Starting phenix.real_space_refine on Wed Feb 14 04:22:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utg_20878/02_2024/6utg_20878.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utg_20878/02_2024/6utg_20878.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/6utg_20878/02_2024/6utg_20878.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utg_20878/02_2024/6utg_20878.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utg_20878/02_2024/6utg_20878.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utg_20878/02_2024/6utg_20878.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= 0.114 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 238 5.16 5 C 36771 2.51 5 N 9926 2.21 5 O 11214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 58149 Number of models: 1 Model: "" Number of chains: 35 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: "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: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1768 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "B" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1768 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "C" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1768 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "D" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1768 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1768 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "F" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1768 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "G" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1768 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} 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: "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: "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: "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: "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: "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: "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: "O" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 1 Chain: "P" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 1 Chain: "Q" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 1 Chain: "R" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 1 Chain: "S" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 1 Chain: "T" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 1 Chain: "U" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 1 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: "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: "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: "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: "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: "a" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1740 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "b" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1740 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "c" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1740 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "d" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1740 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "e" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1740 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "f" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1740 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "g" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1740 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Time building chain proxies: 22.38, per 1000 atoms: 0.38 Number of scatterers: 58149 At special positions: 0 Unit cell: (132.038, 132.038, 238.162, 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 238 16.00 O 11214 8.00 N 9926 7.00 C 36771 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.43 Conformation dependent library (CDL) restraints added in 8.6 seconds 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13874 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 63 sheets defined 48.2% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.78 Creating SS restraints... Processing helix chain '1' and resid 48 through 71 Processing helix chain '1' and resid 75 through 90 removed outlier: 4.005A pdb=" N VAL 1 90 " --> pdb=" O MET 1 86 " (cutoff:3.500A) Processing helix chain '1' and resid 130 through 142 removed outlier: 4.140A pdb=" N VAL 1 134 " --> pdb=" O GLY 1 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR 1 142 " --> pdb=" O LEU 1 138 " (cutoff:3.500A) Processing helix chain '1' and resid 147 through 165 Processing helix chain '1' and resid 188 through 199 Processing helix chain '2' and resid 48 through 71 Processing helix chain '2' and resid 75 through 90 removed outlier: 4.004A pdb=" N VAL 2 90 " --> pdb=" O MET 2 86 " (cutoff:3.500A) Processing helix chain '2' and resid 130 through 142 removed outlier: 4.140A pdb=" N VAL 2 134 " --> pdb=" O GLY 2 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR 2 142 " --> pdb=" O LEU 2 138 " (cutoff:3.500A) Processing helix chain '2' and resid 147 through 165 Processing helix chain '2' and resid 188 through 199 Processing helix chain 'A' and resid 21 through 32 removed outlier: 3.633A pdb=" N VAL A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 104 Processing helix chain 'A' and