVERT: 1 35 PHE cc_start: 0.8356 (m-80) cc_final: 0.7819 (m-80) REVERT: 1 77 GLU cc_start: 0.8455 (tt0) cc_final: 0.7829 (mp0) REVERT: 1 95 TYR cc_start: 0.8820 (m-80) cc_final: 0.8225 (m-80) REVERT: 1 98 GLN cc_start: 0.8917 (mt0) cc_final: 0.8362 (tt0) REVERT: 1 104 ILE cc_start: 0.8981 (tt) cc_final: 0.8459 (tt) REVERT: 1 139 GLU cc_start: 0.8711 (tp30) cc_final: 0.8395 (mm-30) REVERT: 1 150 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8464 (mt-10) REVERT: N 27 MET cc_start: 0.9168 (ttt) cc_final: 0.8190 (ttp) REVERT: N 43 MET cc_start: 0.8283 (ttm) cc_final: 0.8081 (ttp) REVERT: N 95 TYR cc_start: 0.8593 (m-80) cc_final: 0.8118 (m-80) REVERT: N 153 ASP cc_start: 0.8025 (m-30) cc_final: 0.7811 (m-30) REVERT: 2 27 MET cc_start: 0.7371 (ttt) cc_final: 0.6987 (ttt) REVERT: 2 59 MET cc_start: 0.8641 (mmt) cc_final: 0.8317 (mmp) REVERT: 2 77 GLU cc_start: 0.8303 (tt0) cc_final: 0.7746 (mp0) REVERT: 2 98 GLN cc_start: 0.8862 (mt0) cc_final: 0.8272 (tt0) REVERT: 2 124 TYR cc_start: 0.8431 (p90) cc_final: 0.7081 (p90) REVERT: 2 139 GLU cc_start: 0.8576 (tp30) cc_final: 0.8276 (tp30) REVERT: 2 150 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8290 (mt-10) REVERT: H 19 ARG cc_start: 0.8688 (ttm170) cc_final: 0.8475 (ttm-80) REVERT: H 22 MET cc_start: 0.5204 (ttt) cc_final: 0.4853 (ttt) REVERT: H 33 LYS cc_start: 0.8823 (mttm) cc_final: 0.8482 (mttp) REVERT: H 95 TYR cc_start: 0.8717 (m-80) cc_final: 0.8250 (m-80) REVERT: H 149 ASP cc_start: 0.8532 (m-30) cc_final: 0.8295 (t70) REVERT: H 153 ASP cc_start: 0.8134 (m-30) cc_final: 0.7826 (m-30) REVERT: H 166 ASP cc_start: 0.8364 (t70) cc_final: 0.7833 (t0) REVERT: V 27 MET cc_start: 0.7471 (ttt) cc_final: 0.6652 (ttp) REVERT: V 35 PHE cc_start: 0.8466 (m-80) cc_final: 0.7870 (m-80) REVERT: V 37 ILE cc_start: 0.9266 (tp) cc_final: 0.9050 (tp) REVERT: V 98 GLN cc_start: 0.8802 (mt0) cc_final: 0.8398 (tt0) REVERT: V 124 TYR cc_start: 0.8489 (p90) cc_final: 0.7308 (p90) REVERT: V 139 GLU cc_start: 0.8821 (tp30) cc_final: 0.8102 (tp30) REVERT: I 27 MET cc_start: 0.9027 (ttt) cc_final: 0.8711 (ttp) REVERT: I 33 LYS cc_start: 0.8779 (mttm) cc_final: 0.8355 (mtmt) REVERT: I 66 TYR cc_start: 0.8358 (t80) cc_final: 0.6712 (t80) REVERT: I 159 ILE cc_start: 0.8487 (mm) cc_final: 0.8272 (mm) REVERT: I 184 TYR cc_start: 0.8045 (t80) cc_final: 0.7341 (t80) REVERT: W 27 MET cc_start: 0.7299 (ttt) cc_final: 0.6505 (ttp) REVERT: W 35 PHE cc_start: 0.8302 (m-80) cc_final: 0.8098 (m-10) REVERT: W 59 MET cc_start: 0.8456 (mmt) cc_final: 0.8204 (mmp) REVERT: W 104 ILE cc_start: 0.8851 (tt) cc_final: 0.8297 (tt) REVERT: W 124 TYR cc_start: 0.8315 (p90) cc_final: 0.7752 (p90) REVERT: W 139 GLU cc_start: 0.8687 (tp30) cc_final: 0.8233 (tp30) REVERT: W 149 ASP cc_start: 0.7967 (m-30) cc_final: 0.7724 (m-30) REVERT: W 150 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8625 (mt-10) REVERT: J 27 MET cc_start: 0.8809 (ttt) cc_final: 0.8282 (ttt) REVERT: J 33 LYS cc_start: 0.8949 (mttm) cc_final: 0.8612 (mttp) REVERT: J 59 MET cc_start: 0.8610 (mmt) cc_final: 0.8257 (tpp) REVERT: J 66 TYR cc_start: 0.8365 (t80) cc_final: 0.7097 (t80) REVERT: J 76 ILE cc_start: 0.8543 (mm) cc_final: 0.8326 (mm) REVERT: J 112 SER cc_start: 0.9192 (t) cc_final: 0.8874 (t) REVERT: J 149 ASP cc_start: 0.8407 (m-30) cc_final: 0.7726 (t0) REVERT: J 153 ASP cc_start: 0.8259 (m-30) cc_final: 0.7976 (m-30) REVERT: J 159 ILE cc_start: 0.8574 (mm) cc_final: 0.8024 (mm) REVERT: J 166 ASP cc_start: 0.8517 (t70) cc_final: 0.7964 (t0) REVERT: X 27 MET cc_start: 0.7695 (ttt) cc_final: 0.7486 (ttt) REVERT: X 33 LYS cc_start: 0.8551 (mttm) cc_final: 0.8181 (mttt) REVERT: X 35 PHE cc_start: 0.8282 (m-80) cc_final: 0.7897 (m-80) REVERT: X 37 ILE cc_start: 0.9295 (tp) cc_final: 0.9063 (tp) REVERT: X 43 MET cc_start: 0.8125 (ttm) cc_final: 0.7917 (ttp) REVERT: X 90 VAL cc_start: 0.8309 (p) cc_final: 0.8042 (p) REVERT: X 95 TYR cc_start: 0.8787 (m-80) cc_final: 0.8476 (m-80) REVERT: X 124 TYR cc_start: 0.8462 (p90) cc_final: 0.7483 (p90) REVERT: X 139 GLU cc_start: 0.8617 (tp30) cc_final: 0.7798 (tp30) REVERT: X 150 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8359 (mt-10) REVERT: X 160 SER cc_start: 0.8901 (m) cc_final: 0.8635 (p) REVERT: K 9 LYS cc_start: 0.8425 (mttt) cc_final: 0.8213 (mmmt) REVERT: K 149 ASP cc_start: 0.8578 (m-30) cc_final: 0.8113 (t70) REVERT: K 153 ASP cc_start: 0.7998 (m-30) cc_final: 0.7761 (m-30) REVERT: K 166 ASP cc_start: 0.8539 (t70) cc_final: 0.8203 (t0) REVERT: Y 27 MET cc_start: 0.7756 (ttt) cc_final: 0.7387 (ttp) REVERT: Y 35 PHE cc_start: 0.8234 (m-80) cc_final: 0.7607 (m-80) REVERT: Y 37 ILE cc_start: 0.9317 (tp) cc_final: 0.9094 (tp) REVERT: Y 77 GLU cc_start: 0.8445 (tt0) cc_final: 0.8045 (mp0) REVERT: Y 139 GLU cc_start: 0.8757 (tp30) cc_final: 0.8040 (mm-30) REVERT: Y 141 GLN cc_start: 0.8971 (mt0) cc_final: 0.8727 (mt0) REVERT: Y 150 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8453 (mt-10) REVERT: L 33 LYS cc_start: 0.8880 (mttm) cc_final: 0.8617 (mtmt) REVERT: L 59 MET cc_start: 0.8519 (mmt) cc_final: 0.8117 (tpp) REVERT: L 66 TYR cc_start: 0.8295 (t80) cc_final: 0.7170 (t80) REVERT: L 76 ILE cc_start: 0.8596 (mm) cc_final: 0.8396 (mm) REVERT: L 98 GLN cc_start: 0.8520 (mt0) cc_final: 0.8232 (mt0) REVERT: L 131 SER cc_start: 0.8924 (t) cc_final: 0.8570 (t) REVERT: L 135 TYR cc_start: 0.8127 (m-80) cc_final: 0.7669 (m-80) REVERT: L 149 ASP cc_start: 0.8529 (m-30) cc_final: 0.7919 (t0) REVERT: L 153 ASP cc_start: 0.8192 (m-30) cc_final: 0.7747 (m-30) REVERT: L 166 ASP cc_start: 0.8525 (t70) cc_final: 0.8308 (t70) REVERT: A 36 THR cc_start: 0.9008 (m) cc_final: 0.7917 (m) REVERT: A 40 MET cc_start: 0.8493 (pmt) cc_final: 0.8061 (pmm) REVERT: A 51 ASP cc_start: 0.7567 (t70) cc_final: 0.6798 (p0) REVERT: A 71 ASP cc_start: 0.7292 (t70) cc_final: 0.7016 (t70) REVERT: A 72 ASP cc_start: 0.8368 (m-30) cc_final: 0.8135 (m-30) REVERT: A 82 VAL cc_start: 0.8307 (m) cc_final: 0.8063 (p) REVERT: A 95 SER cc_start: 0.7893 (m) cc_final: 0.7148 (p) REVERT: A 100 LYS cc_start: 0.7925 (ttmm) cc_final: 0.7656 (ttmt) REVERT: A 112 LEU cc_start: 0.8837 (tp) cc_final: 0.8625 (tp) REVERT: A 165 ILE cc_start: 0.8032 (pt) cc_final: 0.7766 (pt) REVERT: A 219 ASN cc_start: 0.8443 (m110) cc_final: 0.8240 (m-40) REVERT: A 225 ASP cc_start: 0.7108 (p0) cc_final: 0.6849 (p0) REVERT: B 8 TYR cc_start: 0.5402 (m-10) cc_final: 0.4776 (m-80) REVERT: B 10 ARG cc_start: 0.5052 (mpt-90) cc_final: 0.4203 (ptm-80) REVERT: B 40 MET cc_start: 0.8526 (pmt) cc_final: 0.8051 (pmm) REVERT: B 71 ASP cc_start: 0.7216 (t70) cc_final: 0.6466 (t70) REVERT: B 95 SER cc_start: 0.7670 (m) cc_final: 0.7116 (p) REVERT: B 110 GLU cc_start: 0.7918 (tt0) cc_final: 0.7685 (tm-30) REVERT: B 224 TYR cc_start: 0.7551 (m-10) cc_final: 0.7132 (m-10) REVERT: C 36 THR cc_start: 0.9082 (m) cc_final: 0.8711 (p) REVERT: C 40 MET cc_start: 0.8459 (pmt) cc_final: 0.8038 (pmm) REVERT: C 71 ASP cc_start: 0.7445 (t70) cc_final: 0.7120 (t70) REVERT: C 224 TYR cc_start: 0.7560 (m-10) cc_final: 0.7156 (m-80) REVERT: C 225 ASP cc_start: 0.7261 (p0) cc_final: 0.6810 (p0) REVERT: D 40 MET cc_start: 0.8631 (pmt) cc_final: 0.8179 (pmm) REVERT: D 51 ASP cc_start: 0.7486 (t70) cc_final: 0.7285 (t0) REVERT: D 115 ARG cc_start: 0.8080 (mmt90) cc_final: 0.7858 (mmt-90) REVERT: D 150 ASP cc_start: 0.8335 (p0) cc_final: 0.7708 (p0) REVERT: D 158 ASN cc_start: 0.8067 (m110) cc_final: 0.7742 (m-40) REVERT: D 219 ASN cc_start: 0.8438 (m110) cc_final: 0.8184 (m-40) REVERT: E 29 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7869 (tp30) REVERT: E 40 MET cc_start: 0.8502 (pmt) cc_final: 0.8198 (pmm) REVERT: E 53 LYS cc_start: 0.6281 (mtmm) cc_final: 0.6036 (tmtt) REVERT: E 82 VAL cc_start: 0.8179 (m) cc_final: 0.7923 (p) REVERT: E 95 SER cc_start: 0.7948 (m) cc_final: 0.7195 (p) REVERT: E 108 ASN cc_start: 0.7935 (t0) cc_final: 0.7593 (t0) REVERT: E 142 ASP cc_start: 0.6660 (p0) cc_final: 0.6322 (p0) REVERT: E 147 ARG cc_start: 0.8162 (mmm160) cc_final: 0.7895 (mmm-85) REVERT: E 177 GLU cc_start: 0.7933 (tp30) cc_final: 0.7526 (tt0) REVERT: E 219 ASN cc_start: 0.8361 (m110) cc_final: 0.8069 (m-40) REVERT: E 225 ASP cc_start: 0.7405 (p0) cc_final: 0.6942 (p0) REVERT: F 10 ARG cc_start: 0.5542 (mpt-90) cc_final: 0.4406 (ptm-80) REVERT: F 40 MET cc_start: 0.8713 (pmt) cc_final: 0.8290 (pmm) REVERT: F 95 SER cc_start: 0.7917 (m) cc_final: 0.7355 (m) REVERT: F 150 ASP cc_start: 0.8202 (p0) cc_final: 0.7239 (p0) REVERT: G 8 TYR cc_start: 0.5981 (m-10) cc_final: 0.5618 (m-80) REVERT: G 29 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7945 (tp30) REVERT: G 40 MET cc_start: 0.8231 (pmt) cc_final: 0.7956 (pmm) REVERT: G 71 ASP cc_start: 0.7695 (t70) cc_final: 0.7431 (t70) REVERT: G 95 SER cc_start: 0.7922 (m) cc_final: 0.7325 (p) REVERT: G 115 ARG cc_start: 0.8123 (mmt90) cc_final: 0.7749 (mpt-90) REVERT: G 165 ILE cc_start: 0.7979 (pt) cc_final: 0.7716 (pt) REVERT: G 177 GLU cc_start: 0.7405 (tp30) cc_final: 0.7162 (tt0) REVERT: G 225 ASP cc_start: 0.7786 (p0) cc_final: 0.7103 (p0) REVERT: G 228 GLU cc_start: 0.8418 (tt0) cc_final: 0.8033 (tp30) REVERT: O 17 PRO cc_start: 0.8975 (Cg_endo) cc_final: 0.8700 (Cg_exo) REVERT: O 33 LYS cc_start: 0.8453 (mtpp) cc_final: 0.8184 (pttp) REVERT: O 74 VAL cc_start: 0.9070 (p) cc_final: 0.8717 (m) REVERT: O 122 GLN cc_start: 0.8705 (mt0) cc_final: 0.8457 (tt0) REVERT: O 152 ASP cc_start: 0.7083 (t0) cc_final: 0.6412 (t0) REVERT: O 156 THR cc_start: 0.9100 (m) cc_final: 0.8851 (p) REVERT: O 191 THR cc_start: 0.8634 (m) cc_final: 0.8062 (p) REVERT: O 201 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7957 (tt) REVERT: P 8 TYR cc_start: 0.5737 (t80) cc_final: 0.4793 (m-80) REVERT: P 33 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8648 (pttp) REVERT: P 73 TYR cc_start: 0.8925 (m-80) cc_final: 0.8352 (m-80) REVERT: P 107 VAL cc_start: 0.8164 (t) cc_final: 0.7505 (t) REVERT: P 119 GLN cc_start: 0.8865 (tp-100) cc_final: 0.8406 (tp40) REVERT: P 122 GLN cc_start: 0.8823 (mt0) cc_final: 0.8064 (mt0) REVERT: P 152 ASP cc_start: 0.6941 (t0) cc_final: 0.6357 (t0) REVERT: P 165 ILE cc_start: 0.8745 (tp) cc_final: 0.8372 (mm) REVERT: P 191 THR cc_start: 0.8962 (m) cc_final: 0.8664 (p) REVERT: Q 74 VAL cc_start: 0.9057 (p) cc_final: 0.8572 (p) REVERT: Q 105 SER cc_start: 0.8298 (p) cc_final: 0.8036 (m) REVERT: Q 119 GLN cc_start: 0.8813 (tp-100) cc_final: 0.8403 (tp40) REVERT: Q 121 GLN cc_start: 0.7678 (tm130) cc_final: 0.7342 (tm-30) REVERT: Q 152 ASP cc_start: 0.7163 (t0) cc_final: 0.6571 (t0) REVERT: Q 165 ILE cc_start: 0.8778 (tp) cc_final: 0.8437 (mm) REVERT: Q 191 THR cc_start: 0.8846 (m) cc_final: 0.8475 (p) REVERT: Q 201 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7442 (tt) REVERT: Q 219 ASN cc_start: 0.8530 (m-40) cc_final: 0.8300 (m110) REVERT: R 63 SER cc_start: 0.8243 (m) cc_final: 0.7979 (p) REVERT: R 105 SER cc_start: 0.8124 (p) cc_final: 0.7058 (p) REVERT: R 107 VAL cc_start: 0.8355 (t) cc_final: 0.7661 (m) REVERT: R 119 GLN cc_start: 0.8984 (tp-100) cc_final: 0.8776 (tp40) REVERT: R 121 GLN cc_start: 0.7908 (tm130) cc_final: 0.7617 (tm-30) REVERT: R 122 GLN cc_start: 0.8588 (mt0) cc_final: 0.7903 (mt0) REVERT: R 152 ASP cc_start: 0.7307 (t0) cc_final: 0.6495 (t0) REVERT: R 153 PRO cc_start: 0.7853 (Cg_exo) cc_final: 0.7147 (Cg_endo) REVERT: R 156 THR cc_start: 0.8973 (m) cc_final: 0.8632 (p) REVERT: R 165 ILE cc_start: 0.8382 (tp) cc_final: 0.8012 (mm) REVERT: R 191 THR cc_start: 0.8736 (m) cc_final: 0.8333 (p) REVERT: R 201 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7657 (tt) REVERT: S 72 ASP cc_start: 0.7936 (m-30) cc_final: 0.7457 (p0) REVERT: S 74 VAL cc_start: 0.8825 (p) cc_final: 0.8464 (p) REVERT: S 107 VAL cc_start: 0.8142 (t) cc_final: 0.7858 (m) REVERT: S 119 GLN cc_start: 0.8915 (tp-100) cc_final: 0.8588 (tp40) REVERT: S 122 GLN cc_start: 0.8696 (mt0) cc_final: 0.8441 (mt0) REVERT: S 152 ASP cc_start: 0.7411 (t0) cc_final: 0.6652 (t0) REVERT: S 165 ILE cc_start: 0.8710 (tp) cc_final: 0.8350 (mm) REVERT: S 183 ASN cc_start: 0.7935 (m110) cc_final: 0.7731 (p0) REVERT: S 191 THR cc_start: 0.8883 (m) cc_final: 0.8366 (p) REVERT: T 33 LYS cc_start: 0.8830 (mtpp) cc_final: 0.8553 (pttt) REVERT: T 46 VAL cc_start: 0.8717 (p) cc_final: 0.8494 (m) REVERT: T 49 ILE cc_start: 0.8388 (tt) cc_final: 0.8155 (pt) REVERT: T 72 ASP cc_start: 0.7739 (m-30) cc_final: 0.7095 (p0) REVERT: T 103 TYR cc_start: 0.8265 (m-80) cc_final: 0.7943 (m-80) REVERT: T 119 GLN cc_start: 0.8937 (tp-100) cc_final: 0.8711 (tp40) REVERT: T 151 CYS cc_start: 0.7271 (t) cc_final: 0.6398 (t) REVERT: T 152 ASP cc_start: 0.7108 (t0) cc_final: 0.6426 (t0) REVERT: T 165 ILE cc_start: 0.8895 (tp) cc_final: 0.8554 (mm) REVERT: T 191 THR cc_start: 0.9023 (m) cc_final: 0.8550 (p) REVERT: U 73 TYR cc_start: 0.8835 (m-80) cc_final: 0.8241 (m-10) REVERT: U 84 ASP cc_start: 0.8832 (m-30) cc_final: 0.8529 (m-30) REVERT: U 123 TYR cc_start: 0.8956 (m-10) cc_final: 0.8747 (m-10) REVERT: U 151 CYS cc_start: 0.7333 (t) cc_final: 0.6433 (t) REVERT: U 152 ASP cc_start: 0.6741 (t0) cc_final: 0.6123 (t0) REVERT: U 165 ILE cc_start: 0.8733 (tp) cc_final: 0.8342 (mm) REVERT: U 191 THR cc_start: 0.8834 (m) cc_final: 0.8394 (p) outliers start: 35 outliers final: 11 residues processed: 2586 average time/residue: 0.6765 time to fit residues: 2749.8645 Evaluate side-chains 1325 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1311 time to evaluate : 5.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain U residue 201 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 496 optimal weight: 0.9980 chunk 445 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 152 optimal weight: 0.6980 chunk 300 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 chunk 460 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 chunk 280 optimal weight: 0.9980 chunk 343 optimal weight: 6.9990 chunk 533 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 85 ASN Z 191 GLN M 85 ASN M 89 GLN 1 30 ASN 1 85 ASN ** 1 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 191 GLN 2 30 ASN ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 191 GLN I 191 GLN W 88 ASN W 191 GLN J 89 GLN J 191 GLN K 191 GLN Y 85 ASN Y 191 GLN L 141 GLN A 62 ASN A 219 ASN C 68 GLN C 98 GLN C 183 ASN D 219 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN E 219 ASN F 68 GLN ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN O 23 GLN P 23 GLN P 143 GLN Q 23 GLN Q 143 GLN R 23 GLN S 23 GLN S 143 GLN T 23 GLN T 143 GLN T 226 GLN U 23 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 47096 Z= 0.245 Angle : 0.795 24.010 63588 Z= 0.410 Chirality : 0.047 0.247 7448 Planarity : 0.005 0.116 8162 Dihedral : 6.801 53.063 6627 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.62 % Favored : 95.25 % Rotamer: Outliers : 5.13 % Allowed : 18.86 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.83 (0.10), residues: 5957 helix: 0.29 (0.10), residues: 2303 sheet: -1.39 (0.13), residues: 1274 loop : -2.61 (0.11), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS L 28 PHE 0.020 0.002 PHE P 91 TYR 0.020 0.002 TYR P 221 ARG 0.008 0.001 ARG H 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1743 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1486 time to evaluate : 5.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 10 ASP cc_start: 0.7078 (m-30) cc_final: 0.6791 (m-30) REVERT: Z 14 MET cc_start: 0.7891 (mtm) cc_final: 0.7375 (mtt) REVERT: Z 20 VAL cc_start: 0.9142 (t) cc_final: 0.8860 (p) REVERT: Z 32 LYS cc_start: 0.8459 (tppt) cc_final: 0.8080 (tppt) REVERT: Z 35 PHE cc_start: 0.8356 (m-80) cc_final: 0.8059 (m-10) REVERT: Z 37 ILE cc_start: 0.9206 (tp) cc_final: 0.8846 (tp) REVERT: Z 43 MET cc_start: 0.8106 (ttm) cc_final: 0.7701 (ttp) REVERT: Z 77 GLU cc_start: 0.8470 (tt0) cc_final: 0.7898 (mp0) REVERT: Z 98 GLN cc_start: 0.9043 (mt0) cc_final: 0.8438 (tt0) REVERT: Z 111 PHE cc_start: 0.8433 (m-80) cc_final: 0.8156 (m-80) REVERT: Z 146 MET cc_start: 0.8727 (mtp) cc_final: 0.8467 (mtp) REVERT: Z 180 ARG cc_start: 0.8824 (tpp80) cc_final: 0.8576 (tpp80) REVERT: M 33 LYS cc_start: 0.8807 (mttm) cc_final: 0.8263 (mttp) REVERT: M 92 TYR cc_start: 0.8192 (m-80) cc_final: 0.7673 (m-10) REVERT: M 95 TYR cc_start: 0.8938 (m-80) cc_final: 0.8511 (m-80) REVERT: M 111 PHE cc_start: 0.8579 (m-80) cc_final: 0.8301 (m-80) REVERT: M 193 GLU cc_start: 0.8338 (pt0) cc_final: 0.8001 (tp30) REVERT: 1 35 PHE cc_start: 0.8346 (m-80) cc_final: 0.7795 (m-80) REVERT: 1 95 TYR cc_start: 0.8837 (m-80) cc_final: 0.8139 (m-80) REVERT: 1 98 GLN cc_start: 0.9063 (mt0) cc_final: 0.8502 (tt0) REVERT: 1 124 TYR cc_start: 0.8551 (p90) cc_final: 0.8066 (p90) REVERT: 1 150 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8463 (mt-10) REVERT: 1 193 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7116 (pt0) REVERT: N 92 TYR cc_start: 0.8116 (m-10) cc_final: 0.7679 (m-10) REVERT: N 124 TYR cc_start: 0.8489 (p90) cc_final: 0.8120 (p90) REVERT: N 150 GLU cc_start: 0.8078 (mp0) cc_final: 0.7859 (mp0) REVERT: N 153 ASP cc_start: 0.8202 (m-30) cc_final: 0.7931 (m-30) REVERT: N 193 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8092 (tp30) REVERT: 2 12 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8635 (p) REVERT: 2 63 LEU cc_start: 0.9142 (mm) cc_final: 0.8901 (mm) REVERT: 2 77 GLU cc_start: 0.8506 (tt0) cc_final: 0.7810 (mp0) REVERT: 2 95 TYR cc_start: 0.8903 (m-80) cc_final: 0.8219 (m-80) REVERT: 2 98 GLN cc_start: 0.8935 (mt0) cc_final: 0.8530 (tt0) REVERT: 2 111 PHE cc_start: 0.8096 (m-80) cc_final: 0.7678 (m-80) REVERT: 2 124 TYR cc_start: 0.8435 (p90) cc_final: 0.7045 (p90) REVERT: 2 150 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8334 (mt-10) REVERT: 2 198 LYS cc_start: 0.7779 (mtmt) cc_final: 0.7290 (mtmt) REVERT: H 33 LYS cc_start: 0.8662 (mttm) cc_final: 0.8359 (mttp) REVERT: H 66 TYR cc_start: 0.8671 (t80) cc_final: 0.8042 (t80) REVERT: H 89 GLN cc_start: 0.8766 (mt0) cc_final: 0.8479 (mm-40) REVERT: H 92 TYR cc_start: 0.8208 (m-10) cc_final: 0.7814 (m-10) REVERT: H 95 TYR cc_start: 0.9000 (m-80) cc_final: 0.8559 (m-80) REVERT: H 149 ASP cc_start: 0.8659 (m-30) cc_final: 0.8388 (t0) REVERT: H 153 ASP cc_start: 0.8304 (m-30) cc_final: 0.7950 (m-30) REVERT: V 14 MET cc_start: 0.7903 (mtm) cc_final: 0.7557 (mtt) REVERT: V 32 LYS cc_start: 0.8489 (tppt) cc_final: 0.8242 (tppt) REVERT: V 35 PHE cc_start: 0.8488 (m-80) cc_final: 0.8120 (m-80) REVERT: V 37 ILE cc_start: 0.9232 (tp) cc_final: 0.8953 (tp) REVERT: V 92 TYR cc_start: 0.7945 (m-10) cc_final: 0.7641 (m-10) REVERT: V 95 TYR cc_start: 0.8338 (m-80) cc_final: 0.8124 (m-10) REVERT: V 98 GLN cc_start: 0.8801 (mt0) cc_final: 0.8420 (tt0) REVERT: V 122 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7059 (m-30) REVERT: V 124 TYR cc_start: 0.8467 (p90) cc_final: 0.7357 (p90) REVERT: V 129 SER cc_start: 0.9486 (m) cc_final: 0.9203 (p) REVERT: V 139 GLU cc_start: 0.8744 (tp30) cc_final: 0.8115 (tp30) REVERT: V 141 GLN cc_start: 0.9083 (mt0) cc_final: 0.8368 (mt0) REVERT: V 194 SER cc_start: 0.8148 (m) cc_final: 0.7609 (p) REVERT: I 33 LYS cc_start: 0.8575 (mttm) cc_final: 0.8083 (mtmt) REVERT: I 92 TYR cc_start: 0.8230 (m-10) cc_final: 0.7906 (m-10) REVERT: I 124 TYR cc_start: 0.8657 (p90) cc_final: 0.8269 (p90) REVERT: I 172 MET cc_start: 0.8307 (tpp) cc_final: 0.7915 (tpp) REVERT: I 173 ILE cc_start: 0.8909 (tt) cc_final: 0.8641 (tt) REVERT: W 63 LEU cc_start: 0.9003 (mm) cc_final: 0.8765 (mm) REVERT: W 149 ASP cc_start: 0.8039 (m-30) cc_final: 0.7731 (m-30) REVERT: W 191 GLN cc_start: 0.8928 (mt0) cc_final: 0.8673 (mt0) REVERT: W 193 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6608 (mp0) REVERT: W 197 ARG cc_start: 0.7987 (mtt90) cc_final: 0.7597 (mmt-90) REVERT: J 33 LYS cc_start: 0.8682 (mttm) cc_final: 0.8442 (mttp) REVERT: J 92 TYR cc_start: 0.8303 (m-10) cc_final: 0.7663 (m-10) REVERT: J 149 ASP cc_start: 0.8508 (m-30) cc_final: 0.7947 (t0) REVERT: J 153 ASP cc_start: 0.8461 (m-30) cc_final: 0.7860 (m-30) REVERT: X 35 PHE cc_start: 0.8201 (m-80) cc_final: 0.7912 (m-10) REVERT: X 37 ILE cc_start: 0.9165 (tp) cc_final: 0.8868 (tp) REVERT: X 124 TYR cc_start: 0.8313 (p90) cc_final: 0.7447 (p90) REVERT: X 139 GLU cc_start: 0.8433 (tp30) cc_final: 0.7765 (tp30) REVERT: X 141 GLN cc_start: 0.9025 (mt0) cc_final: 0.8632 (mt0) REVERT: X 146 MET cc_start: 0.8685 (mtp) cc_final: 0.8346 (mtp) REVERT: X 150 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8703 (mt-10) REVERT: X 187 LEU cc_start: 0.8876 (mt) cc_final: 0.8649 (mt) REVERT: X 190 ASP cc_start: 0.7984 (p0) cc_final: 0.7764 (p0) REVERT: X 197 ARG cc_start: 0.7921 (mtt90) cc_final: 0.7498 (mpt180) REVERT: K 38 ASP cc_start: 0.8408 (t0) cc_final: 0.8170 (t70) REVERT: K 93 MET cc_start: 0.8319 (mmt) cc_final: 0.8090 (mmm) REVERT: K 146 MET cc_start: 0.8038 (mtm) cc_final: 0.7810 (mtp) REVERT: K 149 ASP cc_start: 0.8552 (m-30) cc_final: 0.8114 (t0) REVERT: K 153 ASP cc_start: 0.8218 (m-30) cc_final: 0.7871 (m-30) REVERT: K 193 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8030 (pt0) REVERT: Y 27 MET cc_start: 0.8230 (ttt) cc_final: 0.7784 (ttt) REVERT: Y 35 PHE cc_start: 0.8162 (m-80) cc_final: 0.7646 (m-80) REVERT: Y 43 MET cc_start: 0.7908 (ttm) cc_final: 0.7573 (ttm) REVERT: Y 95 TYR cc_start: 0.8418 (m-80) cc_final: 0.7980 (m-10) REVERT: Y 124 TYR cc_start: 0.8434 (p90) cc_final: 0.7767 (p90) REVERT: Y 139 GLU cc_start: 0.8715 (tp30) cc_final: 0.8231 (mm-30) REVERT: Y 141 GLN cc_start: 0.9005 (mt0) cc_final: 0.8694 (mt0) REVERT: Y 150 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8431 (mt-10) REVERT: L 9 LYS cc_start: 0.8759 (pttt) cc_final: 0.8519 (tptp) REVERT: L 33 LYS cc_start: 0.8794 (mttm) cc_final: 0.8185 (mtmt) REVERT: L 38 ASP cc_start: 0.8302 (t0) cc_final: 0.8012 (t0) REVERT: L 98 GLN cc_start: 0.8569 (mt0) cc_final: 0.8339 (mt0) REVERT: L 143 SER cc_start: 0.9126 (t) cc_final: 0.8877 (p) REVERT: L 149 ASP cc_start: 0.8533 (m-30) cc_final: 0.8071 (t0) REVERT: L 153 ASP cc_start: 0.8354 (m-30) cc_final: 0.7847 (m-30) REVERT: L 193 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7978 (pt0) REVERT: A 36 THR cc_start: 0.9074 (m) cc_final: 0.8174 (m) REVERT: A 51 ASP cc_start: 0.7661 (t70) cc_final: 0.7158 (p0) REVERT: A 95 SER