resid 108 through 123 removed outlier: 4.215A pdb=" N LEU A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 180 Processing helix chain 'A' and resid 185 through 199 Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'B' and resid 21 through 32 removed outlier: 3.808A pdb=" N VAL B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 104 Processing helix chain 'B' and resid 108 through 123 removed outlier: 4.191A pdb=" N LEU B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 180 Processing helix chain 'B' and resid 185 through 199 Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'C' and resid 21 through 32 removed outlier: 3.720A pdb=" N VAL C 31 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 104 Processing helix chain 'C' and resid 108 through 123 removed outlier: 4.163A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR C 123 " --> pdb=" O GLN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 Processing helix chain 'C' and resid 185 through 199 Processing helix chain 'C' and resid 225 through 231 Processing helix chain 'D' and resid 21 through 32 removed outlier: 3.856A pdb=" N VAL D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 104 Processing helix chain 'D' and resid 108 through 123 removed outlier: 4.159A pdb=" N LEU D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR D 123 " --> pdb=" O GLN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 180 Processing helix chain 'D' and resid 185 through 199 Processing helix chain 'D' and resid 225 through 231 Processing helix chain 'E' and resid 21 through 32 removed outlier: 3.744A pdb=" N VAL E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 104 Processing helix chain 'E' and resid 108 through 123 removed outlier: 4.151A pdb=" N LEU E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR E 123 " --> pdb=" O GLN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 180 Processing helix chain 'E' and resid 185 through 199 Processing helix chain 'E' and resid 225 through 231 Processing helix chain 'F' and resid 21 through 32 removed outlier: 3.739A pdb=" N VAL F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS F 32 " --> pdb=" O ARG F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 104 Processing helix chain 'F' and resid 108 through 123 removed outlier: 4.174A pdb=" N LEU F 112 " --> pdb=" O ASN F 108 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR F 123 " --> pdb=" O GLN F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 180 Processing helix chain 'F' and resid 185 through 199 Processing helix chain 'F' and resid 225 through 231 Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.833A pdb=" N VAL G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS G 32 " --> pdb=" O ARG G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 104 Processing helix chain 'G' and resid 108 through 123 removed outlier: 4.171A pdb=" N LEU G 112 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 180 Processing helix chain 'G' and resid 185 through 199 Processing helix chain 'G' and resid 225 through 231 Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 90 removed outlier: 4.004A pdb=" N VAL H 90 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 142 removed outlier: 4.139A pdb=" N VAL H 134 " --> pdb=" O GLY H 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR H 142 " --> pdb=" O LEU H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 165 Processing helix chain 'H' and resid 188 through 199 Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 90 removed outlier: 4.005A pdb=" N VAL I 90 " --> pdb=" O MET I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 removed outlier: 4.139A pdb=" N VAL I 134 " --> pdb=" O GLY I 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR I 142 " --> pdb=" O LEU I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 165 Processing helix chain 'I' and resid 188 through 199 Processing helix chain 'J' and resid 48 through 71 Processing helix chain 'J' and resid 75 through 90 removed outlier: 4.005A pdb=" N VAL J 90 " --> pdb=" O MET J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 142 removed outlier: 4.139A pdb=" N VAL J 134 " --> pdb=" O GLY J 130 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR J 142 " --> pdb=" O LEU J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 165 Processing helix chain 'J' and resid 188 through 199 Processing helix chain 'K' and resid 48 through 71 Processing helix chain 'K' and resid 75 through 90 removed outlier: 4.005A pdb=" N VAL K 90 " --> pdb=" O MET K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 142 removed outlier: 4.139A pdb=" N VAL K 134 " --> pdb=" O GLY K 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 165 Processing helix chain 'K' and resid 188 through 199 Processing helix chain 'L' and resid 48 through 71 Processing helix chain 'L' and resid 75 through 90 removed outlier: 4.004A pdb=" N VAL L 90 " --> pdb=" O MET L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 142 removed outlier: 4.139A pdb=" N VAL L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR L 142 " --> pdb=" O LEU L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 165 Processing helix chain 'L' and resid 188 through 199 Processing helix chain 'M' and resid 48 through 71 Processing helix chain 'M' and resid 75 through 90 removed outlier: 4.005A pdb=" N VAL M 90 " --> pdb=" O MET M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 142 removed outlier: 4.139A pdb=" N VAL M 134 " --> pdb=" O GLY M 130 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR M 142 " --> pdb=" O LEU M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 165 Processing helix chain 'M' and resid 188 through 199 Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 90 removed outlier: 4.005A pdb=" N VAL N 90 " --> pdb=" O MET N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 142 removed outlier: 4.139A pdb=" N VAL N 134 " --> pdb=" O GLY N 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR N 142 " --> pdb=" O LEU N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 165 Processing helix chain 'N' and resid 188 through 199 Processing helix chain 'O' and resid 5 through 16 Processing helix chain 'O' and resid 17 through 31 removed outlier: 4.083A pdb=" N SER O 21 " --> pdb=" O THR O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 52 removed outlier: 3.730A pdb=" N ASN O 52 " --> pdb=" O GLY O 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 61 Processing helix chain 'O' and resid 64 through 94 Processing helix chain 'O' and resid 104 through 122 removed outlier: 3.576A pdb=" N ILE O 116 " --> pdb=" O ALA O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 161 removed outlier: 3.789A pdb=" N VAL O 155 " --> pdb=" O ALA O 151 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 221 removed outlier: 3.666A pdb=" N LEU O 180 " --> pdb=" O SER O 176 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG O 184 " --> pdb=" O LEU O 180 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYS O 217 " --> pdb=" O LEU O 213 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LYS O 218 " --> pdb=" O LEU O 214 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 16 Processing helix chain 'P' and resid 17 through 31 removed outlier: 4.083A pdb=" N SER P 21 " --> pdb=" O THR P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 31 through 52 removed outlier: 3.731A pdb=" N ASN P 52 " --> pdb=" O GLY P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 61 Processing helix chain 'P' and resid 64 through 94 Processing helix chain 'P' and resid 104 through 122 removed outlier: 3.577A pdb=" N ILE P 116 " --> pdb=" O ALA P 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 161 removed outlier: 3.789A pdb=" N VAL P 155 " --> pdb=" O ALA P 151 " (cutoff:3.500A) Processing helix chain 'P' and resid 176 through 221 removed outlier: 3.667A pdb=" N LEU P 180 " --> pdb=" O SER P 176 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG P 184 " --> pdb=" O LEU P 180 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS P 217 " --> pdb=" O LEU P 213 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS P 218 " --> pdb=" O LEU P 214 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 16 Processing helix chain 'Q' and resid 17 through 31 removed outlier: 4.082A pdb=" N SER Q 21 " --> pdb=" O THR Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 52 removed outlier: 3.730A pdb=" N ASN Q 52 " --> pdb=" O GLY Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 61 Processing helix chain 'Q' and resid 64 through 94 Processing helix chain 'Q' and resid 104 through 122 removed outlier: 3.577A pdb=" N ILE Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 161 removed outlier: 3.789A pdb=" N VAL Q 155 " --> pdb=" O ALA Q 151 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 221 removed outlier: 3.667A pdb=" N LEU Q 180 " --> pdb=" O SER Q 176 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG Q 184 " --> pdb=" O LEU Q 180 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS Q 217 " --> pdb=" O LEU Q 213 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS Q 218 " --> pdb=" O LEU Q 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 16 Processing helix chain 'R' and resid 17 through 31 removed outlier: 4.083A pdb=" N SER R 21 " --> pdb=" O THR R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 52 removed outlier: 3.730A pdb=" N ASN R 52 " --> pdb=" O GLY R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 61 Processing helix chain 'R' and resid 64 through 94 Processing helix chain 'R' and resid 104 through 122 removed outlier: 3.577A pdb=" N ILE R 116 " --> pdb=" O ALA R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 161 removed outlier: 3.789A pdb=" N VAL R 155 " --> pdb=" O ALA R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 221 removed outlier: 3.666A pdb=" N LEU R 180 " --> pdb=" O SER R 176 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG R 184 " --> pdb=" O LEU R 180 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYS R 217 " --> pdb=" O LEU R 213 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LYS R 218 " --> pdb=" O LEU R 214 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 16 Processing helix chain 'S' and resid 17 through 31 removed outlier: 4.083A pdb=" N SER S 21 " --> pdb=" O THR S 17 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 52 removed outlier: 3.730A pdb=" N ASN S 52 " --> pdb=" O GLY S 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 57 through 61 Processing helix chain 'S' and resid 64 through 94 Processing helix chain 'S' and resid 104 through 122 removed outlier: 3.577A pdb=" N ILE S 116 " --> pdb=" O ALA S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 161 removed outlier: 3.789A pdb=" N VAL