cc_start: 0.7763 (m) cc_final: 0.7278 (p) REVERT: B 36 THR cc_start: 0.8997 (m) cc_final: 0.8769 (p) REVERT: B 40 MET cc_start: 0.7795 (pmt) cc_final: 0.7272 (pmm) REVERT: B 71 ASP cc_start: 0.7170 (t70) cc_final: 0.6902 (t70) REVERT: B 95 SER cc_start: 0.7511 (m) cc_final: 0.7062 (p) REVERT: B 114 LYS cc_start: 0.8172 (mmmm) cc_final: 0.7621 (mmmm) REVERT: B 178 ARG cc_start: 0.7926 (ptt-90) cc_final: 0.7446 (ptt90) REVERT: C 22 PHE cc_start: 0.6792 (m-10) cc_final: 0.6584 (m-10) REVERT: C 36 THR cc_start: 0.9198 (m) cc_final: 0.8974 (p) REVERT: C 40 MET cc_start: 0.7946 (pmt) cc_final: 0.7578 (pmm) REVERT: C 71 ASP cc_start: 0.7510 (t70) cc_final: 0.7198 (t70) REVERT: C 225 ASP cc_start: 0.6876 (p0) cc_final: 0.6505 (p0) REVERT: E 40 MET cc_start: 0.7900 (pmt) cc_final: 0.7621 (pmm) REVERT: E 95 SER cc_start: 0.7533 (m) cc_final: 0.6977 (p) REVERT: E 108 ASN cc_start: 0.7855 (t0) cc_final: 0.7625 (t0) REVERT: E 118 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8092 (p0) REVERT: E 119 GLN cc_start: 0.9005 (tp40) cc_final: 0.8722 (tp40) REVERT: E 177 GLU cc_start: 0.7878 (tp30) cc_final: 0.7525 (tt0) REVERT: E 178 ARG cc_start: 0.8107 (ptt-90) cc_final: 0.7792 (ptt90) REVERT: F 40 MET cc_start: 0.8139 (pmt) cc_final: 0.7743 (pmm) REVERT: F 47 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8374 (pp) REVERT: F 91 PHE cc_start: 0.7798 (t80) cc_final: 0.7475 (t80) REVERT: F 95 SER cc_start: 0.7750 (m) cc_final: 0.7339 (m) REVERT: F 121 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8327 (tm-30) REVERT: F 184 LEU cc_start: 0.8052 (mt) cc_final: 0.7769 (mt) REVERT: F 208 LYS cc_start: 0.7192 (mtpp) cc_final: 0.6977 (mtpp) REVERT: F 224 TYR cc_start: 0.6789 (m-10) cc_final: 0.6437 (m-80) REVERT: G 40 MET cc_start: 0.7596 (pmt) cc_final: 0.7191 (pmm) REVERT: G 71 ASP cc_start: 0.7468 (t70) cc_final: 0.7154 (t70) REVERT: G 95 SER cc_start: 0.7864 (m) cc_final: 0.7383 (p) REVERT: G 119 GLN cc_start: 0.8905 (tp40) cc_final: 0.8482 (tp40) REVERT: G 121 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8447 (tm-30) REVERT: G 147 ARG cc_start: 0.8485 (mmm160) cc_final: 0.8089 (mmm-85) REVERT: G 177 GLU cc_start: 0.7502 (tp30) cc_final: 0.7251 (tt0) REVERT: G 225 ASP cc_start: 0.7746 (p0) cc_final: 0.7027 (p0) REVERT: G 228 GLU cc_start: 0.8669 (tt0) cc_final: 0.8303 (tp30) REVERT: O 33 LYS cc_start: 0.8452 (mtpp) cc_final: 0.8146 (pttp) REVERT: O 72 ASP cc_start: 0.7646 (p0) cc_final: 0.7265 (p0) REVERT: O 73 TYR cc_start: 0.8890 (m-80) cc_final: 0.8352 (m-80) REVERT: O 119 GLN cc_start: 0.8878 (tp40) cc_final: 0.7801 (tp40) REVERT: O 121 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7287 (tm-30) REVERT: O 123 TYR cc_start: 0.8946 (m-10) cc_final: 0.8743 (m-80) REVERT: O 125 GLN cc_start: 0.7796 (tp-100) cc_final: 0.7162 (tt0) REVERT: O 165 ILE cc_start: 0.8572 (tp) cc_final: 0.8212 (mm) REVERT: O 201 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7697 (tt) REVERT: O 220 LYS cc_start: 0.8753 (mttt) cc_final: 0.8332 (mttp) REVERT: P 100 LYS cc_start: 0.8576 (mmmm) cc_final: 0.8238 (mtmm) REVERT: P 107 VAL cc_start: 0.8381 (t) cc_final: 0.7180 (t) REVERT: P 121 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7263 (tm-30) REVERT: P 122 GLN cc_start: 0.8234 (mt0) cc_final: 0.7853 (mt0) REVERT: P 125 GLN cc_start: 0.7002 (tp-100) cc_final: 0.6637 (tt0) REVERT: P 143 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8596 (mp10) REVERT: P 165 ILE cc_start: 0.8674 (tp) cc_final: 0.8214 (mm) REVERT: P 191 THR cc_start: 0.8988 (m) cc_final: 0.8761 (p) REVERT: Q 9 ASP cc_start: 0.6275 (OUTLIER) cc_final: 0.5931 (t0) REVERT: Q 107 VAL cc_start: 0.8811 (t) cc_final: 0.7515 (t) REVERT: Q 121 GLN cc_start: 0.7621 (tm130) cc_final: 0.7348 (tm-30) REVERT: Q 143 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8453 (mp10) REVERT: Q 165 ILE cc_start: 0.8660 (tp) cc_final: 0.8200 (mm) REVERT: Q 191 THR cc_start: 0.8820 (m) cc_final: 0.8532 (p) REVERT: Q 201 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7364 (tt) REVERT: R 40 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7451 (ttm) REVERT: R 84 ASP cc_start: 0.9000 (m-30) cc_final: 0.8723 (t0) REVERT: R 121 GLN cc_start: 0.7910 (tm130) cc_final: 0.7595 (tm-30) REVERT: R 122 GLN cc_start: 0.8376 (mt0) cc_final: 0.7824 (mt0) REVERT: R 152 ASP cc_start: 0.7287 (t0) cc_final: 0.6730 (t0) REVERT: R 187 LYS cc_start: 0.8837 (tmmt) cc_final: 0.8560 (tptt) REVERT: R 191 THR cc_start: 0.8665 (m) cc_final: 0.8342 (p) REVERT: R 201 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7096 (tt) REVERT: R 221 TYR cc_start: 0.8604 (m-80) cc_final: 0.8335 (m-10) REVERT: S 33 LYS cc_start: 0.8824 (mtpp) cc_final: 0.8532 (pttp) REVERT: S 119 GLN cc_start: 0.8770 (tp-100) cc_final: 0.8513 (tp40) REVERT: S 121 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7677 (tm-30) REVERT: S 122 GLN cc_start: 0.8487 (mt0) cc_final: 0.8136 (mt0) REVERT: S 132 TYR cc_start: 0.8566 (m-80) cc_final: 0.8311 (m-10) REVERT: S 143 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8335 (mp10) REVERT: S 152 ASP cc_start: 0.6788 (t0) cc_final: 0.6493 (t0) REVERT: S 165 ILE cc_start: 0.8716 (tp) cc_final: 0.8305 (mm) REVERT: S 191 THR cc_start: 0.8823 (m) cc_final: 0.8479 (p) REVERT: T 33 LYS cc_start: 0.8843 (mtpp) cc_final: 0.8549 (pttp) REVERT: T 72 ASP cc_start: 0.7722 (m-30) cc_final: 0.7269 (m-30) REVERT: T 74 VAL cc_start: 0.8668 (p) cc_final: 0.8402 (p) REVERT: T 143 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8387 (mp10) REVERT: T 147 ARG cc_start: 0.7750 (mtp85) cc_final: 0.7547 (mtp85) REVERT: T 152 ASP cc_start: 0.7005 (t0) cc_final: 0.6572 (t0) REVERT: T 165 ILE cc_start: 0.8851 (tp) cc_final: 0.8421 (mm) REVERT: T 191 THR cc_start: 0.8993 (m) cc_final: 0.8678 (m) REVERT: T 201 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7061 (tt) REVERT: U 33 LYS cc_start: 0.8931 (mtpp) cc_final: 0.8610 (pttp) REVERT: U 119 GLN cc_start: 0.8972 (tp40) cc_final: 0.8469 (tp40) REVERT: U 121 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7131 (tm-30) REVERT: U 125 GLN cc_start: 0.7558 (tp-100) cc_final: 0.7109 (tt0) REVERT: U 165 ILE cc_start: 0.8803 (tp) cc_final: 0.8319 (mm) REVERT: U 191 THR cc_start: 0.8870 (m) cc_final: 0.8504 (p) outliers start: 257 outliers final: 125 residues processed: 1659 average time/residue: 0.6000 time to fit residues: 1660.3759 Evaluate side-chains 1379 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1239 time to evaluate : 6.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 140 SER Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 110 VAL Chi-restraints excluded: chain 1 residue 123 ILE Chi-restraints excluded: chain 1 residue 131 SER Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 17 GLU Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 84 SER Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 123 ILE Chi-restraints excluded: chain 2 residue 135 TYR Chi-restraints excluded: chain 2 residue 140 SER Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 110 VAL Chi-restraints excluded: chain V residue 122 ASP Chi-restraints excluded: chain V residue 131 SER Chi-restraints excluded: chain V residue 140 SER Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain W residue 123 ILE Chi-restraints excluded: chain W residue 193 GLU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 85 ASN Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 119 SER Chi-restraints excluded: chain X residue 127 THR Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 85 ASN Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 122 ASP Chi-restraints excluded: chain Y residue 127 THR Chi-restraints excluded: chain Y residue 140 SER Chi-restraints excluded: chain Y residue 201 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain O residue 9 ASP Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 94 ILE Chi-restraints excluded: chain P residue 105 SER Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 143 GLN Chi-restraints excluded: chain P residue 156 THR Chi-restraints excluded: chain Q residue 9 ASP Chi-restraints excluded: chain Q residue 135 SER Chi-restraints excluded: chain Q residue 143 GLN Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 143 GLN Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 143 GLN Chi-restraints excluded: chain T residue 194 ILE Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 88 LEU Chi-restraints excluded: chain U residue 197 LEU Chi-restraints excluded: chain U residue 201 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 296 optimal weight: 0.5980 chunk 165 optimal weight: 0.9980 chunk 444 optimal weight: 0.8980 chunk 363 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 534 optimal weight: 4.9990 chunk 577 optimal weight: 0.9990 chunk 476 optimal weight: 5.9990 chunk 530 optimal weight: 0.8980 chunk 182 optimal weight: 7.9990 chunk 429 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 ASN ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 30 ASN ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 GLN ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 191 GLN ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN ** W 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 85 ASN X 89 GLN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 191 GLN ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN A 62 ASN C 97 GLN C 98 GLN F 97 GLN ** Q 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 47096 Z= 0.207 Angle : 0.755 27.993 63588 Z= 0.382 Chirality : 0.045 0.211 7448 Planarity : 0.004 0.061 8162 Dihedral : 6.330 52.282 6624 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.64 % Favored : 94.21 % Rotamer: Outliers : 5.39 % Allowed : 20.16 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.30 (0.10), residues: 5957 helix: 1.09 (0.11), residues: 2282 sheet: -1.55 (0.12), residues: 1456 loop : -2.45 (0.11), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS I 28 PHE 0.018 0.001 PHE X 25 TYR 0.026 0.001 TYR O 221 ARG 0.009 0.001 ARG E 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1684 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 1414 time to evaluate : 5.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 20 VAL cc_start: 0.9046 (t) cc_final: 0.8822 (p) REVERT: Z 32 LYS cc_start: 0.8387 (tppt) cc_final: 0.7991 (tppt) REVERT: Z 35 PHE cc_start: 0.8329 (m-80) cc_final: 0.8037 (m-10) REVERT: Z 36 GLN cc_start: 0.8543 (tt0) cc_final: 0.8270 (tt0) REVERT: Z 37 ILE cc_start: 0.9226 (tp) cc_final: 0.8834 (tp) REVERT: Z 77 GLU cc_start: 0.8433 (tt0) cc_final: 0.7875 (mp0) REVERT: Z 98 GLN cc_start: 0.9024 (mt0) cc_final: 0.8354 (tt0) REVERT: Z 111 PHE cc_start: 0.8481 (m-80) cc_final: 0.8109 (m-80) REVERT: Z 139 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8269 (mm-30) REVERT: Z 187 LEU cc_start: 0.8914 (mt) cc_final: 0.8663 (mt) REVERT: M 9 LYS cc_start: 0.8338 (tptp) cc_final: 0.8095 (mmmt) REVERT: M 17 GLU cc_start: 0.7455 (pp20) cc_final: 0.6611 (pp20) REVERT: M 33 LYS cc_start: 0.8717 (mttm) cc_final: 0.8245 (mttp) REVERT: M 95 TYR cc_start: 0.8935 (m-80) cc_final: 0.8535 (m-80) REVERT: M 193 GLU cc_start: 0.8310 (pt0) cc_final: 0.7911 (tp30) REVERT: 1 35 PHE cc_start: 0.8378 (m-80) cc_final: 0.7796 (m-80) REVERT: 1 40 TYR cc_start: 0.8461 (m-10) cc_final: 0.8140 (m-10) REVERT: 1 62 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7477 (mm-30) REVERT: 1 124 TYR cc_start: 0.8441 (p90) cc_final: 0.8085 (p90) REVERT: 1 139 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8076 (mm-30) REVERT: 1 150 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8509 (mt-10) REVERT: 1 174 ASP cc_start: 0.8363 (p0) cc_final: 0.8085 (p0) REVERT: 1 193 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7165 (pt0) REVERT: N 43 MET cc_start: 0.7818 (ttm) cc_final: 0.7608 (ttm) REVERT: N 92 TYR cc_start: 0.7957 (m-10) cc_final: 0.7595 (m-10) REVERT: N 149 ASP cc_start: 0.7657 (t70) cc_final: 0.7439 (t0) REVERT: N 150 GLU cc_start: 0.8021 (mp0) cc_final: 0.7821 (mp0) REVERT: N 153 ASP cc_start: 0.8260 (m-30) cc_final: 0.8041 (m-30) REVERT: N 193 GLU cc_start: 0.8574 (mm-30) cc_final: 0.7993 (tp30) REVERT: N 197 ARG cc_start: 0.8903 (ttm110) cc_final: 0.8659 (ttm110) REVERT: 2 30 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8404 (t0) REVERT: 2 63 LEU cc_start: 0.9123 (mm) cc_final: 0.8819 (mm) REVERT: 2 98 GLN cc_start: 0.8939 (mt0) cc_final: 0.8474 (tt0) REVERT: 2 124 TYR cc_start: 0.8053 (p90) cc_final: 0.7397 (p90) REVERT: 2 150 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8121 (mt-10) REVERT: 2 198 LYS cc_start: 0.7798 (mtmt) cc_final: 0.7433 (mtmm) REVERT: H 33 LYS cc_start: 0.8507 (mttm) cc_final: 0.8207 (mttp) REVERT: H 66 TYR cc_start: 0.8725 (t80) cc_final: 0.7398 (t80) REVERT: H 89 GLN cc_start: 0.8821 (mt0) cc_final: 0.8556 (mm110) REVERT: H 153 ASP cc_start: 0.8358 (m-30) cc_final: 0.8059 (m-30) REVERT: H 172 MET cc_start: 0.8302 (tpp) cc_final: 0.7942 (tpp) REVERT: H 198 LYS cc_start: 0.7925 (mtmm) cc_final: 0.7400 (mtmm) REVERT: V 25 PHE cc_start: 0.7628 (t80) cc_final: 0.7311 (t80) REVERT: V 35 PHE cc_start: 0.8481 (m-80) cc_final: 0.8179 (m-80) REVERT: V 37 ILE cc_start: 0.9195 (tp) cc_final: 0.8917 (tp) REVERT: V 62 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7590 (mm-30) REVERT: V 95 TYR cc_start: 0.8285 (m-80) cc_final: 0.8059 (m-10) REVERT: V 98 GLN cc_start: 0.8750 (mt0) cc_final: 0.8354 (tt0) REVERT: V 124 TYR cc_start: 0.8343 (p90) cc_final: 0.7180 (p90) REVERT: V 139 GLU cc_start: 0.8689 (tp30) cc_final: 0.8010 (tp30) REVERT: V 141 GLN cc_start: 0.9120 (mt0) cc_final: 0.8385 (mt0) REVERT: I 10 ASP cc_start: 0.7972 (p0) cc_final: 0.7749 (p0) REVERT: I 17 GLU cc_start: 0.7137 (pp20) cc_final: 0.6886 (pp20) REVERT: I 33 LYS cc_start: 0.8509 (mttm) cc_final: 0.8022 (mtmt) REVERT: I 59 MET cc_start: 0.8440 (mmp) cc_final: 0.8202 (tpp) REVERT: I 70 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7728 (mtt180) REVERT: I 131 SER cc_start: 0.9025 (p) cc_final: 0.8478 (t) REVERT: I 149 ASP cc_start: 0.8112 (m-30) cc_final: 0.7700 (t0) REVERT: I 150 GLU cc_start: 0.8025 (mp0) cc_final: 0.7767 (mp0) REVERT: I 172 MET cc_start: 0.8323 (tpp) cc_final: 0.7892 (tpp) REVERT: W 10 ASP cc_start: 0.7202 (m-30) cc_final: 0.6942 (m-30) REVERT: W 27 MET cc_start: 0.7454 (ttt) cc_final: 0.6767 (ttt) REVERT: W 114 ASP cc_start: 0.8226 (p0) cc_final: 0.7977 (p0) REVERT: W 149 ASP cc_start: 0.8154 (m-30) cc_final: 0.7798 (m-30) REVERT: W 191 GLN cc_start: 0.8767 (mt0) cc_final: 0.8427 (tm-30) REVERT: W 197 ARG cc_start: 0.8056 (mtt90) cc_final: 0.7650 (mpt180) REVERT: J 20 VAL cc_start: 0.9199 (t) cc_final: 0.8924 (m) REVERT: J 33 LYS cc_start: 0.8603 (mttm) cc_final: 0.8356 (mttp) REVERT: J 149 ASP cc_start: 0.8620 (m-30) cc_final: 0.7891 (t0) REVERT: J 153 ASP cc_start: 0.8439 (m-30) cc_final: 0.7903 (m-30) REVERT: X 10 ASP cc_start: 0.7377 (m-30) cc_final: 0.7034 (m-30) REVERT: X 35 PHE cc_start: 0.8155 (m-80) cc_final: 0.7903 (m-10) REVERT: X 92 TYR cc_start: 0.7623 (m-10) cc_final: 0.7381 (m-10) REVERT: X 124 TYR cc_start: 0.8312 (p90) cc_final: 0.7927 (p90) REVERT: X 139 GLU cc_start: 0.8419 (tp30) cc_final: 0.8085 (tp30) REVERT: X 141 GLN cc_start: 0.8996 (mt0) cc_final: 0.8596 (mt0) REVERT: X 150 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8386 (mt-10) REVERT: X 197 ARG cc_start: 0.7901 (mtt90) cc_final: 0.7523 (mpt180) REVERT: K 9 LYS cc_start: 0.8734 (pttt) cc_final: 0.8475 (mmmt) REVERT: K 59 MET cc_start: 0.8360 (mmp) cc_final: 0.8118 (mmp) REVERT: K 99 LEU cc_start: 0.8253 (mt) cc_final: 0.7970 (mm) REVERT: K 149 ASP cc_start: 0.8707 (m-30) cc_final: 0.8217 (t0) REVERT: K 153 ASP cc_start: 0.8241 (m-30) cc_final: 0.7871 (m-30) REVERT: K 193 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8140 (pt0) REVERT: Y 27 MET cc_start: 0.7794 (ttt) cc_final: 0.7368 (ttt) REVERT: Y 35 PHE cc_start: 0.8161 (m-80) cc_final: 0.7567 (m-80) REVERT: Y 93 MET cc_start: 0.6815 (ttp) cc_final: 0.6386 (tmm) REVERT: Y 95 TYR cc_start: 0.8358 (m-80) cc_final: 0.7819 (m-10) REVERT: Y 139 GLU cc_start: 0.8662 (tp30) cc_final: 0.8058 (mm-30) REVERT: Y 141 GLN cc_start: 0.8995 (mt0) cc_final: 0.8673 (mt0) REVERT: Y 150 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8426 (mt-10) REVERT: L 9 LYS cc_start: 0.8843 (pttt) cc_final: 0.8544 (tptp) REVERT: L 17 GLU cc_start: 0.7852 (pp20) cc_final: 0.7220 (pp20) REVERT: L 33 LYS cc_start: 0.8742 (mttm) cc_final: 0.8057 (mtmt) REVERT: L 38 ASP cc_start: 0.8322 (t0) cc_final: 0.7999 (t70) REVERT: L 98 GLN cc_start: 0.8574 (mt0) cc_final: 0.8313 (mt0) REVERT: L 127 THR cc_start: 0.8325 (p) cc_final: 0.8052 (p) REVERT: L 149 ASP cc_start: 0.8533 (m-30) cc_final: 0.8074 (t0) REVERT: L 153 ASP cc_start: 0.8361 (m-30) cc_final: 0.7870 (m-30) REVERT: A 36 THR cc_start: 0.9033 (m) cc_final: 0.8215 (m) REVERT: A 40 MET cc_start: 0.8239 (pmm) cc_final: 0.6959 (pmm) REVERT: A 51 ASP cc_start: 0.7712 (t70) cc_final: 0.7295 (p0) REVERT: A 95 SER cc_start: 0.7839 (m) cc_final: 0.7302 (p) REVERT: A 119 GLN cc_start: 0.8808 (tp40) cc_final: 0.8503 (tp40) REVERT: B 71 ASP cc_start: 0.7004 (t70) cc_final: 0.6617 (t70) REVERT: B 95 SER cc_start: 0.7679 (m) cc_final: 0.7255 (p) REVERT: B 121 GLN cc_start: 0.8290 (tm-30) cc_final: 0.7896 (tm-30) REVERT: B 178 ARG cc_start: 0.7985 (ptt-90) cc_final: 0.7557 (ptt90) REVERT: B 211 GLU cc_start: 0.7931 (tt0) cc_final: 0.7642 (pt0) REVERT: C 36 THR cc_start: 0.9202 (m) cc_final: 0.8892 (p) REVERT: C 71 ASP cc_start: 0.7474 (t70) cc_final: 0.7106 (t70) REVERT: C 110 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7234 (tm-30) REVERT: C 121 GLN cc_start: 0.8574 (tm-30) cc_final: 0.8270 (tm-30) REVERT: C 188 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8380 (tp30) REVERT: C 225 ASP cc_start: 0.6823 (p0) cc_final: 0.6299 (p0) REVERT: D 36 THR cc_start: 0.9087 (m) cc_final: 0.8763 (p) REVERT: D 114 LYS cc_start: 0.7906 (mmmm) cc_final: 0.7513 (mmmm) REVERT: D 119 GLN cc_start: 0.8883 (tp40) cc_final: 0.8664 (tp40) REVERT: E 44 ASN cc_start: 0.8751 (m-40) cc_final: 0.7963 (t0) REVERT: E 95 SER cc_start: 0.7590 (m) cc_final: 0.7076 (p) REVERT: E 108 ASN cc_start: 0.8015 (t0) cc_final: 0.7700 (t0) REVERT: E 118 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8086 (p0) REVERT: E 121 GLN cc_start: 0.8351 (tm-30) cc_final: 0.8123 (tm-30) REVERT: E 150 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.6839 (p0) REVERT: E 160 TYR cc_start: 0.7979 (m-10) cc_final: 0.7515 (m-80) REVERT: E 177 GLU cc_start: 0.7544 (tp30) cc_final: 0.7276 (tt0) REVERT: E 178 ARG cc_start: 0.8122 (ptt-90) cc_final: 0.7876 (ptt90) REVERT: F 47 LEU cc_start: 0.8543 (pp) cc_final: 0.8236 (pp) REVERT: F 110 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7435 (tm-30) REVERT: F 114 LYS cc_start: 0.8381 (mmtp) cc_final: 0.7998 (mmmm) REVERT: F 118 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8089 (p0) REVERT: F 184 LEU cc_start: 0.8085 (mt) cc_final: 0.7816 (mt) REVERT: G 84 ASP cc_start: 0.8394 (m-30) cc_final: 0.8164 (m-30) REVERT: G 95 SER cc_start: 0.7950 (m) cc_final: 0.7466 (p) REVERT: G 119 GLN cc_start: 0.8861 (tp40) cc_final: 0.8592 (tp40) REVERT: G 121 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8159 (tm-30) REVERT: G 178 ARG cc_start: 0.8111 (ptt-90) cc_final: 0.7787 (ptt90) REVERT: G 228 GLU cc_start: 0.8715 (tt0) cc_final: 0.8018 (tp30) REVERT: O 33 LYS cc_start: 0.8493 (mtpp) cc_final: 0.8161 (pttp) REVERT: O 71 ASP cc_start: 0.7449 (t0) cc_final: 0.7106 (t70) REVERT: O 119 GLN cc_start: 0.8987 (tp40) cc_final: 0.8521 (tp40) REVERT: O 121 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7411 (tm-30) REVERT: O 125 GLN cc_start: 0.7674 (tp-100) cc_final: 0.7221 (tt0) REVERT: O 132 TYR cc_start: 0.8431 (m-80) cc_final: 0.8051 (m-80) REVERT: O 152 ASP cc_start: 0.6800 (t0) cc_final: 0.6560 (t0) REVERT: O 201 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7884 (tt) REVERT: P 40 MET cc_start: 0.7784 (ptp) cc_final: 0.7393 (ttp) REVERT: P 100 LYS cc_start: 0.8634 (mmmm) cc_final: 0.8242 (mtmm) REVERT: P 107 VAL cc_start: 0.8458 (t) cc_final: 0.6953 (t) REVERT: P 115 ARG cc_start: 0.7946 (ttm170) cc_final: 0.7635 (ttm170) REVERT: P 121 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7268 (tm-30) REVERT: P 122 GLN cc_start: 0.8281 (mt0) cc_final: 0.8015 (mt0) REVERT: P 125 GLN cc_start: 0.7042 (tp-100) cc_final: 0.6697 (tt0) REVERT: P 165 ILE cc_start: 0.8551 (tp) cc_final: 0.8048 (mm) REVERT: P 191 THR cc_start: 0.8990 (m) cc_final: 0.8766 (p) REVERT: P 201 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7526 (tm) REVERT: Q 9 ASP cc_start: 0.6365 (OUTLIER) cc_final: 0.6142 (t0) REVERT: Q 40 MET cc_start: 0.7554 (ptp) cc_final: 0.7344 (ttm) REVERT: Q 121 GLN cc_start: 0.7685 (tm130) cc_final: 0.7481 (tm-30) REVERT: Q 152 ASP cc_start: 0.7339 (t0) cc_final: 0.7112 (t0) REVERT: Q 165 ILE cc_start: 0.8537 (tp) cc_final: 0.8199 (mm) REVERT: Q 191 THR cc_start: 0.8775 (m) cc_final: 0.8484 (p) REVERT: Q 201 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7657 (tt) REVERT: R 40 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.6941 (ttp) REVERT: R 72 ASP cc_start: 0.8006 (p0) cc_final: 0.7676 (p0) REVERT: R 143 GLN cc_start: 0.8340 (mp10) cc_final: 0.8095 (mp10) REVERT: R 152 ASP cc_start: 0.7078 (t0) cc_final: 0.6782 (t0) REVERT: R 191 THR cc_start: 0.8637 (m) cc_final: 0.8385 (p) REVERT: R 201 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7086 (tt) REVERT: R 221 TYR cc_start: 0.8623 (m-80) cc_final: 0.8279 (m-10) REVERT: S 33 LYS cc_start: 0.8954 (mtpp) cc_final: 0.8526 (pttp) REVERT: S 119 GLN cc_start: 0.8747 (tp-100) cc_final: 0.8465 (tp40) REVERT: S 121 GLN cc_start: 0.7964 (tm-30) cc_final: 0.7726 (tm-30) REVERT: S 122 GLN cc_start: 0.8458 (mt0) cc_final: 0.8124 (mt0) REVERT: S 125 GLN cc_start: 0.7679 (tp40) cc_final: 0.7344 (tp-100) REVERT: S 165 ILE cc_start: 0.8599 (tp) cc_final: 0.8196 (mm) REVERT: S 183 ASN cc_start: 0.8180 (p0) cc_final: 0.7872 (p0) REVERT: S 191 THR cc_start: 0.8757 (m) cc_final: 0.8404 (p) REVERT: T 33 LYS cc_start: 0.8820 (mtpp) cc_final: 0.8519 (pttp) REVERT: T 49 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8346 (pt) REVERT: T 72 ASP cc_start: 0.7694 (m-30) cc_final: 0.7329 (m-30) REVERT: T 121 GLN cc_start: 0.7782 (tm-30) cc_final: 0.7417 (tm-30) REVERT: T 165 ILE cc_start: 0.8746 (tp) cc_final: 0.8306 (mm) REVERT: T 191 THR cc_start: 0.8855 (m) cc_final: 0.8475 (p) REVERT: U 33 LYS cc_start: 0.8972 (mtpp) cc_final: 0.8521 (pttp) REVERT: U 119 GLN cc_start: 0.9036 (tp40) cc_final: 0.8593 (tp40) REVERT: U 121 GLN cc_start: 0.8258 (tm-30) cc_final: 0.7620 (tm-30) REVERT: U 125 GLN cc_start: 0.7403 (tp-100) cc_final: 0.7160 (tt0) REVERT: U 165 ILE cc_start: 0.8593 (tp) cc_final: 0.8076 (mm) REVERT: U 191 THR cc_start: 0.8857 (m) cc_final: 0.8507 (p) outliers start: 270 outliers final: 160 residues processed: 1596 average time/residue: 0.5431 time to fit residues: 1439.5491 Evaluate side-chains 1444 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1272 time to evaluate : 5.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 64 GLU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 64 GLU Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 123 ILE Chi-restraints excluded: chain 1 residue 131 SER Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 85 ASN Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 104 ILE Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 30 ASN Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 64 GLU Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 123 ILE Chi-restraints excluded: chain 2 residue 135 TYR Chi-restraints excluded: chain 2 residue 177 VAL Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 59 MET Chi-restraints excluded: chain V residue 84 SER Chi-restraints excluded: chain V residue 89 GLN Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 104 ILE Chi-restraints excluded: chain V residue 110 VAL Chi-restraints excluded: chain V residue 131 SER Chi-restraints excluded: chain V residue 177 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 123 ILE Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 177 VAL Chi-restraints excluded: chain W residue 193 GLU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 85 ASN Chi-restraints excluded: chain X residue 104 ILE Chi-restraints excluded: chain X residue 113 ILE Chi-restraints excluded: chain X residue 123 ILE Chi-restraints excluded: chain X residue 127 THR Chi-restraints excluded: chain X residue 177 VAL Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 104 ILE Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 122 ASP Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Y residue 127 THR Chi-restraints excluded: chain Y residue 177 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 192 ILE Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain O residue 9 ASP Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 156 THR Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 219 ASN Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 94 ILE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 105 SER Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 156 THR Chi-restraints excluded: chain P residue 201 LEU Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain Q residue 9 ASP Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 135 SER Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 183 ASN Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 219 ASN Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 157 ILE Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 49 ILE Chi-restraints excluded: chain T residue 194 ILE Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain T residue 219 ASN Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 156 THR Chi-restraints excluded: chain U residue 201 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 528 optimal weight: 8.9990 chunk 402 optimal weight: 10.0000 chunk 277 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 255 optimal weight: 6.9990 chunk 359 optimal weight: 5.9990 chunk 536 optimal weight: 1.9990 chunk 568 optimal weight: 10.0000 chunk 280 optimal weight: 0.0040 chunk 508 optimal weight: 5.9990 chunk 153 optimal weight: 0.8980 overall best weight: 1.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 191 GLN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 191 GLN ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN W 88 ASN ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 85 ASN X 89 GLN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 GLN ** Y 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN C 62 ASN C 68 GLN C 97 GLN ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN R 125 GLN S 125 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 47096 Z= 0.273 Angle : 0.766 28.676 63588 Z= 0.389 Chirality : 0.045 0.213 7448 Planarity : 0.004 0.054 8162 Dihedral : 6.123 53.667 6621 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.83 % Favored : 94.06 % Rotamer: Outliers : 6.41 % Allowed : 20.96 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -0.93 (0.10), residues: 5957 helix: 1.44 (0.11), residues: 2282 sheet: -1.31 (0.13), residues: 1379 loop : -2.32 (0.11), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS Z 28 PHE 0.018 0.002 PHE Y 25 TYR 0.032 0.002 TYR O 221 ARG 0.007 0.001 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1592 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 1271 time to evaluate : 5.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 9 LYS cc_start: 0.7962 (pptt) cc_final: 0.7720 (pptt) REVERT: Z 32 LYS cc_start: 0.8471 (tppt) cc_final: 0.8268 (tppt) REVERT: Z 35 PHE cc_start: 0.8467 (m-80) cc_final: 0.8202 (m-10) REVERT: Z 37 ILE cc_start: 0.9199 (tp) cc_final: 0.8766 (tp) REVERT: Z 77 GLU cc_start: 0.8491 (tt0) cc_final: 0.7976 (mp0) REVERT: Z 98 GLN cc_start: 0.9007 (mt0) cc_final: 0.8363 (tt0) REVERT: Z 122 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.6949 (m-30) REVERT: Z 124 TYR cc_start: 0.8499 (p90) cc_final: 0.8295 (p90) REVERT: Z 150 GLU cc_start: 0.8944 (mt-10) cc_final: 0.7982 (mt-10) REVERT: M 17 GLU cc_start: 0.7539 (pp20) cc_final: 0.7104 (pp20) REVERT: M 33 LYS cc_start: 0.8805 (mttm) cc_final: 0.8275 (mttp) REVERT: M 74 MET cc_start: 0.8041 (mmm) cc_final: 0.7785 (mmm) REVERT: M 95 TYR cc_start: 0.8973 (m-80) cc_final: 0.8609 (m-80) REVERT: M 193 GLU cc_start: 0.8313 (pt0) cc_final: 0.7912 (tp30) REVERT: 1 9 LYS cc_start: 0.7811 (pptt) cc_final: 0.7567 (pptt) REVERT: 1 35 PHE cc_start: 0.8367 (m-80) cc_final: 0.7801 (m-80) REVERT: 1 95 TYR cc_start: 0.8572 (m-80) cc_final: 0.8087 (m-80) REVERT: 1 139 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8203 (mm-30) REVERT: 1 150 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8537 (mt-10) REVERT: 1 174 ASP cc_start: 0.8373 (p0) cc_final: 0.8110 (p0) REVERT: 1 193 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7181 (pt0) REVERT: N 74 MET cc_start: 0.8082 (mmm) cc_final: 0.7839 (mmm) REVERT: N 91 LYS cc_start: 0.8390 (pttm) cc_final: 0.8094 (pttm) REVERT: N 92 TYR cc_start: 0.8068 (m-10) cc_final: 0.7640 (m-10) REVERT: N 153 ASP cc_start: 0.8306 (m-30) cc_final: 0.8012 (m-30) REVERT: N 193 GLU cc_start: 0.8528 (mm-30) cc_final: 0.7997 (tp30) REVERT: 2 98 GLN cc_start: 0.8872 (mt0) cc_final: 0.8398 (tt0) REVERT: 2 111 PHE cc_start: 0.8676 (m-80) cc_final: 0.8428 (m-80) REVERT: 2 124 TYR cc_start: 0.8171 (p90) cc_final: 0.7576 (p90) REVERT: 2 150 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8337 (mt-10) REVERT: 2 198 LYS cc_start: 0.7919 (mtmt) cc_final: 0.7563 (mtmm) REVERT: H 22 MET cc_start: 0.3560 (ttt) cc_final: 0.2574 (ttt) REVERT: H 33 LYS cc_start: 0.8505 (mttm) cc_final: 0.8191 (mttp) REVERT: H 89 GLN cc_start: 0.8881 (mt0) cc_final: 0.8678 (mm110) REVERT: H 193 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7843 (tp30) REVERT: V 22 MET cc_start: 0.4683 (ttt) cc_final: 0.4328 (ttt) REVERT: V 35 PHE cc_start: 0.8549 (m-80) cc_final: 0.8171 (m-10) REVERT: V 37 ILE cc_start: 0.9195 (tp) cc_final: 0.8909 (tp) REVERT: V 88 ASN cc_start: 0.8817 (t0) cc_final: 0.8591 (t0) REVERT: V 98 GLN cc_start: 0.8725 (mt0) cc_final: 0.8356 (tt0) REVERT: V 122 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7268 (m-30) REVERT: V 124 TYR cc_start: 0.8356 (p90) cc_final: 0.7212 (p90) REVERT: V 139 GLU cc_start: 0.8579 (tp30) cc_final: 0.7885 (tp30) REVERT: V 141 GLN cc_start: 0.9141 (mt0) cc_final: 0.8397 (mt0) REVERT: I 17 GLU cc_start: 0.7351 (pp20) cc_final: 0.7109 (pp20) REVERT: I 33 LYS cc_start: 0.8582 (mttm) cc_final: 0.8027 (mtmt) REVERT: I 51 ASP cc_start: 0.8413 (m-30) cc_final: 0.8154 (m-30) REVERT: I 131 SER cc_start: 0.8995 (p) cc_final: 0.8714 (t) REVERT: I 149 ASP cc_start: 0.8278 (m-30) cc_final: 0.7730 (t0) REVERT: I 150 GLU cc_start: 0.8090 (mp0) cc_final: 0.7860 (mp0) REVERT: I 153 ASP cc_start: 0.8067 (m-30) cc_final: 0.7773 (m-30) REVERT: W 22 MET cc_start: 0.5473 (ttm) cc_final: 0.4999 (ttm) REVERT: W 63 LEU cc_start: 0.9172 (mm) cc_final: 0.8894 (mm) REVERT: W 149 ASP cc_start: 0.8265 (m-30) cc_final: 0.7940 (m-30) REVERT: W 180 ARG cc_start: 0.8671 (tpp80) cc_final: 0.8456 (tpp80) REVERT: W 191 GLN cc_start: 0.8752 (mt0) cc_final: 0.8402 (tm-30) REVERT: W 197 ARG cc_start: 0.8111 (mtt90) cc_final: 0.7611 (mpt180) REVERT: J 20 VAL cc_start: 0.9199 (t) cc_final: 0.8923 (m) REVERT: J 33 LYS cc_start: 0.8616 (mttm) cc_final: 0.8328 (mttp) REVERT: J 149 ASP cc_start: 0.8602 (m-30) cc_final: 0.7954 (t0) REVERT: J 153 ASP cc_start: 0.8480 (m-30) cc_final: 0.7958 (m-30) REVERT: J 166 ASP cc_start: 0.8160 (t0) cc_final: 0.7917 (t0) REVERT: X 27 MET cc_start: 0.7738 (ttt) cc_final: 0.7248 (ttt) REVERT: X 35 PHE cc_start: 0.8199 (m-80) cc_final: 0.7962 (m-10) REVERT: X 124 TYR cc_start: 0.8592 (p90) cc_final: 0.8058 (p90) REVERT: X 135 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.7306 (t80) REVERT: X 139 GLU cc_start: 0.8564 (tp30) cc_final: 0.7998 (tp30) REVERT: X 141 GLN cc_start: 0.9056 (mt0) cc_final: 0.8846 (mt0) REVERT: X 145 LYS cc_start: 0.9355 (ttmm) cc_final: 0.9014 (mmmm) REVERT: X 150 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8401 (mt-10) REVERT: X 197 ARG cc_start: 0.8072 (mtt90) cc_final: 0.7793 (mmt-90) REVERT: X 198 LYS cc_start: 0.8041 (mtmt) cc_final: 0.7628 (mtmt) REVERT: K 9 LYS cc_start: 0.8742 (pttt) cc_final: 0.8494 (mmmt) REVERT: K 99 LEU cc_start: 0.8326 (mt) cc_final: 0.8071 (mm) REVERT: K 131 SER cc_start: 0.8981 (p) cc_final: 0.8620 (t) REVERT: Y 9 LYS cc_start: 0.7962 (pptt) cc_final: 0.7609 (pptt) REVERT: Y 27 MET cc_start: 0.7873 (ttt) cc_final: 0.7391 (ttt) REVERT: Y 35 PHE cc_start: 0.8210 (m-80) cc_final: 0.7688 (m-80) REVERT: Y 85 ASN cc_start: 0.8587 (t0) cc_final: 0.8236 (t0) REVERT: Y 93 MET cc_start: 0.6681 (ttp) cc_final: 0.6321 (tmm) REVERT: Y 139 GLU cc_start: 0.8747 (tp30) cc_final: 0.8085 (mm-30) REVERT: Y 141 GLN cc_start: 0.9056 (mt0) cc_final: 0.8777 (mt0) REVERT: Y 150 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8429 (mt-10) REVERT: L 17 GLU cc_start: 0.7853 (pp20) cc_final: 0.7408 (pp20) REVERT: L 33 LYS cc_start: 0.8498 (mttm) cc_final: 0.8026 (mtmt) REVERT: L 35 PHE cc_start: 0.8609 (m-80) cc_final: 0.8030 (m-10) REVERT: L 38 ASP cc_start: 0.8353 (t0) cc_final: 0.8120 (t70) REVERT: L 74 MET cc_start: 0.8048 (mmm) cc_final: 0.7793 (mmm) REVERT: L 98 GLN cc_start: 0.8587 (mt0) cc_final: 0.8329 (mt0) REVERT: L 127 THR cc_start: 0.8475 (p) cc_final: 0.8227 (p) REVERT: L 149 ASP cc_start: 0.8504 (m-30) cc_final: 0.8066 (t0) REVERT: L 153 ASP cc_start: 0.8363 (m-30) cc_final: 0.7751 (m-30) REVERT: A 40 MET cc_start: 0.8432 (pmm) cc_final: 0.8119 (pmm) REVERT: A 225 ASP cc_start: 0.7511 (p0) cc_final: 0.7054 (p0) REVERT: B 95 SER cc_start: 0.7739 (m) cc_final: 0.7311 (p) REVERT: B 178 ARG cc_start: 0.8142 (ptt-90) cc_final: 0.7747 (ptt90) REVERT: B 211 GLU cc_start: 0.8112 (tt0) cc_final: 0.7820 (pt0) REVERT: C 110 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7232 (tm-30) REVERT: C 119 GLN cc_start: 0.8887 (tp40) cc_final: 0.8684 (tp40) REVERT: C 121 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8187 (tm-30) REVERT: C 188 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8391 (tp30) REVERT: D 36 THR cc_start: 0.9208 (m) cc_final: 0.8905 (p) REVERT: D 71 ASP cc_start: 0.7679 (t70) cc_final: 0.7274 (t70) REVERT: D 98 GLN cc_start: 0.7600 (mm-40) cc_final: 0.7150 (tm-30) REVERT: D 114 LYS cc_start: 0.7861 (mmmm) cc_final: 0.7456 (mmmm) REVERT: D 119 GLN cc_start: 0.8868 (tp40) cc_final: 0.8592 (tp40) REVERT: D 163 THR cc_start: 0.7966 (OUTLIER) cc_final: 0.7657 (m) REVERT: E 44 ASN cc_start: 0.8856 (m-40) cc_final: 0.7765 (t0) REVERT: E 118 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.7990 (p0) REVERT: E 121 GLN cc_start: 0.8375 (tm-30) cc_final: 0.8042 (tm-30) REVERT: E 150 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7961 (p0) REVERT: E 178 ARG cc_start: 0.8243 (ptt-90) cc_final: 0.7988 (ptt90) REVERT: E 188 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8118 (tp30) REVERT: F 10 ARG cc_start: 0.5385 (mpt-90) cc_final: 0.4376 (ptm-80) REVERT: F 110 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7329 (tm-30) REVERT: F 114 LYS cc_start: 0.8348 (mmtp) cc_final: 0.8072 (mmtp) REVERT: F 115 ARG cc_start: 0.8083 (tpp-160) cc_final: 0.7747 (tpp80) REVERT: F 121 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7940 (tm-30) REVERT: F 177 GLU cc_start: 0.7201 (tp30) cc_final: 0.6794 (tt0) REVERT: F 208 LYS cc_start: 0.7459 (mtpp) cc_final: 0.6968 (ttpt) REVERT: G 79 SER cc_start: 0.8236 (t) cc_final: 0.7903 (p) REVERT: G 119 GLN cc_start: 0.8833 (tp40) cc_final: 0.8549 (tp40) REVERT: G 121 GLN cc_start: 0.8352 (tm-30) cc_final: 0.8058 (tm-30) REVERT: G 178 ARG cc_start: 0.8214 (ptt-90) cc_final: 0.7651 (ptt90) REVERT: G 225 ASP cc_start: 0.7921 (p0) cc_final: 0.7191 (p0) REVERT: G 228 GLU cc_start: 0.8820 (tt0) cc_final: 0.8266 (tp30) REVERT: O 119 GLN cc_start: 0.9129 (tp40) cc_final: 0.8853 (tp40) REVERT: O 121 GLN cc_start: 0.8406 (tm-30) cc_final: 0.7652 (tm-30) REVERT: O 125 GLN cc_start: 0.7565 (tp-100) cc_final: 0.7209 (tt0) REVERT: O 180 TYR cc_start: 0.7935 (t80) cc_final: 0.7725 (t80) REVERT: O 201 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7898 (tt) REVERT: P 115 ARG cc_start: 0.8014 (ttm170) cc_final: 0.7709 (ttm170) REVERT: P 119 GLN cc_start: 0.8810 (tp40) cc_final: 0.8364 (tp40) REVERT: P 121 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7187 (tm-30) REVERT: P 122 GLN cc_start: 0.8350 (mt0) cc_final: 0.8039 (mt0) REVERT: P 125 GLN cc_start: 0.7158 (tp-100) cc_final: 0.6827 (tt0) REVERT: P 165 ILE cc_start: 0.8563 (tp) cc_final: 0.8090 (mm) REVERT: Q 121 GLN cc_start: 0.7811 (tm130) cc_final: 0.7518 (tm-30) REVERT: Q 152 ASP cc_start: 0.7392 (t0) cc_final: 0.7119 (t0) REVERT: Q 165 ILE cc_start: 0.8535 (tp) cc_final: 0.8209 (mm) REVERT: Q 191 THR cc_start: 0.8785 (m) cc_final: 0.8488 (p) REVERT: Q 201 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7868 (tt) REVERT: R 40 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.6772 (ttp) REVERT: R 67 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8955 (mm) REVERT: R 119 GLN cc_start: 0.8736 (tp40) cc_final: 0.7713 (tp40) REVERT: R 122 GLN cc_start: 0.8301 (mt0) cc_final: 0.7823 (mt0) REVERT: R 123 TYR cc_start: 0.9026 (m-10) cc_final: 0.8583 (m-80) REVERT: R 143 GLN cc_start: 0.8594 (mp10) cc_final: 0.8340 (mp10) REVERT: R 152 ASP cc_start: 0.7026 (t0) cc_final: 0.6763 (t0) REVERT: R 191 THR cc_start: 0.8677 (m) cc_final: 0.8375 (p) REVERT: R 201 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7341 (tt) REVERT: R 211 GLU cc_start: 0.6749 (pt0) cc_final: 0.6048 (pt0) REVERT: R 221 TYR cc_start: 0.8560 (m-80) cc_final: 0.8227 (m-10) REVERT: S 33 LYS cc_start: 0.8941 (mtpp) cc_final: 0.8540 (pttp) REVERT: S 118 ASP cc_start: 0.8615 (t0) cc_final: 0.8393 (t0) REVERT: S 119 GLN cc_start: 0.8836 (tp-100) cc_final: 0.8431 (tp40) REVERT: S 121 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7218 (tm-30) REVERT: S 122 GLN cc_start: 0.8523 (mt0) cc_final: 0.8158 (mt0) REVERT: S 125 GLN cc_start: 0.7680 (tp-100) cc_final: 0.7251 (tp40) REVERT: S 165 ILE cc_start: 0.8538 (tp) cc_final: 0.8190 (mm) REVERT: S 191 THR cc_start: 0.8809 (m) cc_final: 0.8450 (p) REVERT: T 33 LYS cc_start: 0.8930 (mtpp) cc_final: 0.8572 (pttp) REVERT: T 40 MET cc_start: 0.7756 (pmm) cc_final: 0.7489 (pmm) REVERT: T 49 ILE cc_start: 0.8675 (tt) cc_final: 0.8389 (pt) REVERT: T 72 ASP cc_start: 0.7685 (m-30) cc_final: 0.7324 (m-30) REVERT: T 121 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7778 (tm-30) REVERT: T 165 ILE cc_start: 0.8636 (tp) cc_final: 0.8209 (mm) REVERT: T 184 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6547 (tt) REVERT: T 191 THR cc_start: 0.8919 (m) cc_final: 0.8569 (p) REVERT: T 221 TYR cc_start: 0.8851 (m-80) cc_final: 0.8552 (m-10) REVERT: U 119 GLN cc_start: 0.9051 (tp40) cc_final: 0.8657 (tp40) REVERT: U 121 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7487 (tm-30) REVERT: U 165 ILE cc_start: 0.8590 (tp) cc_final: 0.8008 (mm) REVERT: U 191 THR cc_start: 0.8887 (m) cc_final: 0.8547 (p) outliers start: 321 outliers final: 213 residues processed: 1497 average time/residue: 0.5437 time to fit residues: 1355.9185 Evaluate side-chains 1403 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1178 time to evaluate : 5.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 64 GLU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 122 ASP Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 104 ILE Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 23 GLU Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 64 GLU Chi-restraints excluded: chain 1 residue 84 SER Chi-restraints excluded: chain 1 residue 89 GLN Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 123 ILE Chi-restraints excluded: chain 1 residue 131 SER Chi-restraints excluded: chain 1 residue 177 VAL Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 143 SER Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 64 GLU Chi-restraints excluded: chain 2 residue 84 SER Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 123 ILE Chi-restraints excluded: chain 2 residue 135 TYR Chi-restraints excluded: chain 2 residue 177 VAL Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 59 MET Chi-restraints excluded: chain V residue 84 SER Chi-restraints excluded: chain V residue 89 GLN Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 104 ILE Chi-restraints excluded: chain V residue 110 VAL Chi-restraints excluded: chain V residue 122 ASP Chi-restraints excluded: chain V residue 131 SER Chi-restraints excluded: chain V residue 177 VAL Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 84 SER Chi-restraints excluded: chain W residue 85 ASN Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 119 SER Chi-restraints excluded: chain W residue 123 ILE Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 177 VAL Chi-restraints excluded: chain W residue 193 GLU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 104 ILE Chi-restraints excluded: chain X residue 113 ILE Chi-restraints excluded: chain X residue 119 SER Chi-restraints excluded: chain X residue 127 THR Chi-restraints excluded: chain X residue 135 TYR Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 43 MET Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 104 ILE Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Y residue 127 THR Chi-restraints excluded: chain Y residue 135 TYR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 112 SER Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 192 ILE Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain O residue 9 ASP Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 49 ILE Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 156 THR Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 219 ASN Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 94 ILE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 105 SER Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 156 THR Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 135 SER Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 219 ASN Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 157 ILE Chi-restraints excluded: chain S residue 170 ASP Chi-restraints excluded: chain S residue 219 ASN Chi-restraints excluded: chain T residue 184 LEU Chi-restraints excluded: chain T residue 194 ILE Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain T residue 219 ASN Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 156 THR Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 201 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 473 optimal weight: 0.0870 chunk 322 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 423 optimal weight: 6.9990 chunk 234 optimal weight: 6.9990 chunk 485 optimal weight: 5.9990 chunk 392 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 290 optimal weight: 3.9990 chunk 510 optimal weight: 3.9990 chunk 143 optimal weight: 0.1980 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 191 GLN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 ASN ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 36 GLN V 191 GLN I 85 ASN ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN W 88 ASN W 141 GLN ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 36 GLN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 191 GLN ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 ASN D 125 GLN ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN T 226 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 47096 Z= 0.222 Angle : 0.732 26.986 63588 Z= 0.371 Chirality : 0.044 0.198 7448 Planarity : 0.004 0.040 8162 Dihedral : 5.942 53.516 6621 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.76 % Favored : 94.12 % Rotamer: Outliers : 6.13 % Allowed : 22.36 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.73 (0.11), residues: 5957 helix: 1.64 (0.11), residues: 2282 sheet: -1.05 (0.14), residues: 1232 loop : -2.32 (0.11), residues: 2443 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS 1 109 PHE 0.019 0.001 PHE Y 25 TYR 0.019 0.001 TYR O 221 ARG 0.007 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1602 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 1295 time to evaluate : 5.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 9 LYS cc_start: 0.8000 (pptt) cc_final: 0.7792 (pptt) REVERT: Z 25 PHE cc_start: 0.8161 (t80) cc_final: 0.7739 (t80) REVERT: Z 35 PHE cc_start: 0.8470 (m-80) cc_final: 0.8199 (m-10) REVERT: Z 37 ILE cc_start: 0.9184 (tp) cc_final: 0.8757 (tp) REVERT: Z 77 GLU cc_start: 0.8480 (tt0) cc_final: 0.8049 (mp0) REVERT: Z 98 GLN cc_start: 0.8944 (mt0) cc_final: 0.8309 (tt0) REVERT: Z 124 TYR cc_start: 0.8354 (p90) cc_final: 0.7893 (p90) REVERT: Z 139 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8165 (mm-30) REVERT: Z 150 GLU cc_start: 0.8923 (mt-10) cc_final: 0.7977 (mt-10) REVERT: M 33 LYS cc_start: 0.8700 (mttm) cc_final: 0.8419 (mtmm) REVERT: M 74 MET cc_start: 0.8065 (mmm) cc_final: 0.7778 (mmm) REVERT: M 95 TYR cc_start: 0.8967 (m-80) cc_final: 0.8650 (m-80) REVERT: M 150 GLU cc_start: 0.8144 (mp0) cc_final: 0.7892 (mp0) REVERT: M 193 GLU cc_start: 0.8254 (pt0) cc_final: 0.7848 (tp30) REVERT: 1 35 PHE cc_start: 0.8355 (m-80) cc_final: 0.7799 (m-80) REVERT: 1 62 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7465 (mm-30) REVERT: 1 95 TYR cc_start: 0.8480 (m-80) cc_final: 0.7997 (m-80) REVERT: 1 124 TYR cc_start: 0.8533 (p90) cc_final: 0.7867 (p90) REVERT: 1 139 GLU cc_start: 0.8614 (mm-30) cc_final: 0.7926 (mm-30) REVERT: 1 150 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8556 (mt-10) REVERT: 1 174 ASP cc_start: 0.8404 (p0) cc_final: 0.8155 (p0) REVERT: 1 193 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7142 (pt0) REVERT: N 9 LYS cc_start: 0.8601 (pttt) cc_final: 0.8394 (mmmt) REVERT: N 27 MET cc_start: 0.8984 (ttt) cc_final: 0.8366 (ttm) REVERT: N 51 ASP cc_start: 0.8155 (m-30) cc_final: 0.7881 (t0) REVERT: N 66 TYR cc_start: 0.8505 (t80) cc_final: 0.7638 (t80) REVERT: N 74 MET cc_start: 0.8021 (mmm) cc_final: 0.7255 (tpt) REVERT: N 153 ASP cc_start: 0.8296 (m-30) cc_final: 0.8005 (m-30) REVERT: N 193 GLU cc_start: 0.8540 (mm-30) cc_final: 0.7965 (tp30) REVERT: 2 9 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7082 (pttp) REVERT: 2 76 ILE cc_start: 0.8981 (mm) cc_final: 0.8679 (mm) REVERT: 2 98 GLN cc_start: 0.8849 (mt0) cc_final: 0.8334 (tt0) REVERT: 2 124 TYR cc_start: 0.8200 (p90) cc_final: 0.7498 (p90) REVERT: 2 139 GLU cc_start: 0.8307 (tp30) cc_final: 0.8092 (tp30) REVERT: 2 150 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8356 (mt-10) REVERT: 2 181 LYS cc_start: 0.9404 (tttm) cc_final: 0.8977 (tmtt) REVERT: 2 198 LYS cc_start: 0.7898 (mtmt) cc_final: 0.7567 (mtmm) REVERT: H 27 MET cc_start: 0.8900 (ttt) cc_final: 0.8329 (ttt) REVERT: H 33 LYS cc_start: 0.8381 (mttm) cc_final: 0.8128 (mttp) REVERT: H 127 THR cc_start: 0.8638 (p) cc_final: 0.8411 (p) REVERT: H 193 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7630 (tp30) REVERT: V 32 LYS cc_start: 0.8266 (tppt) cc_final: 0.7987 (tppt) REVERT: V 35 PHE cc_start: 0.8554 (m-80) cc_final: 0.8269 (m-80) REVERT: V 37 ILE cc_start: 0.9153 (tp) cc_final: 0.8869 (tp) REVERT: V 88 ASN cc_start: 0.8750 (t0) cc_final: 0.8545 (t0) REVERT: V 98 GLN cc_start: 0.8746 (mt0) cc_final: 0.8360 (tt0) REVERT: V 122 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7483 (m-30) REVERT: V 124 TYR cc_start: 0.8291 (p90) cc_final: 0.7050 (p90) REVERT: V 139 GLU cc_start: 0.8514 (tp30) cc_final: 0.7767 (tp30) REVERT: I 33 LYS cc_start: 0.8648 (mttm) cc_final: 0.8279 (mtmt) REVERT: I 131 SER cc_start: 0.9024 (p) cc_final: 0.8638 (t) REVERT: I 149 ASP cc_start: 0.8150 (m-30) cc_final: 0.7748 (t0) REVERT: I 150 GLU cc_start: 0.8094 (mp0) cc_final: 0.7778 (mp0) REVERT: I 172 MET cc_start: 0.8196 (tpp) cc_final: 0.7863 (tpp) REVERT: I 193 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8034 (tp30) REVERT: W 25 PHE cc_start: 0.7968 (t80) cc_final: 0.7604 (t80) REVERT: W 63 LEU cc_start: 0.9169 (mm) cc_final: 0.8778 (mm) REVERT: W 149 ASP cc_start: 0.8259 (m-30) cc_final: 0.7958 (m-30) REVERT: W 180 ARG cc_start: 0.8698 (tpp80) cc_final: 0.8399 (tpp80) REVERT: W 191 GLN cc_start: 0.8655 (mt0) cc_final: 0.8321 (tm-30) REVERT: W 197 ARG cc_start: 0.8065 (mtt90) cc_final: 0.7707 (mmt-90) REVERT: J 33 LYS cc_start: 0.8531 (mttm) cc_final: 0.8286 (mttp) REVERT: J 149 ASP cc_start: 0.8585 (m-30) cc_final: 0.7914 (t0) REVERT: J 153 ASP cc_start: 0.8474 (m-30) cc_final: 0.7935 (m-30) REVERT: J 166 ASP cc_start: 0.8172 (t0) cc_final: 0.7794 (t0) REVERT: X 27 MET cc_start: 0.7686 (ttt) cc_final: 0.7373 (ttm) REVERT: X 35 PHE cc_start: 0.8216 (m-80) cc_final: 0.7935 (m-10) REVERT: X 124 TYR cc_start: 0.8554 (p90) cc_final: 0.7466 (p90) REVERT: X 139 GLU cc_start: 0.8524 (tp30) cc_final: 0.7843 (tp30) REVERT: X 141 GLN cc_start: 0.9024 (mt0) cc_final: 0.8794 (mt0) REVERT: X 145 LYS cc_start: 0.9265 (ttmm) cc_final: 0.8987 (mmmm) REVERT: X 150 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8410 (mt-10) REVERT: X 197 ARG cc_start: 0.8088 (mtt90) cc_final: 0.7868 (mmt-90) REVERT: X 198 LYS cc_start: 0.8158 (mtmt) cc_final: 0.7719 (mtmt) REVERT: K 35 PHE cc_start: 0.8460 (m-80) cc_final: 0.8077 (m-10) REVERT: K 131 SER cc_start: 0.8931 (p) cc_final: 0.8583 (t) REVERT: Y 9 LYS cc_start: 0.7858 (pptt) cc_final: 0.7549 (pptt) REVERT: Y 25 PHE cc_start: 0.8218 (t80) cc_final: 0.7948 (t80) REVERT: Y 27 MET cc_start: 0.7668 (ttt) cc_final: 0.7226 (ttt) REVERT: Y 35 PHE cc_start: 0.8187 (m-80) cc_final: 0.7633 (m-80) REVERT: Y 85 ASN cc_start: 0.8594 (t0) cc_final: 0.8251 (t0) REVERT: Y 93 MET cc_start: 0.6472 (ttp) cc_final: 0.6129 (tmm) REVERT: Y 139 GLU cc_start: 0.8729 (tp30) cc_final: 0.7980 (tp30) REVERT: Y 141 GLN cc_start: 0.9032 (mt0) cc_final: 0.8779 (mt0) REVERT: Y 150 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8419 (mt-10) REVERT: L 17 GLU cc_start: 0.7856 (pp20) cc_final: 0.7479 (pp20) REVERT: L 33 LYS cc_start: 0.8418 (mttm) cc_final: 0.8107 (mtmm) REVERT: L 35 PHE cc_start: 0.8555 (m-80) cc_final: 0.8059 (m-10) REVERT: L 38 ASP cc_start: 0.8423 (t0) cc_final: 0.8214 (t70) REVERT: L 74 MET cc_start: 0.8034 (mmm) cc_final: 0.7565 (tpt) REVERT: L 98 GLN cc_start: 0.8529 (mt0) cc_final: 0.8281 (mt0) REVERT: L 127 THR cc_start: 0.8403 (p) cc_final: 0.8128 (p) REVERT: L 149 ASP cc_start: 0.8459 (m-30) cc_final: 0.7932 (t0) REVERT: L 153 ASP cc_start: 0.8394 (m-30) cc_final: 0.7836 (m-30) REVERT: A 40 MET cc_start: 0.8444 (pmm) cc_final: 0.8121 (pmm) REVERT: A 118 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.8047 (p0) REVERT: B 40 MET cc_start: 0.7924 (pmm) cc_final: 0.7354 (pmm) REVERT: B 71 ASP cc_start: 0.7191 (t70) cc_final: 0.6954 (t70) REVERT: B 95 SER cc_start: 0.7816 (m) cc_final: 0.7434 (p) REVERT: B 158 ASN cc_start: 0.7737 (m-40) cc_final: 0.7386 (m-40) REVERT: B 178 ARG cc_start: 0.8156 (ptt-90) cc_final: 0.7706 (ptt90) REVERT: B 182 GLU cc_start: 0.8469 (pm20) cc_final: 0.8111 (pm20) REVERT: B 205 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7209 (mp0) REVERT: B 211 GLU cc_start: 0.7987 (tt0) cc_final: 0.7644 (pt0) REVERT: C 40 MET cc_start: 0.8393 (pmm) cc_final: 0.7766 (pmm) REVERT: C 89 VAL cc_start: 0.8518 (t) cc_final: 0.8234 (p) REVERT: C 98 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7281 (tm-30) REVERT: C 121 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8203 (tm-30) REVERT: C 159 GLU cc_start: 0.6170 (tt0) cc_final: 0.5571 (tt0) REVERT: C 178 ARG cc_start: 0.7854 (ptt-90) cc_final: 0.7564 (ptt90) REVERT: C 188 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8344 (tp30) REVERT: D 71 ASP cc_start: 0.7551 (t70) cc_final: 0.7222 (t70) REVERT: D 98 GLN cc_start: 0.7564 (mm-40) cc_final: 0.7115 (tm-30) REVERT: D 114 LYS cc_start: 0.7984 (mmmm) cc_final: 0.7667 (mmmm) REVERT: D 119 GLN cc_start: 0.8781 (tp40) cc_final: 0.8482 (tp40) REVERT: D 163 THR cc_start: 0.7926 (OUTLIER) cc_final: 0.7647 (m) REVERT: D 177 GLU cc_start: 0.7160 (tp30) cc_final: 0.6681 (pt0) REVERT: E 40 MET cc_start: 0.8241 (pmm) cc_final: 0.7670 (pmm) REVERT: E 44 ASN cc_start: 0.8804 (m-40) cc_final: 0.7775 (t0) REVERT: E 108 ASN cc_start: 0.8282 (t0) cc_final: 0.7727 (t0) REVERT: E 118 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8048 (p0) REVERT: E 150 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7365 (p0) REVERT: E 160 TYR cc_start: 0.8138 (m-10) cc_final: 0.7579 (m-10) REVERT: E 178 ARG cc_start: 0.8219 (ptt-90) cc_final: 0.7899 (ptt90) REVERT: E 188 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8159 (tp30) REVERT: E 225 ASP cc_start: 0.7269 (p0) cc_final: 0.6708 (p0) REVERT: F 40 MET cc_start: 0.8442 (pmm) cc_final: 0.7945 (pmm) REVERT: F 110 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7366 (tm-30) REVERT: F 114 LYS cc_start: 0.8417 (mmtp) cc_final: 0.7916 (mmmm) REVERT: F 118 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8299 (p0) REVERT: F 121 GLN cc_start: 0.8266 (tm-30) cc_final: 0.8053 (tm-30) REVERT: F 177 GLU cc_start: 0.7302 (tp30) cc_final: 0.6952 (tt0) REVERT: F 208 LYS cc_start: 0.7739 (mtpp) cc_final: 0.7327 (ttpt) REVERT: G 40 MET cc_start: 0.8053 (pmm) cc_final: 0.7260 (pmm) REVERT: G 47 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8221 (pt) REVERT: G 79 SER cc_start: 0.8088 (t) cc_final: 0.7804 (p) REVERT: G 115 ARG cc_start: 0.7833 (mpt-90) cc_final: 0.7414 (mtt90) REVERT: G 119 GLN cc_start: 0.8820 (tp40) cc_final: 0.8471 (tp40) REVERT: G 178 ARG cc_start: 0.8275 (ptt-90) cc_final: 0.7670 (ptt90) REVERT: G 179 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7715 (mm-30) REVERT: G 225 ASP cc_start: 0.8018 (p0) cc_final: 0.7316 (p0) REVERT: G 228 GLU cc_start: 0.8715 (tt0) cc_final: 0.8292 (tp30) REVERT: O 121 GLN cc_start: 0.8329 (tm-30) cc_final: 0.7476 (tm-30) REVERT: O 122 GLN cc_start: 0.8407 (mt0) cc_final: 0.8191 (tt0) REVERT: O 123 TYR cc_start: 0.9018 (m-10) cc_final: 0.8427 (m-10) REVERT: O 125 GLN cc_start: 0.7514 (tp-100) cc_final: 0.7200 (tt0) REVERT: O 132 TYR cc_start: 0.8340 (m-80) cc_final: 0.7400 (m-80) REVERT: O 158 ASN cc_start: 0.7445 (m110) cc_final: 0.6952 (m110) REVERT: O 160 TYR cc_start: 0.8314 (m-80) cc_final: 0.7742 (m-80) REVERT: O 180 TYR cc_start: 0.7987 (t80) cc_final: 0.7721 (t80) REVERT: O 201 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7924 (tt) REVERT: P 115 ARG cc_start: 0.8085 (ttm170) cc_final: 0.7771 (ttm170) REVERT: P 121 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7419 (tm-30) REVERT: P 165 ILE cc_start: 0.8545 (tp) cc_final: 0.8193 (mm) REVERT: Q 121 GLN cc_start: 0.7797 (tm130) cc_final: 0.7530 (tm-30) REVERT: Q 165 ILE cc_start: 0.8515 (tp) cc_final: 0.8212 (mm) REVERT: Q 191 THR cc_start: 0.8787 (m) cc_final: 0.8488 (p) REVERT: Q 201 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7879 (tt) REVERT: R 40 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7064 (ttm) REVERT: R 119 GLN cc_start: 0.8812 (tp40) cc_final: 0.8189 (tp40) REVERT: R 143 GLN cc_start: 0.8652 (mp10) cc_final: 0.8383 (mp10) REVERT: R 191 THR cc_start: 0.8671 (m) cc_final: 0.8372 (p) REVERT: R 201 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7249 (tt) REVERT: R 211 GLU cc_start: 0.6673 (pt0) cc_final: 0.6137 (pt0) REVERT: R 221 TYR cc_start: 0.8398 (m-80) cc_final: 0.8074 (m-10) REVERT: S 33 LYS cc_start: 0.8946 (mtpp) cc_final: 0.8509 (pttp) REVERT: S 54 VAL cc_start: 0.5919 (OUTLIER) cc_final: 0.5718 (p) REVERT: S 119 GLN cc_start: 0.8832 (tp-100) cc_final: 0.8472 (tp40) REVERT: S 121 GLN cc_start: 0.7911 (tm-30) cc_final: 0.7292 (tm-30) REVERT: S 122 GLN cc_start: 0.8582 (mt0) cc_final: 0.8296 (mt0) REVERT: S 125 GLN cc_start: 0.7415 (tp-100) cc_final: 0.7196 (tp40) REVERT: S 165 ILE cc_start: 0.8524 (tp) cc_final: 0.8191 (mm) REVERT: S 191 THR cc_start: 0.8797 (m) cc_final: 0.8443 (p) REVERT: T 33 LYS cc_start: 0.8924 (mtpp) cc_final: 0.8554 (pttp) REVERT: T 40 MET cc_start: 0.7758 (pmm) cc_final: 0.7283 (pmm) REVERT: T 49 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8457 (pt) REVERT: T 121 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7563 (tm-30) REVERT: T 165 ILE cc_start: 0.8590 (tp) cc_final: 0.8159 (mm) REVERT: T 191 THR cc_start: 0.8907 (m) cc_final: 0.8563 (p) REVERT: T 221 TYR cc_start: 0.8714 (m-80) cc_final: 0.8494 (m-10) REVERT: U 40 MET cc_start: 0.7207 (ttp) cc_final: 0.6972 (ttp) REVERT: U 119 GLN cc_start: 0.9008 (tp40) cc_final: 0.8600 (tp40) REVERT: U 121 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7838 (tm-30) REVERT: U 165 ILE cc_start: 0.8576 (tp) cc_final: 0.8022 (mm) REVERT: U 191 THR cc_start: 0.8889 (m) cc_final: 0.8558 (p) REVERT: U 201 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7752 (tt) outliers start: 307 outliers final: 210 residues processed: 1513 average time/residue: 0.5880 time to fit residues: 1487.1333 Evaluate side-chains 1396 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1170 time to evaluate : 5.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 64 GLU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 64 GLU Chi-restraints excluded: chain 1 residue 84 SER Chi-restraints excluded: chain 1 residue 85 ASN Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 131 SER Chi-restraints excluded: chain 1 residue 177 VAL Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 143 SER Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 192 ILE Chi-restraints excluded: chain 2 residue 9 LYS Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 55 LEU Chi-restraints excluded: chain 2 residue 84 SER Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 122 ASP Chi-restraints excluded: chain 2 residue 123 ILE Chi-restraints excluded: chain 2 residue 135 TYR Chi-restraints excluded: chain 2 residue 177 VAL Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 45 ILE Chi-restraints excluded: chain V residue 84 SER Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 104 ILE Chi-restraints excluded: chain V residue 110 VAL Chi-restraints excluded: chain V residue 122 ASP Chi-restraints excluded: chain V residue 140 SER Chi-restraints excluded: chain V residue 177 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 64 GLU Chi-restraints excluded: chain W residue 85 ASN Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 123 ILE Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 177 VAL Chi-restraints excluded: chain W residue 193 GLU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 104 ILE Chi-restraints excluded: chain X residue 113 ILE Chi-restraints excluded: chain X residue 119 SER Chi-restraints excluded: chain X residue 123 ILE Chi-restraints excluded: chain X residue 127 THR Chi-restraints excluded: chain X residue 135 TYR Chi-restraints excluded: chain X residue 187 LEU Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 43 MET Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 104 ILE Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Y residue 127 THR Chi-restraints excluded: chain Y residue 135 TYR Chi-restraints excluded: chain Y residue 140 SER Chi-restraints excluded: chain Y residue 177 VAL Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 112 SER Chi-restraints excluded: chain L residue 146 MET Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 192 ILE Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 179 GLU Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 49 ILE Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 156 THR Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 105 SER Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 156 THR Chi-restraints excluded: chain P residue 158 ASN Chi-restraints excluded: chain P residue 191 THR Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 135 SER Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 219 ASN Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 219 ASN Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 170 ASP Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 219 ASN Chi-restraints excluded: chain T residue 49 ILE Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 194 ILE Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain T residue 219 ASN Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 156 THR Chi-restraints excluded: chain U residue 201 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 191 optimal weight: 2.9990 chunk 511 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 333 optimal weight: 8.9990 chunk 140 optimal weight: 6.9990 chunk 568 optimal weight: 10.0000 chunk 472 optimal weight: 6.9990 chunk 263 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 36 GLN ** Z 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 191 GLN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 ASN ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 141 GLN ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN W 88 ASN W 141 GLN J 85 ASN ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 191 GLN L 85 ASN ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN G 62 ASN O 98 GLN Q 121 GLN ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 122 GLN ** R 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 158 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 47096 Z= 0.491 Angle : 0.888 27.456 63588 Z= 0.454 Chirality : 0.049 0.281 7448 Planarity : 0.004 0.053 8162 Dihedral : 6.456 57.974 6620 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.80 % Favored : 92.98 % Rotamer: Outliers : 7.89 % Allowed : 22.92 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.02 (0.10), residues: 5957 helix: 1.17 (0.10), residues: 2275 sheet: -1.23 (0.13), residues: 1351 loop : -2.20 (0.12), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS W 28 PHE 0.030 0.002 PHE R 91 TYR 0.026 0.002 TYR D 160 ARG 0.008 0.001 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1541 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 395 poor density : 1146 time to evaluate : 5.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 32 LYS cc_start: 0.8634 (tppt) cc_final: 0.8351 (tppt) REVERT: Z 37 ILE cc_start: 0.9269 (tp) cc_final: 0.8862 (tp) REVERT: Z 98 GLN cc_start: 0.8780 (mt0) cc_final: 0.8236 (tt0) REVERT: Z 111 PHE cc_start: 0.8786 (m-80) cc_final: 0.8488 (m-80) REVERT: Z 122 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7277 (m-30) REVERT: Z 124 TYR cc_start: 0.8554 (p90) cc_final: 0.8174 (p90) REVERT: Z 139 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8375 (mm-30) REVERT: Z 166 ASP cc_start: 0.8478 (t0) cc_final: 0.8268 (t0) REVERT: M 33 LYS cc_start: 0.8827 (mttm) cc_final: 0.8618 (mttp) REVERT: M 124 TYR cc_start: 0.8577 (p90) cc_final: 0.8217 (p90) REVERT: M 150 GLU cc_start: 0.8303 (mp0) cc_final: 0.8029 (mp0) REVERT: M 193 GLU cc_start: 0.8212 (pt0) cc_final: 0.7997 (tp30) REVERT: 1 9 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7642 (pptt) REVERT: 1 10 ASP cc_start: 0.7555 (m-30) cc_final: 0.7333 (m-30) REVERT: 1 35 PHE cc_start: 0.8642 (m-80) cc_final: 0.8070 (m-80) REVERT: 1 62 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7680 (mm-30) REVERT: 1 63 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8810 (mm) REVERT: 1 139 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8274 (mm-30) REVERT: 1 144 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7944 (mm-30) REVERT: 1 174 ASP cc_start: 0.8632 (p0) cc_final: 0.8327 (p0) REVERT: 1 190 ASP cc_start: 0.8040 (p0) cc_final: 0.7827 (p0) REVERT: 1 193 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7168 (pt0) REVERT: N 27 MET cc_start: 0.9077 (ttt) cc_final: 0.8465 (ttt) REVERT: N 193 GLU cc_start: 0.8574 (mm-30) cc_final: 0.7979 (tp30) REVERT: 2 9 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7180 (pttp) REVERT: 2 10 ASP cc_start: 0.7875 (m-30) cc_final: 0.7433 (m-30) REVERT: 2 62 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7431 (mp0) REVERT: 2 76 ILE cc_start: 0.9187 (mm) cc_final: 0.8959 (mt) REVERT: 2 121 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7828 (tt0) REVERT: 2 124 TYR cc_start: 0.8465 (p90) cc_final: 0.7766 (p90) REVERT: 2 127 THR cc_start: 0.9168 (p) cc_final: 0.8897 (p) REVERT: 2 135 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.7128 (t80) REVERT: 2 139 GLU cc_start: 0.8433 (tp30) cc_final: 0.8160 (tp30) REVERT: 2 198 LYS cc_start: 0.7946 (mtmt) cc_final: 0.7631 (mtmm) REVERT: H 33 LYS cc_start: 0.8518 (mttm) cc_final: 0.7759 (mttp) REVERT: H 135 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.7449 (t80) REVERT: H 153 ASP cc_start: 0.8438 (m-30) cc_final: 0.7893 (m-30) REVERT: H 193 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7974 (tp30) REVERT: V 9 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8033 (pptt) REVERT: V 25 PHE cc_start: 0.8466 (t80) cc_final: 0.8230 (t80) REVERT: V 37 ILE cc_start: 0.9222 (tp) cc_final: 0.8927 (tp) REVERT: V 98 GLN cc_start: 0.8755 (mt0) cc_final: 0.8403 (tt0) REVERT: V 122 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7172 (m-30) REVERT: V 139 GLU cc_start: 0.8788 (tp30) cc_final: 0.7985 (tp30) REVERT: V 146 MET cc_start: 0.8588 (mtp) cc_final: 0.8184 (mtp) REVERT: I 33 LYS cc_start: 0.8820 (mttm) cc_final: 0.8430 (mtmt) REVERT: I 131 SER cc_start: 0.9155 (p) cc_final: 0.8700 (t) REVERT: I 149 ASP cc_start: 0.8408 (m-30) cc_final: 0.7987 (t0) REVERT: I 193 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7882 (tp30) REVERT: W 9 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7703 (pptt) REVERT: W 10 ASP cc_start: 0.7534 (m-30) cc_final: 0.7317 (m-30) REVERT: W 25 PHE cc_start: 0.8503 (t80) cc_final: 0.8267 (t80) REVERT: W 27 MET cc_start: 0.7831 (ttt) cc_final: 0.7282 (ttt) REVERT: W 53 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7888 (mt0) REVERT: W 122 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7723 (m-30) REVERT: W 139 GLU cc_start: 0.8925 (tp30) cc_final: 0.7849 (tp30) REVERT: W 141 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8759 (pt0) REVERT: W 149 ASP cc_start: 0.8437 (m-30) cc_final: 0.8128 (m-30) REVERT: W 191 GLN cc_start: 0.8780 (mt0) cc_final: 0.8560 (mt0) REVERT: W 193 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: W 197 ARG cc_start: 0.8359 (mtt90) cc_final: 0.8123 (mmt-90) REVERT: J 33 LYS cc_start: 0.8710 (mttm) cc_final: 0.8333 (mttp) REVERT: J 149 ASP cc_start: 0.8520 (m-30) cc_final: 0.8000 (t0) REVERT: J 153 ASP cc_start: 0.8549 (m-30) cc_final: 0.7959 (m-30) REVERT: J 166 ASP cc_start: 0.8322 (t0) cc_final: 0.7750 (t0) REVERT: J 193 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8219 (pt0) REVERT: X 9 LYS cc_start: 0.8209 (pptt) cc_final: 0.7962 (pptt) REVERT: X 25 PHE cc_start: 0.8772 (t80) cc_final: 0.8468 (t80) REVERT: X 27 MET cc_start: 0.8251 (ttt) cc_final: 0.7448 (ttt) REVERT: X 122 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7560 (m-30) REVERT: X 123 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8392 (tt) REVERT: X 139 GLU cc_start: 0.8876 (tp30) cc_final: 0.8117 (tp30) REVERT: X 197 ARG cc_start: 0.8161 (mtt90) cc_final: 0.7800 (mmt-90) REVERT: K 38 ASP cc_start: 0.8123 (t0) cc_final: 0.7852 (t0) REVERT: K 74 MET cc_start: 0.8270 (mmm) cc_final: 0.7778 (tpt) REVERT: K 95 TYR cc_start: 0.9191 (m-80) cc_final: 0.8820 (m-80) REVERT: K 131 SER cc_start: 0.9149 (p) cc_final: 0.8614 (t) REVERT: Y 9 LYS cc_start: 0.8192 (pptt) cc_final: 0.7947 (pptt) REVERT: Y 27 MET cc_start: 0.7877 (ttt) cc_final: 0.7077 (ttt) REVERT: Y 93 MET cc_start: 0.6824 (ttp) cc_final: 0.6379 (tmm) REVERT: Y 139 GLU cc_start: 0.8876 (tp30) cc_final: 0.8329 (mm-30) REVERT: Y 141 GLN cc_start: 0.9171 (mt0) cc_final: 0.8893 (mt0) REVERT: L 17 GLU cc_start: 0.8021 (pp20) cc_final: 0.7815 (pp20) REVERT: L 33 LYS cc_start: 0.8546 (mttm) cc_final: 0.8180 (mtmm) REVERT: L 35 PHE cc_start: 0.8687 (m-80) cc_final: 0.8354 (m-80) REVERT: L 127 THR cc_start: 0.8713 (p) cc_final: 0.8480 (p) REVERT: L 153 ASP cc_start: 0.8511 (m-30) cc_final: 0.7995 (m-30) REVERT: L 187 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8851 (mm) REVERT: A 60 GLU cc_start: 0.6807 (tp30) cc_final: 0.6490 (tm-30) REVERT: A 61 GLN cc_start: 0.6898 (OUTLIER) cc_final: 0.6370 (mm-40) REVERT: A 98 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7273 (tm-30) REVERT: A 115 ARG cc_start: 0.7967 (mpt180) cc_final: 0.7761 (tpp80) REVERT: A 208 LYS cc_start: 0.7627 (mttt) cc_final: 0.7338 (ttmt) REVERT: B 40 MET cc_start: 0.8387 (pmm) cc_final: 0.7477 (pmm) REVERT: B 98 GLN cc_start: 0.7850 (tp40) cc_final: 0.6997 (tm-30) REVERT: B 119 GLN cc_start: 0.8765 (tp40) cc_final: 0.8494 (tp40) REVERT: B 121 GLN cc_start: 0.8392 (tm-30) cc_final: 0.8189 (tm-30) REVERT: B 143 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8455 (mp10) REVERT: B 211 GLU cc_start: 0.7931 (tt0) cc_final: 0.7538 (pt0) REVERT: C 58 LEU cc_start: 0.6113 (mt) cc_final: 0.5865 (mt) REVERT: C 98 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7096 (tm-30) REVERT: C 178 ARG cc_start: 0.8055 (ptt-90) cc_final: 0.7708 (ptt90) REVERT: D 60 GLU cc_start: 0.7001 (tp30) cc_final: 0.6584 (tm-30) REVERT: D 72 ASP cc_start: 0.8351 (m-30) cc_final: 0.8029 (m-30) REVERT: D 98 GLN cc_start: 0.7468 (mm-40) cc_final: 0.6930 (tm-30) REVERT: D 119 GLN cc_start: 0.8821 (tp40) cc_final: 0.8534 (tp40) REVERT: D 158 ASN cc_start: 0.8134 (m-40) cc_final: 0.7916 (m-40) REVERT: D 163 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8214 (m) REVERT: E 40 MET cc_start: 0.8496 (pmm) cc_final: 0.7714 (pmm) REVERT: E 118 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8020 (p0) REVERT: E 188 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8384 (tp30) REVERT: E 208 LYS cc_start: 0.7828 (mttt) cc_final: 0.7213 (mtpp) REVERT: F 40 MET cc_start: 0.8605 (pmm) cc_final: 0.7910 (pmm) REVERT: F 60 GLU cc_start: 0.6739 (tp30) cc_final: 0.6353 (tm-30) REVERT: F 91 PHE cc_start: 0.8428 (t80) cc_final: 0.8187 (t80) REVERT: F 98 GLN cc_start: 0.7876 (mm110) cc_final: 0.7104 (tm-30) REVERT: F 114 LYS cc_start: 0.8424 (mmtp) cc_final: 0.7989 (mmmm) REVERT: F 118 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8379 (p0) REVERT: F 121 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8245 (tm-30) REVERT: G 114 LYS cc_start: 0.8251 (mmtp) cc_final: 0.7954 (mmmm) REVERT: G 115 ARG cc_start: 0.8013 (mpt-90) cc_final: 0.7541 (mtt90) REVERT: G 119 GLN cc_start: 0.8858 (tp40) cc_final: 0.8485 (tp40) REVERT: G 178 ARG cc_start: 0.8220 (ptt-90) cc_final: 0.7746 (ptt90) REVERT: G 179 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8230 (mm-30) REVERT: G 228 GLU cc_start: 0.8845 (tt0) cc_final: 0.8457 (tp30) REVERT: O 119 GLN cc_start: 0.9170 (tp40) cc_final: 0.8794 (tp40) REVERT: O 121 GLN cc_start: 0.8433 (tm-30) cc_final: 0.7991 (tm-30) REVERT: O 122 GLN cc_start: 0.8336 (mt0) cc_final: 0.8113 (mt0) REVERT: O 125 GLN cc_start: 0.7459 (tp-100) cc_final: 0.7090 (tp-100) REVERT: O 143 GLN cc_start: 0.8662 (mp10) cc_final: 0.7935 (mp10) REVERT: O 158 ASN cc_start: 0.7597 (m110) cc_final: 0.7339 (m110) REVERT: O 160 TYR cc_start: 0.8447 (m-80) cc_final: 0.7894 (m-80) REVERT: O 183 ASN cc_start: 0.8413 (m110) cc_final: 0.7668 (p0) REVERT: P 40 MET cc_start: 0.7832 (ptp) cc_final: 0.7460 (pmm) REVERT: P 47 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8390 (pt) REVERT: P 115 ARG cc_start: 0.8147 (ttm170) cc_final: 0.7838 (ttm170) REVERT: P 119 GLN cc_start: 0.9020 (tp40) cc_final: 0.8666 (tp40) REVERT: P 121 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7783 (tm-30) REVERT: P 125 GLN cc_start: 0.7802 (tt0) cc_final: 0.7598 (tt0) REVERT: P 165 ILE cc_start: 0.8531 (tp) cc_final: 0.8162 (mm) REVERT: Q 81 LEU cc_start: 0.8123 (mt) cc_final: 0.7769 (tt) REVERT: Q 119 GLN cc_start: 0.8811 (tp-100) cc_final: 0.8463 (tp40) REVERT: Q 121 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7973 (tm-30) REVERT: Q 132 TYR cc_start: 0.8448 (m-80) cc_final: 0.7484 (m-80) REVERT: Q 160 TYR cc_start: 0.8763 (m-80) cc_final: 0.8028 (m-80) REVERT: Q 165 ILE cc_start: 0.8549 (tp) cc_final: 0.8239 (mm) REVERT: Q 191 THR cc_start: 0.8887 (m) cc_final: 0.8552 (p) REVERT: R 40 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.6629 (ttp) REVERT: R 119 GLN cc_start: 0.9086 (tp40) cc_final: 0.8552 (tp40) REVERT: R 191 THR cc_start: 0.8856 (m) cc_final: 0.8587 (p) REVERT: R 201 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7434 (tt) REVERT: R 221 TYR cc_start: 0.8272 (m-80) cc_final: 0.8050 (m-10) REVERT: S 81 LEU cc_start: 0.8001 (mt) cc_final: 0.7728 (tt) REVERT: S 107 VAL cc_start: 0.8876 (t) cc_final: 0.7574 (p) REVERT: S 118 ASP cc_start: 0.8969 (t0) cc_final: 0.8645 (t0) REVERT: S 119 GLN cc_start: 0.9001 (tp-100) cc_final: 0.8641 (tp40) REVERT: S 121 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7287 (tm-30) REVERT: S 122 GLN cc_start: 0.8271 (mt0) cc_final: 0.7927 (mt0) REVERT: S 125 GLN cc_start: 0.7568 (tp-100) cc_final: 0.7342 (tp40) REVERT: S 143 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8340 (mp10) REVERT: S 160 TYR cc_start: 0.8323 (m-80) cc_final: 0.7736 (m-10) REVERT: S 165 ILE cc_start: 0.8560 (tp) cc_final: 0.8225 (mm) REVERT: S 191 THR cc_start: 0.8877 (m) cc_final: 0.8536 (p) REVERT: T 40 MET cc_start: 0.8136 (pmm) cc_final: 0.7889 (pmm) REVERT: T 121 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7828 (tm-30) REVERT: T 165 ILE cc_start: 0.8538 (tp) cc_final: 0.8089 (mm) REVERT: T 191 THR cc_start: 0.8994 (m) cc_final: 0.8681 (p) REVERT: U 40 MET cc_start: 0.7453 (ttp) cc_final: 0.7242 (ttp) REVERT: U 119 GLN cc_start: 0.9092 (tp40) cc_final: 0.8699 (tp40) REVERT: U 151 CYS cc_start: 0.7885 (t) cc_final: 0.7228 (t) REVERT: U 191 THR cc_start: 0.9028 (m) cc_final: 0.8697 (p) REVERT: U 201 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7775 (tt) outliers start: 395 outliers final: 290 residues processed: 1437 average time/residue: 0.5477 time to fit residues: 1305.5543 Evaluate side-chains 1383 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 1068 time to evaluate : 4.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 45 ILE Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 122 ASP Chi-restraints excluded: chain Z residue 135 TYR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 59 MET Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 85 ASN Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 104 ILE Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain 1 residue 9 LYS Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 43 MET Chi-restraints excluded: chain 1 residue 45 ILE Chi-restraints excluded: chain 1 residue 59 MET Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 64 GLU Chi-restraints excluded: chain 1 residue 85 ASN Chi-restraints excluded: chain 1 residue 89 GLN Chi-restraints excluded: chain 1 residue 99 LEU Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 110 VAL Chi-restraints excluded: chain 1 residue 131 SER Chi-restraints excluded: chain 1 residue 177 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 85 ASN Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 140 SER Chi-restraints excluded: chain N residue 143 SER Chi-restraints excluded: chain N residue 165 ARG Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain 2 residue 9 LYS Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 55 LEU Chi-restraints excluded: chain 2 residue 83 LEU Chi-restraints excluded: chain 2 residue 84 SER Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 122 ASP Chi-restraints excluded: chain 2 residue 123 ILE Chi-restraints excluded: chain 2 residue 135 TYR Chi-restraints excluded: chain 2 residue 146 MET Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain V residue 9 LYS Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 45 ILE Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 63 LEU Chi-restraints excluded: chain V residue 84 SER Chi-restraints excluded: chain V residue 89 GLN Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 104 ILE Chi-restraints excluded: chain V residue 110 VAL Chi-restraints excluded: chain V residue 119 SER Chi-restraints excluded: chain V residue 122 ASP Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 190 ASP Chi-restraints excluded: chain W residue 9 LYS Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 53 GLN Chi-restraints excluded: chain W residue 55 LEU Chi-restraints excluded: chain W residue 59 MET Chi-restraints excluded: chain W residue 64 GLU Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 119 SER Chi-restraints excluded: chain W residue 122 ASP Chi-restraints excluded: chain W residue 123 ILE Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 141 GLN Chi-restraints excluded: chain W residue 177 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 193 GLU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 37 ILE Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 104 ILE Chi-restraints excluded: chain X residue 119 SER Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 123 ILE Chi-restraints excluded: chain X residue 127 THR Chi-restraints excluded: chain X residue 135 TYR Chi-restraints excluded: chain X residue 187 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 104 ILE Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Y residue 127 THR Chi-restraints excluded: chain Y residue 135 TYR Chi-restraints excluded: chain Y residue 177 VAL Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 85 ASN Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 192 ILE Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 179 GLU Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 49 ILE Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 156 THR Chi-restraints excluded: chain O residue 219 ASN Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 94 ILE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 105 SER Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 156 THR Chi-restraints excluded: chain P residue 158 ASN Chi-restraints excluded: chain P residue 191 THR Chi-restraints excluded: chain P residue 197 LEU Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 94 ILE Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 158 ASN Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 215 ILE Chi-restraints excluded: chain Q residue 219 ASN Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 170 ASP Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 219 ASN Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 157 ILE Chi-restraints excluded: chain S residue 170 ASP Chi-restraints excluded: chain S residue 172 VAL Chi-restraints excluded: chain S residue 219 ASN Chi-restraints excluded: chain T residue 49 ILE Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 156 THR Chi-restraints excluded: chain T residue 158 ASN Chi-restraints excluded: chain T residue 194 ILE Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain T residue 215 ILE Chi-restraints excluded: chain T residue 219 ASN Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 88 LEU Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 156 THR Chi-restraints excluded: chain U residue 158 ASN Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 197 LEU Chi-restraints excluded: chain U residue 201 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 548 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 324 optimal weight: 9.9990 chunk 415 optimal weight: 5.9990 chunk 321 optimal weight: 9.9990 chunk 478 optimal weight: 0.0040 chunk 317 optimal weight: 0.9990 chunk 566 optimal weight: 9.9990 chunk 354 optimal weight: 2.9990 chunk 345 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 overall best weight: 1.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 191 GLN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 ASN ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 36 GLN W 88 ASN J 85 ASN ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 88 ASN Y 191 GLN L 85 ASN ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 62 ASN C 62 ASN D 62 ASN D 125 GLN D 183 ASN E 183 ASN G 125 GLN ** P 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 226 GLN ** R 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 226 GLN ** U 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 143 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.6327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 47096 Z= 0.270 Angle : 0.782 25.093 63588 Z= 0.398 Chirality : 0.045 0.228 7448 Planarity : 0.004 0.042 8162 Dihedral : 6.139 57.073 6618 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.79 % Favored : 94.07 % Rotamer: Outliers : 6.31 % Allowed : 25.13 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.80 (0.11), residues: 5957 helix: 1.52 (0.11), residues: 2275 sheet: -1.11 (0.13), residues: 1309 loop : -2.27 (0.12), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS Y 28 PHE 0.024 0.002 PHE R 91 TYR 0.031 0.001 TYR T 221 ARG 0.008 0.000 ARG O 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1522 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 1206 time to evaluate : 7.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 32 LYS cc_start: 0.8606 (tppt) cc_final: 0.8286 (tppt) REVERT: Z 35 PHE cc_start: 0.8692 (m-80) cc_final: 0.8330 (m-10) REVERT: Z 37 ILE cc_start: 0.9228 (tp) cc_final: 0.8837 (tp) REVERT: Z 98 GLN cc_start: 0.8767 (mt0) cc_final: 0.8269 (tt0) REVERT: Z 111 PHE cc_start: 0.8680 (m-80) cc_final: 0.8374 (m-80) REVERT: M 17 GLU cc_start: 0.7593 (pp20) cc_final: 0.6920 (pp20) REVERT: M 27 MET cc_start: 0.7970 (ptm) cc_final: 0.7219 (ptm) REVERT: M 33 LYS cc_start: 0.8707 (mttm) cc_final: 0.8241 (mttp) REVERT: M 66 TYR cc_start: 0.8711 (t80) cc_final: 0.8457 (t80) REVERT: M 150 GLU cc_start: 0.8289 (mp0) cc_final: 0.8020 (mp0) REVERT: M 193 GLU cc_start: 0.8239 (pt0) cc_final: 0.7940 (tp30) REVERT: 1 9 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7424 (pptt) REVERT: 1 10 ASP cc_start: 0.7499 (m-30) cc_final: 0.7217 (m-30) REVERT: 1 27 MET cc_start: 0.6991 (ttt) cc_final: 0.6102 (ttt) REVERT: 1 35 PHE cc_start: 0.8547 (m-80) cc_final: 0.7868 (m-80) REVERT: 1 62 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7755 (mm-30) REVERT: 1 63 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8735 (mm) REVERT: 1 95 TYR cc_start: 0.8626 (m-80) cc_final: 0.8260 (m-80) REVERT: 1 139 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8066 (mm-30) REVERT: 1 150 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8596 (mt-10) REVERT: 1 174 ASP cc_start: 0.8626 (p0) cc_final: 0.8373 (p0) REVERT: N 51 ASP cc_start: 0.8415 (m-30) cc_final: 0.7984 (t0) REVERT: N 124 TYR cc_start: 0.8447 (p90) cc_final: 0.8224 (p90) REVERT: N 135 TYR cc_start: 0.8345 (m-80) cc_final: 0.7403 (t80) REVERT: N 146 MET cc_start: 0.7459 (mtp) cc_final: 0.7255 (mtp) REVERT: N 153 ASP cc_start: 0.8393 (m-30) cc_final: 0.8138 (m-30) REVERT: N 165 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7760 (tpp-160) REVERT: N 193 GLU cc_start: 0.8617 (mm-30) cc_final: 0.7970 (tp30) REVERT: 2 9 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.6986 (pttp) REVERT: 2 124 TYR cc_start: 0.8388 (p90) cc_final: 0.7483 (p90) REVERT: 2 127 THR cc_start: 0.8981 (p) cc_final: 0.8728 (p) REVERT: 2 135 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.7086 (t80) REVERT: 2 139 GLU cc_start: 0.8263 (tp30) cc_final: 0.7877 (tp30) REVERT: 2 150 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8418 (mt-10) REVERT: 2 198 LYS cc_start: 0.7981 (mtmt) cc_final: 0.7620 (mtmt) REVERT: H 27 MET cc_start: 0.8817 (ttt) cc_final: 0.8440 (ttt) REVERT: H 33 LYS cc_start: 0.8400 (mttm) cc_final: 0.8109 (mttp) REVERT: H 127 THR cc_start: 0.8583 (p) cc_final: 0.8343 (p) REVERT: H 135 TYR cc_start: 0.8240 (m-80) cc_final: 0.7350 (t80) REVERT: H 153 ASP cc_start: 0.8341 (m-30) cc_final: 0.8068 (m-30) REVERT: H 193 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7940 (tp30) REVERT: H 198 LYS cc_start: 0.7922 (mtmm) cc_final: 0.7420 (mtmm) REVERT: V 9 LYS cc_start: 0.8175 (pptt) cc_final: 0.7863 (pptt) REVERT: V 32 LYS cc_start: 0.8419 (tppt) cc_final: 0.8186 (tppt) REVERT: V 35 PHE cc_start: 0.8751 (m-80) cc_final: 0.8321 (m-10) REVERT: V 37 ILE cc_start: 0.9174 (tp) cc_final: 0.8894 (tp) REVERT: V 98 GLN cc_start: 0.8731 (mt0) cc_final: 0.8255 (tt0) REVERT: V 122 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7450 (m-30) REVERT: V 139 GLU cc_start: 0.8676 (tp30) cc_final: 0.7800 (tp30) REVERT: V 144 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7922 (tp30) REVERT: V 146 MET cc_start: 0.8550 (mtp) cc_final: 0.8348 (mtp) REVERT: I 2 THR cc_start: 0.9326 (t) cc_final: 0.9034 (m) REVERT: I 33 LYS cc_start: 0.8731 (mttm) cc_final: 0.8411 (mtmt) REVERT: I 51 ASP cc_start: 0.8519 (m-30) cc_final: 0.8186 (m-30) REVERT: I 131 SER cc_start: 0.9127 (p) cc_final: 0.8642 (t) REVERT: I 149 ASP cc_start: 0.8281 (m-30) cc_final: 0.7528 (t0) REVERT: I 153 ASP cc_start: 0.8233 (m-30) cc_final: 0.7731 (m-30) REVERT: I 193 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8123 (pt0) REVERT: W 9 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7831 (pptt) REVERT: W 18 ARG cc_start: 0.8268 (mtm180) cc_final: 0.7974 (mtp85) REVERT: W 22 MET cc_start: 0.5750 (ttt) cc_final: 0.5522 (ttt) REVERT: W 25 PHE cc_start: 0.8452 (t80) cc_final: 0.8202 (t80) REVERT: W 53 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7723 (mt0) REVERT: W 122 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7592 (m-30) REVERT: W 139 GLU cc_start: 0.8807 (tp30) cc_final: 0.7779 (tp30) REVERT: W 149 ASP cc_start: 0.8294 (m-30) cc_final: 0.8020 (m-30) REVERT: W 191 GLN cc_start: 0.8763 (mt0) cc_final: 0.8406 (tm-30) REVERT: W 193 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: J 27 MET cc_start: 0.8733 (ttt) cc_final: 0.8266 (ttm) REVERT: J 149 ASP cc_start: 0.8571 (m-30) cc_final: 0.7967 (t0) REVERT: J 153 ASP cc_start: 0.8557 (m-30) cc_final: 0.8020 (m-30) REVERT: J 193 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8195 (pt0) REVERT: X 9 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7803 (pptt) REVERT: X 27 MET cc_start: 0.7962 (ttt) cc_final: 0.7479 (ttt) REVERT: X 124 TYR cc_start: 0.8584 (p90) cc_final: 0.7846 (p90) REVERT: X 139 GLU cc_start: 0.8657 (tp30) cc_final: 0.7799 (tp30) REVERT: X 150 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8392 (mt-10) REVERT: X 197 ARG cc_start: 0.8088 (mtt90) cc_final: 0.7836 (mmt-90) REVERT: X 198 LYS cc_start: 0.8173 (mtmt) cc_final: 0.7744 (mtmt) REVERT: K 38 ASP cc_start: 0.8209 (t0) cc_final: 0.7934 (t0) REVERT: K 74 MET cc_start: 0.8209 (mmm) cc_final: 0.7968 (tpt) REVERT: K 131 SER cc_start: 0.9050 (p) cc_final: 0.8577 (t) REVERT: Y 27 MET cc_start: 0.7738 (ttt) cc_final: 0.7097 (ttt) REVERT: Y 35 PHE cc_start: 0.8398 (m-80) cc_final: 0.7944 (m-80) REVERT: Y 93 MET cc_start: 0.6574 (ttp) cc_final: 0.6106 (tmm) REVERT: Y 95 TYR cc_start: 0.8401 (m-80) cc_final: 0.8028 (m-10) REVERT: Y 139 GLU cc_start: 0.8791 (tp30) cc_final: 0.7960 (tp30) REVERT: Y 141 GLN cc_start: 0.9131 (mt0) cc_final: 0.8809 (mt0) REVERT: Y 150 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8371 (mt-10) REVERT: L 17 GLU cc_start: 0.7972 (pp20) cc_final: 0.7754 (pp20) REVERT: L 33 LYS cc_start: 0.8291 (mttm) cc_final: 0.8018 (mtmm) REVERT: L 35 PHE cc_start: 0.8608 (m-80) cc_final: 0.8258 (m-80) REVERT: L 127 THR cc_start: 0.8534 (p) cc_final: 0.8320 (p) REVERT: L 153 ASP cc_start: 0.8345 (m-30) cc_final: 0.7875 (m-30) REVERT: A 60 GLU cc_start: 0.6860 (tp30) cc_final: 0.6493 (tm-30) REVERT: A 98 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7184 (tm-30) REVERT: A 110 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7457 (tm-30) REVERT: A 121 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8167 (tm-30) REVERT: A 160 TYR cc_start: 0.8295 (m-10) cc_final: 0.7335 (m-10) REVERT: A 208 LYS cc_start: 0.7761 (mttt) cc_final: 0.7225 (mtpp) REVERT: A 225 ASP cc_start: 0.7846 (p0) cc_final: 0.7296 (p0) REVERT: B 23 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7107 (tp-100) REVERT: B 60 GLU cc_start: 0.7108 (mm-30) cc_final: 0.5967 (tm-30) REVERT: B 98 GLN cc_start: 0.7849 (tp40) cc_final: 0.7051 (tm-30) REVERT: B 119 GLN cc_start: 0.8696 (tp40) cc_final: 0.8443 (tp40) REVERT: B 208 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7656 (ttpt) REVERT: B 211 GLU cc_start: 0.7925 (tt0) cc_final: 0.7557 (pt0) REVERT: C 40 MET cc_start: 0.8418 (pmm) cc_final: 0.7670 (pmm) REVERT: C 98 GLN cc_start: 0.7654 (mm-40) cc_final: 0.6938 (tm-30) REVERT: C 149 PHE cc_start: 0.8040 (m-10) cc_final: 0.7704 (m-10) REVERT: C 178 ARG cc_start: 0.8159 (ptt-90) cc_final: 0.7883 (ptt90) REVERT: C 188 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8386 (tp30) REVERT: C 208 LYS cc_start: 0.8236 (mtpp) cc_final: 0.7901 (ttpt) REVERT: D 60 GLU cc_start: 0.6567 (tp30) cc_final: 0.6237 (tm-30) REVERT: D 72 ASP cc_start: 0.8368 (m-30) cc_final: 0.8158 (m-30) REVERT: D 98 GLN cc_start: 0.7175 (mm-40) cc_final: 0.6722 (tm-30) REVERT: D 110 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7307 (tm-30) REVERT: D 114 LYS cc_start: 0.7978 (mmmm) cc_final: 0.7540 (mmmm) REVERT: D 119 GLN cc_start: 0.8806 (tp40) cc_final: 0.8496 (tp40) REVERT: D 158 ASN cc_start: 0.8119 (m-40) cc_final: 0.7870 (m-40) REVERT: D 163 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.8074 (m) REVERT: E 40 MET cc_start: 0.8433 (pmm) cc_final: 0.7573 (pmm) REVERT: E 118 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8049 (p0) REVERT: E 188 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8190 (tp30) REVERT: E 208 LYS cc_start: 0.7973 (mttt) cc_final: 0.7558 (mtpp) REVERT: F 60 GLU cc_start: 0.6511 (tp30) cc_final: 0.6224 (tm-30) REVERT: F 91 PHE cc_start: 0.8383 (t80) cc_final: 0.8129 (t80) REVERT: F 98 GLN cc_start: 0.7707 (mm110) cc_final: 0.7017 (tm-30) REVERT: F 121 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7967 (tm-30) REVERT: F 208 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7641 (ptmt) REVERT: F 221 TYR cc_start: 0.7973 (m-80) cc_final: 0.7515 (m-10) REVERT: G 115 ARG cc_start: 0.7963 (mpt-90) cc_final: 0.7601 (mtt90) REVERT: G 119 GLN cc_start: 0.8866 (tp40) cc_final: 0.8541 (tp40) REVERT: G 178 ARG cc_start: 0.8195 (ptt-90) cc_final: 0.7658 (ptt90) REVERT: G 179 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8137 (mm-30) REVERT: G 228 GLU cc_start: 0.8884 (tt0) cc_final: 0.8199 (tp30) REVERT: O 121 GLN cc_start: 0.8432 (tm-30) cc_final: 0.8016 (tm-30) REVERT: O 123 TYR cc_start: 0.9182 (m-10) cc_final: 0.8416 (m-10) REVERT: O 132 TYR cc_start: 0.8601 (m-80) cc_final: 0.7587 (m-80) REVERT: O 158 ASN cc_start: 0.7717 (m110) cc_final: 0.7496 (m-40) REVERT: O 160 TYR cc_start: 0.8413 (m-80) cc_final: 0.7870 (m-80) REVERT: O 183 ASN cc_start: 0.8307 (m110) cc_final: 0.7534 (p0) REVERT: P 40 MET cc_start: 0.7433 (ptp) cc_final: 0.7176 (pmm) REVERT: P 47 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8390 (pt) REVERT: P 119 GLN cc_start: 0.8955 (tp40) cc_final: 0.8533 (tp40) REVERT: P 165 ILE cc_start: 0.8520 (tp) cc_final: 0.8212 (mm) REVERT: Q 119 GLN cc_start: 0.8749 (tp-100) cc_final: 0.8143 (tp40) REVERT: Q 121 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7800 (tm-30) REVERT: Q 123 TYR cc_start: 0.9040 (m-80) cc_final: 0.7878 (m-10) REVERT: Q 132 TYR cc_start: 0.8436 (m-80) cc_final: 0.7233 (m-80) REVERT: Q 160 TYR cc_start: 0.8711 (m-80) cc_final: 0.7866 (m-10) REVERT: Q 165 ILE cc_start: 0.8552 (tp) cc_final: 0.8246 (mm) REVERT: Q 191 THR cc_start: 0.8877 (m) cc_final: 0.8547 (p) REVERT: R 40 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6991 (ttm) REVERT: R 122 GLN cc_start: 0.8385 (mt0) cc_final: 0.8030 (mt0) REVERT: R 132 TYR cc_start: 0.8569 (m-10) cc_final: 0.8329 (m-10) REVERT: R 191 THR cc_start: 0.8841 (m) cc_final: 0.8588 (p) REVERT: R 201 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7459 (tt) REVERT: S 81 LEU cc_start: 0.7888 (mt) cc_final: 0.7594 (tt) REVERT: S 118 ASP cc_start: 0.8811 (t0) cc_final: 0.8466 (t0) REVERT: S 119 GLN cc_start: 0.8928 (tp-100) cc_final: 0.8448 (tp40) REVERT: S 121 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7338 (tm-30) REVERT: S 122 GLN cc_start: 0.8270 (mt0) cc_final: 0.7890 (mt0) REVERT: S 165 ILE cc_start: 0.8542 (tp) cc_final: 0.8311 (mm) REVERT: S 191 THR cc_start: 0.8882 (m) cc_final: 0.8546 (p) REVERT: T 40 MET cc_start: 0.7994 (pmm) cc_final: 0.7765 (pmm) REVERT: T 121 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7882 (tm-30) REVERT: T 165 ILE cc_start: 0.8513 (tp) cc_final: 0.8037 (mm) REVERT: T 191 THR cc_start: 0.8968 (m) cc_final: 0.8662 (p) REVERT: U 119 GLN cc_start: 0.9074 (tp40) cc_final: 0.8713 (tp40) REVERT: U 151 CYS cc_start: 0.7850 (t) cc_final: 0.7009 (t) REVERT: U 191 THR cc_start: 0.8981 (m) cc_final: 0.8664 (p) REVERT: U 201 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7741 (tt) outliers start: 316 outliers final: 240 residues processed: 1429 average time/residue: 0.6039 time to fit residues: 1443.1241 Evaluate side-chains 1357 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1097 time to evaluate : 5.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 104 ILE Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 122 ASP Chi-restraints excluded: chain Z residue 135 TYR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 85 ASN Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 104 ILE Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain 1 residue 9 LYS Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 43 MET Chi-restraints excluded: chain 1 residue 45 ILE Chi-restraints excluded: chain 1 residue 55 LEU Chi-restraints excluded: chain 1 residue 59 MET Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 64 GLU Chi-restraints excluded: chain 1 residue 85 ASN Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 131 SER Chi-restraints excluded: chain 1 residue 177 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 85 ASN Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 143 SER Chi-restraints excluded: chain N residue 165 ARG Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain 2 residue 9 LYS Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 55 LEU Chi-restraints excluded: chain 2 residue 84 SER Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 122 ASP Chi-restraints excluded: chain 2 residue 123 ILE Chi-restraints excluded: chain 2 residue 135 TYR Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 45 ILE Chi-restraints excluded: chain V residue 63 LEU Chi-restraints excluded: chain V residue 84 SER Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 104 ILE Chi-restraints excluded: chain V residue 110 VAL Chi-restraints excluded: chain V residue 122 ASP Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain W residue 9 LYS Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 53 GLN Chi-restraints excluded: chain W residue 59 MET Chi-restraints excluded: chain W residue 64 GLU Chi-restraints excluded: chain W residue 84 SER Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 122 ASP Chi-restraints excluded: chain W residue 123 ILE Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 177 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 193 GLU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain X residue 9 LYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 104 ILE Chi-restraints excluded: chain X residue 113 ILE Chi-restraints excluded: chain X residue 119 SER Chi-restraints excluded: chain X residue 123 ILE Chi-restraints excluded: chain X residue 127 THR Chi-restraints excluded: chain X residue 135 TYR Chi-restraints excluded: chain X residue 177 VAL Chi-restraints excluded: chain X residue 187 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 104 ILE Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 122 ASP Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Y residue 127 THR Chi-restraints excluded: chain Y residue 135 TYR Chi-restraints excluded: chain Y residue 177 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 85 ASN Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 140 SER Chi-restraints excluded: chain L residue 146 MET Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 192 ILE Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 208 LYS Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 179 GLU Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 49 ILE Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 156 THR Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 94 ILE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 156 THR Chi-restraints excluded: chain P residue 158 ASN Chi-restraints excluded: chain P residue 197 LEU Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 158 ASN Chi-restraints excluded: chain Q residue 183 ASN Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 219 ASN Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 170 ASP Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 219 ASN Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 170 ASP Chi-restraints excluded: chain S residue 219 ASN Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 156 THR Chi-restraints excluded: chain T residue 158 ASN Chi-restraints excluded: chain T residue 194 ILE Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain T residue 219 ASN Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 88 LEU Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 156 THR Chi-restraints excluded: chain U residue 158 ASN Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 201 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 350 optimal weight: 10.0000 chunk 226 optimal weight: 7.9990 chunk 338 optimal weight: 4.9990 chunk 170 optimal weight: 0.0060 chunk 111 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 360 optimal weight: 6.9990 chunk 386 optimal weight: 1.9990 chunk 280 optimal weight: 0.1980 chunk 52 optimal weight: 5.9990 chunk 445 optimal weight: 7.9990 overall best weight: 2.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 191 GLN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 36 GLN ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 GLN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 85 ASN Y 88 ASN Y 191 GLN ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN G 62 ASN O 226 GLN P 98 GLN R 98 GLN ** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 143 GLN ** S 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.6507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 47096 Z= 0.278 Angle : 0.783 24.937 63588 Z= 0.398 Chirality : 0.046 0.256 7448 Planarity : 0.004 0.050 8162 Dihedral : 6.066 56.274 6618 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.36 % Favored : 93.50 % Rotamer: Outliers : 6.33 % Allowed : 26.21 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.75 (0.11), residues: 5957 helix: 1.59 (0.11), residues: 2275 sheet: -1.13 (0.13), residues: 1309 loop : -2.26 (0.12), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS Y 28 PHE 0.030 0.002 PHE V 25 TYR 0.028 0.002 TYR T 221 ARG 0.008 0.000 ARG O 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1475 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 1158 time to evaluate : 5.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 9 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7750 (pptt) REVERT: Z 10 ASP cc_start: 0.7355 (m-30) cc_final: 0.7064 (m-30) REVERT: Z 32 LYS cc_start: 0.8463 (tppt) cc_final: 0.8118 (tppt) REVERT: Z 35 PHE cc_start: 0.8703 (m-80) cc_final: 0.8348 (m-10) REVERT: Z 37 ILE cc_start: 0.9249 (tp) cc_final: 0.8855 (tp) REVERT: Z 98 GLN cc_start: 0.8734 (mt0) cc_final: 0.8458 (tt0) REVERT: Z 139 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8134 (mm-30) REVERT: Z 180 ARG cc_start: 0.8665 (tpp80) cc_final: 0.8411 (tpp80) REVERT: M 17 GLU cc_start: 0.7410 (pp20) cc_final: 0.6687 (pp20) REVERT: M 27 MET cc_start: 0.7872 (ptm) cc_final: 0.7256 (ptm) REVERT: M 33 LYS cc_start: 0.8744 (mttm) cc_final: 0.8287 (mttp) REVERT: M 150 GLU cc_start: 0.8253 (mp0) cc_final: 0.7966 (mp0) REVERT: M 193 GLU cc_start: 0.8260 (pt0) cc_final: 0.7937 (tp30) REVERT: 1 27 MET cc_start: 0.7098 (ttt) cc_final: 0.6171 (ttt) REVERT: 1 35 PHE cc_start: 0.8417 (m-80) cc_final: 0.7835 (m-80) REVERT: 1 36 GLN cc_start: 0.8441 (tt0) cc_final: 0.8175 (tp40) REVERT: 1 62 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7764 (mm-30) REVERT: 1 63 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8771 (mm) REVERT: 1 139 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8336 (mm-30) REVERT: 1 150 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8606 (mt-10) REVERT: 1 174 ASP cc_start: 0.8565 (p0) cc_final: 0.8317 (p0) REVERT: N 14 MET cc_start: 0.8398 (mtm) cc_final: 0.8191 (mtt) REVERT: N 74 MET cc_start: 0.8287 (mmm) cc_final: 0.7684 (tpt) REVERT: N 135 TYR cc_start: 0.8333 (m-80) cc_final: 0.7425 (t80) REVERT: N 146 MET cc_start: 0.7488 (mtp) cc_final: 0.7277 (mtp) REVERT: N 153 ASP cc_start: 0.8328 (m-30) cc_final: 0.8078 (m-30) REVERT: N 193 GLU cc_start: 0.8647 (mm-30) cc_final: 0.7993 (tp30) REVERT: 2 9 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.6868 (pttp) REVERT: 2 25 PHE cc_start: 0.8534 (t80) cc_final: 0.8054 (t80) REVERT: 2 124 TYR cc_start: 0.8402 (p90) cc_final: 0.7429 (p90) REVERT: 2 127 THR cc_start: 0.9000 (OUTLIER) cc_final: 0.8751 (p) REVERT: 2 135 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.7091 (t80) REVERT: 2 198 LYS cc_start: 0.7933 (mtmt) cc_final: 0.7573 (mtmm) REVERT: H 27 MET cc_start: 0.8833 (ttt) cc_final: 0.8500 (ttt) REVERT: H 33 LYS cc_start: 0.8402 (mttm) cc_final: 0.7660 (mttp) REVERT: H 127 THR cc_start: 0.8568 (p) cc_final: 0.8310 (p) REVERT: H 135 TYR cc_start: 0.8220 (m-80) cc_final: 0.7349 (t80) REVERT: H 153 ASP cc_start: 0.8331 (m-30) cc_final: 0.8067 (m-30) REVERT: H 172 MET cc_start: 0.8386 (tpp) cc_final: 0.8115 (tpp) REVERT: H 193 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8008 (tp30) REVERT: H 198 LYS cc_start: 0.7929 (mtmm) cc_final: 0.7426 (mtmm) REVERT: V 9 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7729 (pptt) REVERT: V 32 LYS cc_start: 0.8414 (tppt) cc_final: 0.8162 (tppt) REVERT: V 35 PHE cc_start: 0.8751 (m-80) cc_final: 0.8332 (m-10) REVERT: V 37 ILE cc_start: 0.9193 (tp) cc_final: 0.8901 (tp) REVERT: V 95 TYR cc_start: 0.7792 (m-10) cc_final: 0.7588 (m-10) REVERT: V 98 GLN cc_start: 0.8675 (mt0) cc_final: 0.8310 (tt0) REVERT: V 122 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7541 (m-30) REVERT: V 139 GLU cc_start: 0.8597 (tp30) cc_final: 0.7729 (tp30) REVERT: V 144 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7945 (tp30) REVERT: I 2 THR cc_start: 0.9308 (t) cc_final: 0.9047 (m) REVERT: I 33 LYS cc_start: 0.8767 (mttm) cc_final: 0.8463 (mtmt) REVERT: I 51 ASP cc_start: 0.8503 (m-30) cc_final: 0.8140 (m-30) REVERT: I 70 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7863 (mtt180) REVERT: I 131 SER cc_start: 0.9100 (p) cc_final: 0.8643 (t) REVERT: I 149 ASP cc_start: 0.8284 (m-30) cc_final: 0.7658 (t0) REVERT: I 153 ASP cc_start: 0.8180 (m-30) cc_final: 0.7839 (m-30) REVERT: I 172 MET cc_start: 0.8148 (tpp) cc_final: 0.7944 (tpp) REVERT: I 193 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7896 (tp30) REVERT: W 9 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7818 (pptt) REVERT: W 25 PHE cc_start: 0.8504 (t80) cc_final: 0.8217 (t80) REVERT: W 27 MET cc_start: 0.7866 (ttt) cc_final: 0.7357 (ttt) REVERT: W 53 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7526 (mt0) REVERT: W 77 GLU cc_start: 0.8575 (tt0) cc_final: 0.8035 (mp0) REVERT: W 122 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7452 (m-30) REVERT: W 139 GLU cc_start: 0.8741 (tp30) cc_final: 0.7739 (tp30) REVERT: W 149 ASP cc_start: 0.8309 (m-30) cc_final: 0.8036 (m-30) REVERT: W 191 GLN cc_start: 0.8722 (mt0) cc_final: 0.8403 (tm-30) REVERT: W 193 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: J 149 ASP cc_start: 0.8568 (m-30) cc_final: 0.7956 (t0) REVERT: J 153 ASP cc_start: 0.8517 (m-30) cc_final: 0.7971 (m-30) REVERT: J 193 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8256 (pt0) REVERT: X 9 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7710 (pptt) REVERT: X 27 MET cc_start: 0.8251 (ttt) cc_final: 0.7676 (ttt) REVERT: X 74 MET cc_start: 0.8519 (ttt) cc_final: 0.8314 (ttt) REVERT: X 123 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8405 (tt) REVERT: X 124 TYR cc_start: 0.8581 (p90) cc_final: 0.7833 (p90) REVERT: X 139 GLU cc_start: 0.8608 (tp30) cc_final: 0.7810 (tp30) REVERT: X 145 LYS cc_start: 0.9319 (ttmm) cc_final: 0.9036 (tppp) REVERT: X 150 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8401 (mt-10) REVERT: X 197 ARG cc_start: 0.8084 (mtt90) cc_final: 0.7829 (mmt-90) REVERT: X 198 LYS cc_start: 0.8195 (mtmt) cc_final: 0.7842 (mtmm) REVERT: K 38 ASP cc_start: 0.8162 (t0) cc_final: 0.7875 (t0) REVERT: K 74 MET cc_start: 0.8182 (mmm) cc_final: 0.7970 (tpt) REVERT: K 131 SER cc_start: 0.9065 (p) cc_final: 0.8628 (t) REVERT: Y 27 MET cc_start: 0.7743 (ttt) cc_final: 0.7047 (ttt) REVERT: Y 35 PHE cc_start: 0.8389 (m-80) cc_final: 0.7899 (m-80) REVERT: Y 93 MET cc_start: 0.6622 (ttp) cc_final: 0.6040 (tmm) REVERT: Y 95 TYR cc_start: 0.8352 (m-80) cc_final: 0.7987 (m-10) REVERT: Y 139 GLU cc_start: 0.8738 (tp30) cc_final: 0.7883 (tp30) REVERT: Y 141 GLN cc_start: 0.9126 (mt0) cc_final: 0.8804 (mt0) REVERT: Y 150 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8684 (mt-10) REVERT: L 17 GLU cc_start: 0.7971 (pp20) cc_final: 0.7731 (pp20) REVERT: L 33 LYS cc_start: 0.8271 (mttm) cc_final: 0.7993 (mtmm) REVERT: L 35 PHE cc_start: 0.8603 (m-80) cc_final: 0.8263 (m-80) REVERT: L 135 TYR cc_start: 0.8292 (m-80) cc_final: 0.7647 (m-80) REVERT: A 60 GLU cc_start: 0.6966 (tp30) cc_final: 0.6599 (tm-30) REVERT: A 98 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7139 (tm-30) REVERT: A 110 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7416 (tm-30) REVERT: A 160 TYR cc_start: 0.8281 (m-10) cc_final: 0.7438 (m-10) REVERT: A 178 ARG cc_start: 0.7982 (ptp90) cc_final: 0.7586 (ptp90) REVERT: A 208 LYS cc_start: 0.7823 (mttt) cc_final: 0.7480 (mtpp) REVERT: A 221 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.7676 (m-80) REVERT: B 40 MET cc_start: 0.8483 (pmm) cc_final: 0.7467 (pmm) REVERT: B 59 ILE cc_start: 0.6558 (mt) cc_final: 0.6273 (mm) REVERT: B 98 GLN cc_start: 0.7815 (tp40) cc_final: 0.7048 (tm-30) REVERT: B 119 GLN cc_start: 0.8665 (tp40) cc_final: 0.8404 (tp40) REVERT: B 208 LYS cc_start: 0.7947 (mtpp) cc_final: 0.7554 (ttpt) REVERT: B 211 GLU cc_start: 0.7710 (tt0) cc_final: 0.7260 (pt0) REVERT: C 40 MET cc_start: 0.8331 (pmm) cc_final: 0.7654 (pmm) REVERT: C 98 GLN cc_start: 0.7590 (mm-40) cc_final: 0.6833 (tm-30) REVERT: C 149 PHE cc_start: 0.7996 (m-10) cc_final: 0.7569 (m-10) REVERT: C 178 ARG cc_start: 0.8118 (ptt-90) cc_final: 0.7820 (ptt90) REVERT: C 208 LYS cc_start: 0.8572 (mtpp) cc_final: 0.7780 (ptmt) REVERT: D 72 ASP cc_start: 0.8364 (m-30) cc_final: 0.8004 (m-30) REVERT: D 98 GLN cc_start: 0.7120 (mm-40) cc_final: 0.6705 (tm-30) REVERT: D 110 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7405 (tm-30) REVERT: D 114 LYS cc_start: 0.8011 (mmmm) cc_final: 0.7658 (mmmt) REVERT: D 119 GLN cc_start: 0.8798 (tp40) cc_final: 0.8523 (tp40) REVERT: D 158 ASN cc_start: 0.8117 (m-40) cc_final: 0.7915 (m-40) REVERT: D 163 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.8087 (m) REVERT: E 40 MET cc_start: 0.8474 (pmm) cc_final: 0.7551 (pmm) REVERT: E 118 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8022 (p0) REVERT: E 121 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7963 (tm-30) REVERT: E 160 TYR cc_start: 0.8467 (m-10) cc_final: 0.8033 (m-10) REVERT: E 188 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8188 (tp30) REVERT: E 208 LYS cc_start: 0.8005 (mttt) cc_final: 0.7561 (mtpp) REVERT: F 91 PHE cc_start: 0.8387 (t80) cc_final: 0.8111 (t80) REVERT: F 98 GLN cc_start: 0.7726 (mm110) cc_final: 0.7050 (tm-30) REVERT: F 121 GLN cc_start: 0.8353 (tm-30) cc_final: 0.8097 (tm-30) REVERT: F 208 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7536 (ptmt) REVERT: G 98 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7461 (tm-30) REVERT: G 115 ARG cc_start: 0.7956 (mpt-90) cc_final: 0.7558 (mtt90) REVERT: G 119 GLN cc_start: 0.8876 (tp40) cc_final: 0.8550 (tp40) REVERT: G 178 ARG cc_start: 0.8162 (ptt-90) cc_final: 0.7631 (ptt90) REVERT: G 179 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8175 (mm-30) REVERT: G 228 GLU cc_start: 0.8652 (tt0) cc_final: 0.8198 (tp30) REVERT: O 121 GLN cc_start: 0.8432 (tm-30) cc_final: 0.8013 (tm-30) REVERT: O 123 TYR cc_start: 0.9187 (m-10) cc_final: 0.8541 (m-10) REVERT: O 132 TYR cc_start: 0.8551 (m-80) cc_final: 0.7607 (m-80) REVERT: O 158 ASN cc_start: 0.7774 (m110) cc_final: 0.7536 (m-40) REVERT: O 160 TYR cc_start: 0.8354 (m-80) cc_final: 0.7786 (m-80) REVERT: O 183 ASN cc_start: 0.8328 (m110) cc_final: 0.7562 (p0) REVERT: P 40 MET cc_start: 0.7473 (ptp) cc_final: 0.7242 (pmm) REVERT: P 47 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8444 (pt) REVERT: P 115 ARG cc_start: 0.8067 (ttm170) cc_final: 0.7787 (ttm170) REVERT: P 119 GLN cc_start: 0.8968 (tp40) cc_final: 0.8578 (tp40) REVERT: P 165 ILE cc_start: 0.8512 (tp) cc_final: 0.8202 (mm) REVERT: P 208 LYS cc_start: 0.6205 (OUTLIER) cc_final: 0.5593 (ttmt) REVERT: Q 119 GLN cc_start: 0.8713 (tp-100) cc_final: 0.8434 (tp40) REVERT: Q 121 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7728 (tm-30) REVERT: Q 132 TYR cc_start: 0.8453 (m-80) cc_final: 0.7591 (m-80) REVERT: Q 160 TYR cc_start: 0.8666 (m-80) cc_final: 0.8433 (m-80) REVERT: Q 165 ILE cc_start: 0.8519 (tp) cc_final: 0.8226 (mm) REVERT: Q 191 THR cc_start: 0.8875 (m) cc_final: 0.8543 (p) REVERT: R 119 GLN cc_start: 0.9050 (tp40) cc_final: 0.8520 (tp40) REVERT: R 122 GLN cc_start: 0.8316 (mt0) cc_final: 0.8090 (mt0) REVERT: R 191 THR cc_start: 0.8845 (m) cc_final: 0.8589 (p) REVERT: R 201 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7478 (tt) REVERT: S 81 LEU cc_start: 0.7959 (mt) cc_final: 0.7703 (tt) REVERT: S 118 ASP cc_start: 0.8840 (t0) cc_final: 0.8498 (t0) REVERT: S 119 GLN cc_start: 0.8928 (tp-100) cc_final: 0.8474 (tp40) REVERT: S 121 GLN cc_start: 0.7770 (tm-30) cc_final: 0.7336 (tm-30) REVERT: S 122 GLN cc_start: 0.8259 (mt0) cc_final: 0.7859 (mt0) REVERT: S 143 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8474 (mp10) REVERT: S 165 ILE cc_start: 0.8467 (tp) cc_final: 0.8237 (mm) REVERT: S 191 THR cc_start: 0.8887 (m) cc_final: 0.8545 (p) REVERT: T 40 MET cc_start: 0.7970 (pmm) cc_final: 0.7695 (pmm) REVERT: T 121 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7903 (tm-30) REVERT: T 123 TYR cc_start: 0.8160 (m-10) cc_final: 0.7857 (m-10) REVERT: T 160 TYR cc_start: 0.8417 (m-80) cc_final: 0.7131 (m-10) REVERT: T 165 ILE cc_start: 0.8437 (tp) cc_final: 0.7972 (mm) REVERT: T 191 THR cc_start: 0.8957 (m) cc_final: 0.8633 (p) REVERT: T 208 LYS cc_start: 0.6352 (OUTLIER) cc_final: 0.6142 (mttt) REVERT: U 119 GLN cc_start: 0.9068 (tp40) cc_final: 0.8633 (tp40) REVERT: U 120 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8156 (mtm) REVERT: U 151 CYS cc_start: 0.8231 (t) cc_final: 0.7494 (t) REVERT: U 191 THR cc_start: 0.9024 (m) cc_final: 0.8696 (p) REVERT: U 201 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7621 (tt) outliers start: 317 outliers final: 254 residues processed: 1384 average time/residue: 0.5484 time to fit residues: 1262.8251 Evaluate side-chains 1392 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1111 time to evaluate : 5.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 64 GLU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 104 ILE Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 122 ASP Chi-restraints excluded: chain Z residue 135 TYR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 59 MET Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 85 ASN Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 104 ILE Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 43 MET Chi-restraints excluded: chain 1 residue 45 ILE Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 64 GLU Chi-restraints excluded: chain 1 residue 85 ASN Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 110 VAL Chi-restraints excluded: chain 1 residue 131 SER Chi-restraints excluded: chain 1 residue 177 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 123 ILE Chi-restraints excluded: chain N residue 143 SER Chi-restraints excluded: chain N residue 165 ARG Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain 2 residue 9 LYS Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 55 LEU Chi-restraints excluded: chain 2 residue 84 SER Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 122 ASP Chi-restraints excluded: chain 2 residue 123 ILE Chi-restraints excluded: chain 2 residue 127 THR Chi-restraints excluded: chain 2 residue 135 TYR Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain V residue 9 LYS Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 45 ILE Chi-restraints excluded: chain V residue 63 LEU Chi-restraints excluded: chain V residue 84 SER Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 104 ILE Chi-restraints excluded: chain V residue 110 VAL Chi-restraints excluded: chain V residue 122 ASP Chi-restraints excluded: chain I residue 9 LYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 70 ARG Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain W residue 9 LYS Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 53 GLN Chi-restraints excluded: chain W residue 59 MET Chi-restraints excluded: chain W residue 64 GLU Chi-restraints excluded: chain W residue 84 SER Chi-restraints excluded: chain W residue 85 ASN Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 119 SER Chi-restraints excluded: chain W residue 122 ASP Chi-restraints excluded: chain W residue 123 ILE Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 177 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 193 GLU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain X residue 9 LYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 104 ILE Chi-restraints excluded: chain X residue 113 ILE Chi-restraints excluded: chain X residue 119 SER Chi-restraints excluded: chain X residue 123 ILE Chi-restraints excluded: chain X residue 127 THR Chi-restraints excluded: chain X residue 135 TYR Chi-restraints excluded: chain X residue 187 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 104 ILE Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 122 ASP Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Y residue 127 THR Chi-restraints excluded: chain Y residue 135 TYR Chi-restraints excluded: chain Y residue 177 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 85 ASN Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 140 SER Chi-restraints excluded: chain L residue 146 MET Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 192 ILE Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 208 LYS Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 179 GLU Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 49 ILE Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 156 THR Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 94 ILE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 156 THR Chi-restraints excluded: chain P residue 158 ASN Chi-restraints excluded: chain P residue 208 LYS Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 8 TYR Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 94 ILE Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 158 ASN Chi-restraints excluded: chain Q residue 170 ASP Chi-restraints excluded: chain Q residue 183 ASN Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 219 ASN Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 143 GLN Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 158 ASN Chi-restraints excluded: chain S residue 170 ASP Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 219 ASN Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 156 THR Chi-restraints excluded: chain T residue 158 ASN Chi-restraints excluded: chain T residue 194 ILE Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain T residue 208 LYS Chi-restraints excluded: chain T residue 219 ASN Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 120 MET Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 156 THR Chi-restraints excluded: chain U residue 158 ASN Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 201 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 515 optimal weight: 8.9990 chunk 542 optimal weight: 0.4980 chunk 495 optimal weight: 10.0000 chunk 528 optimal weight: 2.9990 chunk 317 optimal weight: 1.9990 chunk 230 optimal weight: 0.1980 chunk 414 optimal weight: 7.9990 chunk 162 optimal weight: 0.7980 chunk 477 optimal weight: 0.2980 chunk 499 optimal weight: 5.9990 chunk 526 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 36 GLN Z 191 GLN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 ASN ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 88 ASN H 36 GLN ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 36 GLN ** W 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 ASN ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 36 GLN Y 88 ASN L 85 ASN ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN B 23 GLN D 62 ASN D 125 GLN F 62 ASN ** G 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 183 ASN R 98 GLN ** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 125 GLN ** T 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.6631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 47096 Z= 0.203 Angle : 0.759 24.021 63588 Z= 0.384 Chirality : 0.045 0.243 7448 Planarity : 0.004 0.050 8162 Dihedral : 5.867 54.563 6618 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.13 % Favored : 93.79 % Rotamer: Outliers : 5.45 % Allowed : 27.37 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.61 (0.11), residues: 5957 helix: 1.82 (0.11), residues: 2247 sheet: -1.15 (0.14), residues: 1232 loop : -2.18 (0.11), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS W 109 PHE 0.025 0.001 PHE V 25 TYR 0.030 0.001 TYR I 66 ARG 0.009 0.000 ARG O 178 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1531 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1258 time to evaluate : 5.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 9 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7628 (pptt) REVERT: Z 25 PHE cc_start: 0.8282 (t80) cc_final: 0.7648 (t80) REVERT: Z 27 MET cc_start: 0.7501 (ptm) cc_final: 0.6857 (ptm) REVERT: Z 32 LYS cc_start: 0.8435 (tppt) cc_final: 0.8110 (tppt) REVERT: Z 35 PHE cc_start: 0.8624 (m-80) cc_final: 0.8325 (m-10) REVERT: Z 37 ILE cc_start: 0.9230 (tp) cc_final: 0.8895 (tp) REVERT: Z 98 GLN cc_start: 0.8849 (mt0) cc_final: 0.8510 (tt0) REVERT: Z 146 MET cc_start: 0.8726 (mtp) cc_final: 0.8522 (ptm) REVERT: Z 180 ARG cc_start: 0.8673 (tpp80) cc_final: 0.8377 (tpp80) REVERT: M 17 GLU cc_start: 0.7317 (pp20) cc_final: 0.6632 (pp20) REVERT: M 27 MET cc_start: 0.7508 (ptm) cc_final: 0.6941 (ptm) REVERT: M 33 LYS cc_start: 0.8659 (mttm) cc_final: 0.8210 (mttp) REVERT: M 36 GLN cc_start: 0.9047 (tt0) cc_final: 0.8837 (tt0) REVERT: M 95 TYR cc_start: 0.8919 (m-80) cc_final: 0.8613 (m-80) REVERT: M 98 GLN cc_start: 0.8670 (mt0) cc_final: 0.8184 (mp10) REVERT: M 149 ASP cc_start: 0.8023 (t0) cc_final: 0.7661 (t0) REVERT: M 153 ASP cc_start: 0.8094 (m-30) cc_final: 0.7697 (m-30) REVERT: M 193 GLU cc_start: 0.8209 (pt0) cc_final: 0.7860 (tp30) REVERT: 1 35 PHE cc_start: 0.8373 (m-80) cc_final: 0.7755 (m-80) REVERT: 1 36 GLN cc_start: 0.8411 (tt0) cc_final: 0.8113 (tp40) REVERT: 1 62 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7788 (mm-30) REVERT: 1 95 TYR cc_start: 0.8434 (m-80) cc_final: 0.8079 (m-80) REVERT: 1 139 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8041 (mm-30) REVERT: 1 150 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8636 (mt-10) REVERT: 1 174 ASP cc_start: 0.8550 (p0) cc_final: 0.8331 (p0) REVERT: 1 193 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6989 (mt-10) REVERT: N 2 THR cc_start: 0.9313 (t) cc_final: 0.9046 (m) REVERT: N 51 ASP cc_start: 0.8191 (m-30) cc_final: 0.7876 (t0) REVERT: N 74 MET cc_start: 0.8127 (mmm) cc_final: 0.7498 (tpt) REVERT: N 135 TYR cc_start: 0.8298 (m-80) cc_final: 0.7371 (t80) REVERT: N 153 ASP cc_start: 0.8222 (m-30) cc_final: 0.8017 (m-30) REVERT: N 193 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7955 (tp30) REVERT: 2 9 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.6905 (pttp) REVERT: 2 12 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8468 (p) REVERT: 2 124 TYR cc_start: 0.8343 (p90) cc_final: 0.7802 (p90) REVERT: 2 127 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8685 (p) REVERT: 2 141 GLN cc_start: 0.8853 (mt0) cc_final: 0.8363 (mt0) REVERT: 2 150 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8377 (mt-10) REVERT: 2 198 LYS cc_start: 0.7844 (mtmt) cc_final: 0.7486 (mtmt) REVERT: H 33 LYS cc_start: 0.8280 (mttm) cc_final: 0.7563 (mttp) REVERT: H 127 THR cc_start: 0.8539 (p) cc_final: 0.8299 (p) REVERT: H 135 TYR cc_start: 0.8074 (m-80) cc_final: 0.7216 (t80) REVERT: H 153 ASP cc_start: 0.8372 (m-30) cc_final: 0.8145 (m-30) REVERT: H 172 MET cc_start: 0.8317 (tpp) cc_final: 0.8051 (tpp) REVERT: H 193 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7981 (tp30) REVERT: H 198 LYS cc_start: 0.7921 (mtmm) cc_final: 0.7413 (mtmm) REVERT: V 32 LYS cc_start: 0.8354 (tppt) cc_final: 0.8114 (tppt) REVERT: V 35 PHE cc_start: 0.8665 (m-80) cc_final: 0.8290 (m-10) REVERT: V 37 ILE cc_start: 0.9135 (tp) cc_final: 0.8834 (tp) REVERT: V 95 TYR cc_start: 0.7615 (m-10) cc_final: 0.7406 (m-10) REVERT: V 139 GLU cc_start: 0.8449 (tp30) cc_final: 0.7631 (tp30) REVERT: V 144 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7964 (tp30) REVERT: I 2 THR cc_start: 0.9308 (t) cc_final: 0.9045 (m) REVERT: I 33 LYS cc_start: 0.8690 (mttm) cc_final: 0.8422 (mtmt) REVERT: I 43 MET cc_start: 0.7907 (ttm) cc_final: 0.7639 (ttp) REVERT: I 51 ASP cc_start: 0.8281 (m-30) cc_final: 0.8002 (m-30) REVERT: I 131 SER cc_start: 0.9095 (p) cc_final: 0.8666 (t) REVERT: I 149 ASP cc_start: 0.8259 (m-30) cc_final: 0.7714 (t0) REVERT: I 153 ASP cc_start: 0.8160 (m-30) cc_final: 0.7857 (m-30) REVERT: I 172 MET cc_start: 0.8209 (tpp) cc_final: 0.7956 (tpp) REVERT: I 193 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8103 (pt0) REVERT: W 25 PHE cc_start: 0.8483 (t80) cc_final: 0.8133 (t80) REVERT: W 53 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7571 (mt0) REVERT: W 62 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7611 (mm-30) REVERT: W 77 GLU cc_start: 0.8443 (tt0) cc_final: 0.7978 (mp0) REVERT: W 95 TYR cc_start: 0.8666 (m-80) cc_final: 0.8296 (m-80) REVERT: W 122 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7098 (m-30) REVERT: W 124 TYR cc_start: 0.8386 (p90) cc_final: 0.7714 (p90) REVERT: W 139 GLU cc_start: 0.8677 (tp30) cc_final: 0.8051 (tp30) REVERT: W 149 ASP cc_start: 0.8160 (m-30) cc_final: 0.7879 (m-30) REVERT: W 191 GLN cc_start: 0.8723 (mt0) cc_final: 0.8407 (tm-30) REVERT: W 193 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: J 97 VAL cc_start: 0.9340 (p) cc_final: 0.9111 (m) REVERT: J 149 ASP cc_start: 0.8573 (m-30) cc_final: 0.8007 (t0) REVERT: J 153 ASP cc_start: 0.8505 (m-30) cc_final: 0.8025 (m-30) REVERT: J 193 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8227 (pt0) REVERT: X 123 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8405 (tt) REVERT: X 124 TYR cc_start: 0.8461 (p90) cc_final: 0.7409 (p90) REVERT: X 135 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.7247 (t80) REVERT: X 139 GLU cc_start: 0.8452 (tp30) cc_final: 0.7567 (tp30) REVERT: X 145 LYS cc_start: 0.9271 (ttmm) cc_final: 0.9051 (mmmm) REVERT: X 150 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8428 (mt-10) REVERT: X 197 ARG cc_start: 0.8089 (mtt90) cc_final: 0.7663 (mpt180) REVERT: X 198 LYS cc_start: 0.8157 (mtmt) cc_final: 0.7796 (mtmm) REVERT: K 38 ASP cc_start: 0.7969 (t0) cc_final: 0.7737 (t0) REVERT: K 51 ASP cc_start: 0.7868 (m-30) cc_final: 0.7657 (m-30) REVERT: K 74 MET cc_start: 0.8096 (mmm) cc_final: 0.7880 (tpt) REVERT: K 131 SER cc_start: 0.9006 (p) cc_final: 0.8628 (t) REVERT: K 149 ASP cc_start: 0.8006 (t0) cc_final: 0.7331 (t0) REVERT: K 153 ASP cc_start: 0.8298 (m-30) cc_final: 0.7809 (m-30) REVERT: Y 9 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7604 (pptt) REVERT: Y 27 MET cc_start: 0.7671 (ttt) cc_final: 0.7244 (ttt) REVERT: Y 35 PHE cc_start: 0.8278 (m-80) cc_final: 0.7731 (m-80) REVERT: Y 93 MET cc_start: 0.6539 (ttp) cc_final: 0.6187 (tmm) REVERT: Y 95 TYR cc_start: 0.8131 (m-80) cc_final: 0.7837 (m-10) REVERT: Y 139 GLU cc_start: 0.8547 (tp30) cc_final: 0.7657 (tp30) REVERT: Y 141 GLN cc_start: 0.9062 (mt0) cc_final: 0.8755 (mt0) REVERT: Y 150 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8346 (mt-10) REVERT: L 17 GLU cc_start: 0.7925 (pp20) cc_final: 0.7483 (pp20) REVERT: L 33 LYS cc_start: 0.8101 (mttm) cc_final: 0.7888 (mtmm) REVERT: L 35 PHE cc_start: 0.8515 (m-80) cc_final: 0.8125 (m-10) REVERT: L 66 TYR cc_start: 0.8582 (t80) cc_final: 0.8380 (t80) REVERT: L 135 TYR cc_start: 0.8246 (m-80) cc_final: 0.7624 (m-80) REVERT: L 149 ASP cc_start: 0.7758 (t0) cc_final: 0.7136 (t0) REVERT: L 153 ASP cc_start: 0.8187 (m-30) cc_final: 0.7789 (m-30) REVERT: A 60 GLU cc_start: 0.6714 (tp30) cc_final: 0.6349 (tm-30) REVERT: A 98 GLN cc_start: 0.7615 (mm-40) cc_final: 0.7127 (tm-30) REVERT: A 125 GLN cc_start: 0.8031 (tt0) cc_final: 0.7738 (tt0) REVERT: A 158 ASN cc_start: 0.8186 (m-40) cc_final: 0.6508 (m110) REVERT: A 160 TYR cc_start: 0.8392 (m-10) cc_final: 0.7857 (m-10) REVERT: A 188 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8122 (tp30) REVERT: A 208 LYS cc_start: 0.7879 (mttt) cc_final: 0.7446 (mtpp) REVERT: A 221 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.7383 (m-10) REVERT: A 225 ASP cc_start: 0.7916 (p0) cc_final: 0.7349 (p0) REVERT: B 40 MET cc_start: 0.8368 (pmm) cc_final: 0.7356 (pmm) REVERT: B 59 ILE cc_start: 0.6655 (mt) cc_final: 0.6368 (mm) REVERT: B 98 GLN cc_start: 0.7728 (tp40) cc_final: 0.7002 (tm-30) REVERT: B 115 ARG cc_start: 0.7603 (mpt180) cc_final: 0.7196 (mtt90) REVERT: B 119 GLN cc_start: 0.8666 (tp40) cc_final: 0.8378 (tp40) REVERT: B 211 GLU cc_start: 0.7904 (tt0) cc_final: 0.7444 (pt0) REVERT: C 40 MET cc_start: 0.8420 (pmm) cc_final: 0.7743 (pmm) REVERT: C 98 GLN cc_start: 0.7421 (mm-40) cc_final: 0.6782 (tm-30) REVERT: C 119 GLN cc_start: 0.8928 (tp40) cc_final: 0.8723 (tp40) REVERT: C 121 GLN cc_start: 0.8312 (tm-30) cc_final: 0.8099 (tm-30) REVERT: C 178 ARG cc_start: 0.8113 (ptt-90) cc_final: 0.7769 (ptt90) REVERT: C 188 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8431 (tp30) REVERT: D 72 ASP cc_start: 0.8326 (m-30) cc_final: 0.7978 (m-30) REVERT: D 98 GLN cc_start: 0.7075 (mm-40) cc_final: 0.6667 (tm-30) REVERT: D 110 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7260 (tm-30) REVERT: D 114 LYS cc_start: 0.8170 (mmmm) cc_final: 0.7842 (mmmm) REVERT: D 158 ASN cc_start: 0.8128 (m-40) cc_final: 0.7916 (m-40) REVERT: D 163 THR cc_start: 0.8230 (OUTLIER) cc_final: 0.7999 (m) REVERT: E 40 MET cc_start: 0.8476 (pmm) cc_final: 0.8033 (pmm) REVERT: E 118 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8091 (p0) REVERT: E 188 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8207 (tp30) REVERT: E 208 LYS cc_start: 0.7929 (mttt) cc_final: 0.7548 (mtpp) REVERT: F 98 GLN cc_start: 0.7655 (mm110) cc_final: 0.7043 (tm-30) REVERT: F 114 LYS cc_start: 0.8182 (mmmm) cc_final: 0.7949 (mmmm) REVERT: F 121 GLN cc_start: 0.8293 (tm-30) cc_final: 0.8007 (tm-30) REVERT: F 208 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7611 (ptmt) REVERT: F 221 TYR cc_start: 0.8102 (m-80) cc_final: 0.7619 (m-80) REVERT: G 98 GLN cc_start: 0.8007 (mm110) cc_final: 0.7429 (tm-30) REVERT: G 115 ARG cc_start: 0.7907 (mpt-90) cc_final: 0.7549 (mtt90) REVERT: G 119 GLN cc_start: 0.8806 (tp40) cc_final: 0.8536 (tp40) REVERT: G 178 ARG cc_start: 0.8159 (ptt-90) cc_final: 0.7677 (ptt90) REVERT: G 179 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8095 (mm-30) REVERT: G 228 GLU cc_start: 0.8669 (tt0) cc_final: 0.8162 (tp30) REVERT: O 121 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7642 (tm-30) REVERT: O 123 TYR cc_start: 0.9096 (m-10) cc_final: 0.8456 (m-10) REVERT: O 132 TYR cc_start: 0.8665 (m-80) cc_final: 0.7739 (m-80) REVERT: O 158 ASN cc_start: 0.7842 (m110) cc_final: 0.7634 (m-40) REVERT: O 160 TYR cc_start: 0.8349 (m-80) cc_final: 0.7740 (m-80) REVERT: O 165 ILE cc_start: 0.8760 (tp) cc_final: 0.8340 (pt) REVERT: O 180 TYR cc_start: 0.8344 (t80) cc_final: 0.8052 (t80) REVERT: O 183 ASN cc_start: 0.8310 (m-40) cc_final: 0.7390 (p0) REVERT: P 40 MET cc_start: 0.7324 (ptp) cc_final: 0.7023 (pmm) REVERT: P 47 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8407 (pt) REVERT: P 115 ARG cc_start: 0.8038 (ttm170) cc_final: 0.7763 (ttm170) REVERT: P 160 TYR cc_start: 0.8618 (m-80) cc_final: 0.7520 (m-80) REVERT: P 165 ILE cc_start: 0.8481 (tp) cc_final: 0.8168 (mm) REVERT: P 208 LYS cc_start: 0.6012 (OUTLIER) cc_final: 0.5494 (ttmt) REVERT: Q 8 TYR cc_start: 0.5286 (OUTLIER) cc_final: 0.3771 (t80) REVERT: Q 121 GLN cc_start: 0.7811 (tm-30) cc_final: 0.7557 (tm-30) REVERT: Q 123 TYR cc_start: 0.9034 (m-80) cc_final: 0.8139 (m-10) REVERT: Q 132 TYR cc_start: 0.8493 (m-80) cc_final: 0.7479 (m-80) REVERT: Q 160 TYR cc_start: 0.8555 (m-80) cc_final: 0.7784 (m-80) REVERT: Q 165 ILE cc_start: 0.8464 (tp) cc_final: 0.8218 (mm) REVERT: Q 191 THR cc_start: 0.8835 (m) cc_final: 0.8494 (p) REVERT: Q 201 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7786 (tt) REVERT: R 122 GLN cc_start: 0.8272 (mt0) cc_final: 0.7927 (mt0) REVERT: R 191 THR cc_start: 0.8800 (m) cc_final: 0.8549 (p) REVERT: R 211 GLU cc_start: 0.6697 (pt0) cc_final: 0.6493 (pt0) REVERT: S 81 LEU cc_start: 0.7989 (mt) cc_final: 0.7687 (tt) REVERT: S 119 GLN cc_start: 0.8812 (tp-100) cc_final: 0.8403 (tp40) REVERT: S 122 GLN cc_start: 0.8298 (mt0) cc_final: 0.7878 (mt0) REVERT: S 165 ILE cc_start: 0.8419 (tp) cc_final: 0.8195 (mm) REVERT: S 191 THR cc_start: 0.8850 (m) cc_final: 0.8506 (p) REVERT: T 121 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7858 (tm-30) REVERT: T 123 TYR cc_start: 0.8068 (m-10) cc_final: 0.7719 (m-10) REVERT: T 125 GLN cc_start: 0.7100 (tp-100) cc_final: 0.6811 (tp-100) REVERT: T 160 TYR cc_start: 0.8421 (m-80) cc_final: 0.7078 (m-10) REVERT: T 165 ILE cc_start: 0.8426 (tp) cc_final: 0.8011 (mm) REVERT: T 191 THR cc_start: 0.8926 (m) cc_final: 0.8568 (p) REVERT: T 201 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7411 (tt) REVERT: U 119 GLN cc_start: 0.9108 (tp40) cc_final: 0.8679 (tp40) REVERT: U 120 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8067 (mtm) REVERT: U 151 CYS cc_start: 0.8161 (t) cc_final: 0.7637 (t) REVERT: U 191 THR cc_start: 0.8984 (m) cc_final: 0.8652 (p) REVERT: U 201 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7624 (tt) outliers start: 273 outliers final: 192 residues processed: 1443 average time/residue: 0.5555 time to fit residues: 1334.8247 Evaluate side-chains 1380 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1166 time to evaluate : 5.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain Z residue 64 GLU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 104 ILE Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 135 TYR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 85 ASN Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 43 MET Chi-restraints excluded: chain 1 residue 64 GLU Chi-restraints excluded: chain 1 residue 85 ASN Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 110 VAL Chi-restraints excluded: chain 1 residue 131 SER Chi-restraints excluded: chain 1 residue 177 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 85 ASN Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 123 ILE Chi-restraints excluded: chain N residue 143 SER Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain 2 residue 9 LYS Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 55 LEU Chi-restraints excluded: chain 2 residue 84 SER Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 122 ASP Chi-restraints excluded: chain 2 residue 123 ILE Chi-restraints excluded: chain 2 residue 127 THR Chi-restraints excluded: chain 2 residue 135 TYR Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 45 ILE Chi-restraints excluded: chain V residue 84 SER Chi-restraints excluded: chain V residue 104 ILE Chi-restraints excluded: chain V residue 110 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 53 GLN Chi-restraints excluded: chain W residue 64 GLU Chi-restraints excluded: chain W residue 84 SER Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 122 ASP Chi-restraints excluded: chain W residue 123 ILE Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 177 VAL Chi-restraints excluded: chain W residue 193 GLU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 104 ILE Chi-restraints excluded: chain X residue 119 SER Chi-restraints excluded: chain X residue 123 ILE Chi-restraints excluded: chain X residue 127 THR Chi-restraints excluded: chain X residue 135 TYR Chi-restraints excluded: chain X residue 187 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain Y residue 9 LYS Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 104 ILE Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Y residue 127 THR Chi-restraints excluded: chain Y residue 135 TYR Chi-restraints excluded: chain Y residue 177 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 85 ASN Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 146 MET Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 192 ILE Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 208 LYS Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 179 GLU Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 156 THR Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 94 ILE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 156 THR Chi-restraints excluded: chain P residue 158 ASN Chi-restraints excluded: chain P residue 191 THR Chi-restraints excluded: chain P residue 197 LEU Chi-restraints excluded: chain P residue 208 LYS Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 8 TYR Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 158 ASN Chi-restraints excluded: chain Q residue 170 ASP Chi-restraints excluded: chain Q residue 183 ASN Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 219 ASN Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 170 ASP Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 158 ASN Chi-restraints excluded: chain S residue 170 ASP Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 219 ASN Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 156 THR Chi-restraints excluded: chain T residue 158 ASN Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 120 MET Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 156 THR Chi-restraints excluded: chain U residue 158 ASN Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 346 optimal weight: 0.0770 chunk 558 optimal weight: 0.0670 chunk 340 optimal weight: 0.9990 chunk 264 optimal weight: 9.9990 chunk 388 optimal weight: 0.0980 chunk 585 optimal weight: 4.9990 chunk 539 optimal weight: 5.9990 chunk 466 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 360 optimal weight: 6.9990 chunk 286 optimal weight: 2.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 191 GLN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 ASN ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 88 ASN H 36 GLN ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 36 GLN ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 ASN ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 85 ASN X 98 GLN ** Y 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 ASN ** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.6770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 47096 Z= 0.204 Angle : 0.789 24.192 63588 Z= 0.397 Chirality : 0.046 0.291 7448 Planarity : 0.004 0.050 8162 Dihedral : 5.746 54.132 6615 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.99 % Favored : 93.92 % Rotamer: Outliers : 4.34 % Allowed : 28.63 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.60 (0.11), residues: 5957 helix: 1.83 (0.11), residues: 2247 sheet: -1.27 (0.13), residues: 1260 loop : -2.10 (0.11), residues: 2450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS 2 28 PHE 0.026 0.001 PHE V 25 TYR 0.023 0.001 TYR Z 66 ARG 0.009 0.000 ARG O 178 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11914 Ramachandran restraints generated. 5957 Oldfield, 0 Emsley, 5957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1482 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1265 time to evaluate : 5.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 9 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7527 (pptt) REVERT: Z 25 PHE cc_start: 0.8156 (t80) cc_final: 0.7506 (t80) REVERT: Z 27 MET cc_start: 0.7357 (ptm) cc_final: 0.6771 (ptm) REVERT: Z 32 LYS cc_start: 0.8409 (tppt) cc_final: 0.7983 (tppt) REVERT: Z 35 PHE cc_start: 0.8596 (m-80) cc_final: 0.8286 (m-10) REVERT: Z 37 ILE cc_start: 0.9252 (tp) cc_final: 0.8951 (tp) REVERT: Z 98 GLN cc_start: 0.8835 (mt0) cc_final: 0.8508 (tt0) REVERT: Z 141 GLN cc_start: 0.8870 (mt0) cc_final: 0.8545 (mt0) REVERT: Z 146 MET cc_start: 0.8699 (mtp) cc_final: 0.8493 (ptm) REVERT: Z 150 GLU cc_start: 0.8941 (mt-10) cc_final: 0.7997 (mt-10) REVERT: Z 180 ARG cc_start: 0.8658 (tpp80) cc_final: 0.8362 (tpp80) REVERT: M 17 GLU cc_start: 0.7298 (pp20) cc_final: 0.6707 (pp20) REVERT: M 27 MET cc_start: 0.7769 (ptm) cc_final: 0.7220 (ptm) REVERT: M 33 LYS cc_start: 0.8617 (mttm) cc_final: 0.8397 (mtmm) REVERT: M 95 TYR cc_start: 0.8845 (m-80) cc_final: 0.8456 (m-80) REVERT: M 98 GLN cc_start: 0.8741 (mt0) cc_final: 0.8380 (mp10) REVERT: M 149 ASP cc_start: 0.7829 (t0) cc_final: 0.7340 (t0) REVERT: M 153 ASP cc_start: 0.8050 (m-30) cc_final: 0.7658 (m-30) REVERT: M 193 GLU cc_start: 0.8240 (pt0) cc_final: 0.7830 (tp30) REVERT: 1 25 PHE cc_start: 0.8438 (t80) cc_final: 0.8238 (t80) REVERT: 1 35 PHE cc_start: 0.8313 (m-80) cc_final: 0.7664 (m-80) REVERT: 1 36 GLN cc_start: 0.8392 (tt0) cc_final: 0.8103 (tp40) REVERT: 1 62 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7789 (mm-30) REVERT: 1 95 TYR cc_start: 0.8354 (m-80) cc_final: 0.7993 (m-80) REVERT: 1 139 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8119 (mm-30) REVERT: 1 150 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8524 (mt-10) REVERT: 1 174 ASP cc_start: 0.8448 (p0) cc_final: 0.8232 (p0) REVERT: 1 193 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6985 (mt-10) REVERT: N 2 THR cc_start: 0.9298 (t) cc_final: 0.9038 (m) REVERT: N 74 MET cc_start: 0.8107 (mmm) cc_final: 0.7463 (tpt) REVERT: N 98 GLN cc_start: 0.8687 (mt0) cc_final: 0.8302 (mp10) REVERT: N 135 TYR cc_start: 0.8314 (m-80) cc_final: 0.7441 (t80) REVERT: N 153 ASP cc_start: 0.8189 (m-30) cc_final: 0.7861 (m-30) REVERT: N 193 GLU cc_start: 0.8616 (mm-30) cc_final: 0.7953 (tp30) REVERT: 2 9 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.6845 (pttp) REVERT: 2 10 ASP cc_start: 0.7166 (m-30) cc_final: 0.6821 (m-30) REVERT: 2 12 VAL cc_start: 0.8705 (OUTLIER) cc_final: 0.8453 (p) REVERT: 2 124 TYR cc_start: 0.8465 (p90) cc_final: 0.7042 (p90) REVERT: 2 127 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8724 (p) REVERT: 2 139 GLU cc_start: 0.8255 (tp30) cc_final: 0.7295 (tp30) REVERT: 2 141 GLN cc_start: 0.8834 (mt0) cc_final: 0.8338 (mt0) REVERT: 2 150 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8366 (mt-10) REVERT: 2 198 LYS cc_start: 0.7931 (mtmt) cc_final: 0.7578 (mtmm) REVERT: H 33 LYS cc_start: 0.8196 (mttm) cc_final: 0.7499 (mttp) REVERT: H 127 THR cc_start: 0.8584 (p) cc_final: 0.8351 (p) REVERT: H 153 ASP cc_start: 0.8357 (m-30) cc_final: 0.8112 (m-30) REVERT: H 172 MET cc_start: 0.8337 (tpp) cc_final: 0.8037 (tpp) REVERT: H 193 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7919 (tp30) REVERT: H 198 LYS cc_start: 0.7848 (mtmm) cc_final: 0.7321 (mtmm) REVERT: V 32 LYS cc_start: 0.8327 (tppt) cc_final: 0.8087 (tppt) REVERT: V 35 PHE cc_start: 0.8547 (m-80) cc_final: 0.8188 (m-10) REVERT: V 37 ILE cc_start: 0.9107 (tp) cc_final: 0.8805 (tp) REVERT: V 95 TYR cc_start: 0.7570 (m-10) cc_final: 0.7323 (m-10) REVERT: V 139 GLU cc_start: 0.8340 (tp30) cc_final: 0.7531 (tp30) REVERT: V 144 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7955 (tp30) REVERT: I 2 THR cc_start: 0.9368 (t) cc_final: 0.9100 (m) REVERT: I 36 GLN cc_start: 0.8753 (tt0) cc_final: 0.8528 (tt0) REVERT: I 43 MET cc_start: 0.7786 (ttm) cc_final: 0.7503 (ttp) REVERT: I 131 SER cc_start: 0.9079 (p) cc_final: 0.8495 (t) REVERT: I 135 TYR cc_start: 0.8055 (m-80) cc_final: 0.7637 (m-80) REVERT: I 149 ASP cc_start: 0.8248 (m-30) cc_final: 0.7680 (t0) REVERT: I 153 ASP cc_start: 0.8085 (m-30) cc_final: 0.7800 (m-30) REVERT: I 172 MET cc_start: 0.8171 (tpp) cc_final: 0.7909 (tpp) REVERT: I 193 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7773 (tp30) REVERT: W 25 PHE cc_start: 0.8653 (t80) cc_final: 0.8317 (t80) REVERT: W 62 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7582 (mm-30) REVERT: W 77 GLU cc_start: 0.8372 (tt0) cc_final: 0.8085 (mp0) REVERT: W 95 TYR cc_start: 0.8634 (m-80) cc_final: 0.8284 (m-80) REVERT: W 122 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7058 (m-30) REVERT: W 124 TYR cc_start: 0.8304 (p90) cc_final: 0.7968 (p90) REVERT: W 139 GLU cc_start: 0.8526 (tp30) cc_final: 0.8140 (tp30) REVERT: W 149 ASP cc_start: 0.8129 (m-30) cc_final: 0.7870 (m-30) REVERT: W 180 ARG cc_start: 0.8876 (tpp80) cc_final: 0.8512 (tpp80) REVERT: W 191 GLN cc_start: 0.8736 (mt0) cc_final: 0.8422 (tm-30) REVERT: J 149 ASP cc_start: 0.8576 (m-30) cc_final: 0.7995 (t0) REVERT: J 153 ASP cc_start: 0.8486 (m-30) cc_final: 0.8015 (m-30) REVERT: J 193 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8154 (pt0) REVERT: X 123 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8419 (tt) REVERT: X 124 TYR cc_start: 0.8464 (p90) cc_final: 0.7328 (p90) REVERT: X 135 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7274 (t80) REVERT: X 139 GLU cc_start: 0.8389 (tp30) cc_final: 0.7587 (tp30) REVERT: X 145 LYS cc_start: 0.9312 (ttmm) cc_final: 0.9058 (tppp) REVERT: X 150 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8411 (mt-10) REVERT: X 197 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7656 (mpt180) REVERT: X 198 LYS cc_start: 0.8151 (mtmt) cc_final: 0.7782 (mtmm) REVERT: K 38 ASP cc_start: 0.7802 (t0) cc_final: 0.7481 (t0) REVERT: K 74 MET cc_start: 0.8058 (mmm) cc_final: 0.7840 (tpt) REVERT: K 131 SER cc_start: 0.8942 (p) cc_final: 0.8633 (t) REVERT: K 149 ASP cc_start: 0.7947 (t0) cc_final: 0.7245 (t0) REVERT: K 153 ASP cc_start: 0.8160 (m-30) cc_final: 0.7692 (m-30) REVERT: K 181 LYS cc_start: 0.9303 (tppp) cc_final: 0.8843 (tppt) REVERT: Y 9 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7412 (pptt) REVERT: Y 27 MET cc_start: 0.7888 (ttt) cc_final: 0.7540 (ttt) REVERT: Y 35 PHE cc_start: 0.8256 (m-80) cc_final: 0.7675 (m-80) REVERT: Y 36 GLN cc_start: 0.8384 (tt0) cc_final: 0.8063 (tp40) REVERT: Y 37 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8861 (tp) REVERT: Y 93 MET cc_start: 0.6439 (ttp) cc_final: 0.6070 (tmm) REVERT: Y 95 TYR cc_start: 0.8043 (m-80) cc_final: 0.7744 (m-10) REVERT: Y 139 GLU cc_start: 0.8554 (tp30) cc_final: 0.7673 (tp30) REVERT: Y 141 GLN cc_start: 0.9019 (mt0) cc_final: 0.8751 (mt0) REVERT: Y 150 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8394 (mt-10) REVERT: L 17 GLU cc_start: 0.7862 (pp20) cc_final: 0.7436 (pp20) REVERT: L 33 LYS cc_start: 0.8075 (mttm) cc_final: 0.7799 (mtmt) REVERT: L 35 PHE cc_start: 0.8488 (m-80) cc_final: 0.8096 (m-10) REVERT: L 98 GLN cc_start: 0.8598 (mt0) cc_final: 0.8224 (mp10) REVERT: L 135 TYR cc_start: 0.8186 (m-80) cc_final: 0.7690 (m-80) REVERT: L 153 ASP cc_start: 0.8116 (m-30) cc_final: 0.7658 (m-30) REVERT: L 166 ASP cc_start: 0.8506 (t70) cc_final: 0.8206 (t70) REVERT: A 98 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7127 (tm-30) REVERT: A 125 GLN cc_start: 0.8215 (tt0) cc_final: 0.7889 (tt0) REVERT: A 158 ASN cc_start: 0.8173 (m-40) cc_final: 0.6677 (m110) REVERT: A 160 TYR cc_start: 0.8337 (m-10) cc_final: 0.7991 (m-80) REVERT: A 188 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8148 (tp30) REVERT: A 208 LYS cc_start: 0.7898 (mttt) cc_final: 0.7468 (mtpp) REVERT: A 221 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.7469 (m-10) REVERT: A 225 ASP cc_start: 0.7902 (p0) cc_final: 0.7323 (p0) REVERT: B 40 MET cc_start: 0.8303 (pmm) cc_final: 0.7244 (pmm) REVERT: B 47 LEU cc_start: 0.8593 (pp) cc_final: 0.8272 (pt) REVERT: B 98 GLN cc_start: 0.7800 (tp40) cc_final: 0.7094 (tm-30) REVERT: B 119 GLN cc_start: 0.8681 (tp40) cc_final: 0.8433 (tp40) REVERT: B 178 ARG cc_start: 0.8016 (ptp90) cc_final: 0.7756 (ptt90) REVERT: B 205 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7414 (mp0) REVERT: B 211 GLU cc_start: 0.7879 (tt0) cc_final: 0.7422 (pt0) REVERT: B 221 TYR cc_start: 0.7975 (m-80) cc_final: 0.7579 (m-80) REVERT: C 40 MET cc_start: 0.8353 (pmm) cc_final: 0.7699 (pmm) REVERT: C 98 GLN cc_start: 0.7419 (mm-40) cc_final: 0.6819 (tm-30) REVERT: C 119 GLN cc_start: 0.8911 (tp40) cc_final: 0.8655 (tp40) REVERT: C 121 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7952 (tm-30) REVERT: C 178 ARG cc_start: 0.8055 (ptt-90) cc_final: 0.7714 (ptt90) REVERT: C 188 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8497 (tp30) REVERT: D 72 ASP cc_start: 0.8321 (m-30) cc_final: 0.7947 (m-30) REVERT: D 98 GLN cc_start: 0.7039 (mm-40) cc_final: 0.6649 (tm-30) REVERT: D 110 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7304 (tm-30) REVERT: D 114 LYS cc_start: 0.8233 (mmmm) cc_final: 0.7883 (mmmm) REVERT: D 163 THR cc_start: 0.8230 (OUTLIER) cc_final: 0.8009 (m) REVERT: E 40 MET cc_start: 0.8381 (pmm) cc_final: 0.7480 (pmm) REVERT: E 91 PHE cc_start: 0.8532 (t80) cc_final: 0.8331 (t80) REVERT: E 110 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7226 (tm-30) REVERT: E 118 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8087 (p0) REVERT: E 188 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8221 (tp30) REVERT: E 208 LYS cc_start: 0.7868 (mttt) cc_final: 0.7496 (mtpp) REVERT: F 98 GLN cc_start: 0.7594 (mm110) cc_final: 0.7051 (tm-30) REVERT: F 114 LYS cc_start: 0.8231 (mmmm) cc_final: 0.7999 (mmmm) REVERT: F 121 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7932 (tm-30) REVERT: F 208 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7611 (ptmt) REVERT: F 221 TYR cc_start: 0.8112 (m-80) cc_final: 0.7575 (m-80) REVERT: G 98 GLN cc_start: 0.7960 (mm110) cc_final: 0.7421 (tm-30) REVERT: G 115 ARG cc_start: 0.7955 (mpt-90) cc_final: 0.7627 (mtt90) REVERT: G 178 ARG cc_start: 0.8116 (ptt-90) cc_final: 0.7662 (ptt90) REVERT: G 179 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8020 (mm-30) REVERT: G 228 GLU cc_start: 0.8712 (tt0) cc_final: 0.8187 (tp30) REVERT: O 123 TYR cc_start: 0.9087 (m-10) cc_final: 0.8523 (m-10) REVERT: O 132 TYR cc_start: 0.8693 (m-80) cc_final: 0.7746 (m-80) REVERT: O 160 TYR cc_start: 0.8277 (m-80) cc_final: 0.7702 (m-80) REVERT: O 165 ILE cc_start: 0.8649 (tp) cc_final: 0.8225 (pt) REVERT: P 40 MET cc_start: 0.7234 (ptp) cc_final: 0.6929 (pmm) REVERT: P 47 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8323 (pt) REVERT: P 115 ARG cc_start: 0.8108 (ttm170) cc_final: 0.7860 (ttm170) REVERT: P 160 TYR cc_start: 0.8572 (m-80) cc_final: 0.7957 (m-80) REVERT: P 165 ILE cc_start: 0.8467 (tp) cc_final: 0.8160 (mm) REVERT: P 181 LYS cc_start: 0.9126 (mmmt) cc_final: 0.8842 (mmmt) REVERT: P 182 GLU cc_start: 0.8313 (mp0) cc_final: 0.7958 (mp0) REVERT: P 208 LYS cc_start: 0.5937 (OUTLIER) cc_final: 0.5430 (ttmt) REVERT: Q 8 TYR cc_start: 0.5314 (OUTLIER) cc_final: 0.3719 (t80) REVERT: Q 40 MET cc_start: 0.7642 (ttp) cc_final: 0.7305 (ttp) REVERT: Q 121 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7526 (tm-30) REVERT: Q 123 TYR cc_start: 0.9011 (m-80) cc_final: 0.8132 (m-10) REVERT: Q 132 TYR cc_start: 0.8543 (m-80) cc_final: 0.7518 (m-80) REVERT: Q 160 TYR cc_start: 0.8468 (m-80) cc_final: 0.7761 (m-80) REVERT: Q 165 ILE cc_start: 0.8454 (tp) cc_final: 0.8197 (mm) REVERT: Q 191 THR cc_start: 0.8838 (m) cc_final: 0.8487 (p) REVERT: Q 201 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7798 (tt) REVERT: Q 232 PHE cc_start: 0.8889 (m-80) cc_final: 0.8601 (m-80) REVERT: R 122 GLN cc_start: 0.8306 (mt0) cc_final: 0.7922 (mt0) REVERT: R 165 ILE cc_start: 0.8728 (tp) cc_final: 0.8313 (pt) REVERT: R 191 THR cc_start: 0.8785 (m) cc_final: 0.8530 (p) REVERT: S 81 LEU cc_start: 0.7970 (mt) cc_final: 0.7671 (tt) REVERT: S 118 ASP cc_start: 0.8854 (t0) cc_final: 0.8549 (t0) REVERT: S 119 GLN cc_start: 0.8840 (tp-100) cc_final: 0.8471 (tp40) REVERT: S 165 ILE cc_start: 0.8403 (tp) cc_final: 0.8182 (mm) REVERT: S 191 THR cc_start: 0.8842 (m) cc_final: 0.8490 (p) REVERT: T 33 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8388 (pttp) REVERT: T 121 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7828 (tm-30) REVERT: T 123 TYR cc_start: 0.7990 (m-10) cc_final: 0.7604 (m-10) REVERT: T 160 TYR cc_start: 0.8393 (m-80) cc_final: 0.7119 (m-10) REVERT: T 165 ILE cc_start: 0.8423 (tp) cc_final: 0.8038 (mm) REVERT: T 191 THR cc_start: 0.8891 (m) cc_final: 0.8521 (p) REVERT: T 201 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7480 (tt) REVERT: U 119 GLN cc_start: 0.9105 (tp40) cc_final: 0.8679 (tp40) REVERT: U 120 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8036 (mtm) REVERT: U 151 CYS cc_start: 0.8080 (t) cc_final: 0.7591 (t) REVERT: U 191 THR cc_start: 0.8965 (m) cc_final: 0.8636 (p) REVERT: U 201 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7863 (tt) outliers start: 217 outliers final: 167 residues processed: 1419 average time/residue: 0.5565 time to fit residues: 1311.4046 Evaluate side-chains 1400 residues out of total 5005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1212 time to evaluate : 5.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain Z residue 64 GLU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 104 ILE Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 43 MET Chi-restraints excluded: chain 1 residue 64 GLU Chi-restraints excluded: chain 1 residue 85 ASN Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 110 VAL Chi-restraints excluded: chain 1 residue 131 SER Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 85 ASN Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 143 SER Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain 2 residue 9 LYS Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 16 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 55 LEU Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 123 ILE Chi-restraints excluded: chain 2 residue 127 THR Chi-restraints excluded: chain 2 residue 135 TYR Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 62 GLU Chi-restraints excluded: chain V residue 104 ILE Chi-restraints excluded: chain V residue 110 VAL Chi-restraints excluded: chain I residue 27 MET Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 64 GLU Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 122 ASP Chi-restraints excluded: chain W residue 123 ILE Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 177 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 85 ASN Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 104 ILE Chi-restraints excluded: chain X residue 119 SER Chi-restraints excluded: chain X residue 123 ILE Chi-restraints excluded: chain X residue 127 THR Chi-restraints excluded: chain X residue 135 TYR Chi-restraints excluded: chain X residue 187 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain Y residue 9 LYS Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 104 ILE Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 123 ILE Chi-restraints excluded: chain Y residue 127 THR Chi-restraints excluded: chain Y residue 135 TYR Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 146 MET Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 192 ILE Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 208 LYS Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 179 GLU Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain O residue 49 ILE Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 156 THR Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 156 THR Chi-restraints excluded: chain P residue 158 ASN Chi-restraints excluded: chain P residue 191 THR Chi-restraints excluded: chain P residue 197 LEU Chi-restraints excluded: chain P residue 208 LYS Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 8 TYR Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 158 ASN Chi-restraints excluded: chain Q residue 183 ASN Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 219 ASN Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 158 ASN Chi-restraints excluded: chain S residue 170 ASP Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 219 ASN Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 156 THR Chi-restraints excluded: chain T residue 158 ASN Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 120 MET Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 156 THR Chi-restraints excluded: chain U residue 158 ASN Chi-restraints excluded: chain U residue 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 370 optimal weight: 10.0000 chunk 496 optimal weight: 0.9980 chunk 142 optimal weight: 0.3980 chunk 430 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 467 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 479 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 88 ASN Z 191 GLN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 ASN ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 36 GLN 2 88 ASN ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 ASN ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 85 ASN X 98 GLN ** Y 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 ASN ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 GLN ** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.113439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.093638 restraints weight = 86449.216| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.84 r_work: 0.3222 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.6840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 47096 Z= 0.238 Angle : 0.798 24.593 63588 Z= 0.401 Chirality : 0.046 0.302 7448 Planarity : 0.004 0.072 8162 Dihedral : 5.738 54.259 6615 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.89 % Favored : 94.04 % Rotamer: Outliers : 4.50 % Allowed : 29.35 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.60 (0.11), residues: 5957 helix: 1.77 (0.11), residues: 2275 sheet: -1.09 (0.14), residues: 1127 loop : -2.17 (0.11), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS 2 28 PHE 0.023 0.001 PHE V 25 TYR 0.028 0.001 TYR V 92 ARG 0.014 0.000 ARG A 178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19953.78 seconds wall clock time: 352 minutes 4.59 seconds (21124.59 seconds total)