S 155 " --> pdb=" O ALA S 151 " (cutoff:3.500A) Processing helix chain 'S' and resid 176 through 221 removed outlier: 3.667A pdb=" N LEU S 180 " --> pdb=" O SER S 176 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG S 184 " --> pdb=" O LEU S 180 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYS S 217 " --> pdb=" O LEU S 213 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS S 218 " --> pdb=" O LEU S 214 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 16 Processing helix chain 'T' and resid 17 through 31 removed outlier: 4.083A pdb=" N SER T 21 " --> pdb=" O THR T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 52 removed outlier: 3.730A pdb=" N ASN T 52 " --> pdb=" O GLY T 48 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 61 Processing helix chain 'T' and resid 64 through 94 Processing helix chain 'T' and resid 104 through 122 removed outlier: 3.576A pdb=" N ILE T 116 " --> pdb=" O ALA T 112 " (cutoff:3.500A) Processing helix chain 'T' and resid 143 through 161 removed outlier: 3.789A pdb=" N VAL T 155 " --> pdb=" O ALA T 151 " (cutoff:3.500A) Processing helix chain 'T' and resid 176 through 221 removed outlier: 3.667A pdb=" N LEU T 180 " --> pdb=" O SER T 176 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG T 184 " --> pdb=" O LEU T 180 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS T 217 " --> pdb=" O LEU T 213 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LYS T 218 " --> pdb=" O LEU T 214 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 16 Processing helix chain 'U' and resid 17 through 31 removed outlier: 4.082A pdb=" N SER U 21 " --> pdb=" O THR U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 52 removed outlier: 3.730A pdb=" N ASN U 52 " --> pdb=" O GLY U 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 57 through 61 Processing helix chain 'U' and resid 64 through 94 Processing helix chain 'U' and resid 104 through 122 removed outlier: 3.577A pdb=" N ILE U 116 " --> pdb=" O ALA U 112 " (cutoff:3.500A) Processing helix chain 'U' and resid 143 through 161 removed outlier: 3.790A pdb=" N VAL U 155 " --> pdb=" O ALA U 151 " (cutoff:3.500A) Processing helix chain 'U' and resid 176 through 221 removed outlier: 3.667A pdb=" N LEU U 180 " --> pdb=" O SER U 176 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG U 184 " --> pdb=" O LEU U 180 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS U 217 " --> pdb=" O LEU U 213 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS U 218 " --> pdb=" O LEU U 214 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 90 removed outlier: 4.005A pdb=" N VAL V 90 " --> pdb=" O MET V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 142 removed outlier: 4.139A pdb=" N VAL V 134 " --> pdb=" O GLY V 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR V 142 " --> pdb=" O LEU V 138 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 165 Processing helix chain 'V' and resid 188 through 199 Processing helix chain 'W' and resid 48 through 71 Processing helix chain 'W' and resid 75 through 90 removed outlier: 4.005A pdb=" N VAL W 90 " --> pdb=" O MET W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 142 removed outlier: 4.139A pdb=" N VAL W 134 " --> pdb=" O GLY W 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR W 142 " --> pdb=" O LEU W 138 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 165 Processing helix chain 'W' and resid 188 through 199 Processing helix chain 'X' and resid 48 through 71 Processing helix chain 'X' and resid 75 through 90 removed outlier: 4.005A pdb=" N VAL X 90 " --> pdb=" O MET X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 142 removed outlier: 4.140A pdb=" N VAL X 134 " --> pdb=" O GLY X 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR X 142 " --> pdb=" O LEU X 138 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 165 Processing helix chain 'X' and resid 188 through 199 Processing helix chain 'Y' and resid 48 through 71 Processing helix chain 'Y' and resid 75 through 90 removed outlier: 4.004A pdb=" N VAL Y 90 " --> pdb=" O MET Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 142 removed outlier: 4.139A pdb=" N VAL Y 134 " --> pdb=" O GLY Y 130 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 165 Processing helix chain 'Y' and resid 188 through 199 Processing helix chain 'Z' and resid 48 through 71 Processing helix chain 'Z' and resid 75 through 90 removed outlier: 4.004A pdb=" N VAL Z 90 " --> pdb=" O MET Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 142 removed outlier: 4.139A pdb=" N VAL Z 134 " --> pdb=" O GLY Z 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR Z 142 " --> pdb=" O LEU Z 138 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 165 Processing helix chain 'Z' and resid 188 through 199 Processing helix chain 'a' and resid 21 through 33 Processing helix chain 'a' and resid 81 through 104 Processing helix chain 'a' and resid 108 through 126 removed outlier: 3.739A pdb=" N LEU a 112 " --> pdb=" O ASN a 108 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR a 123 " --> pdb=" O GLN a 119 " (cutoff:3.500A) Processing helix chain 'a' and resid 169 through 180 Processing helix chain 'a' and resid 185 through 202 removed outlier: 3.535A pdb=" N SER a 200 " --> pdb=" O ALA a 196 " (cutoff:3.500A) Processing helix chain 'a' and resid 225 through 233 removed outlier: 3.701A pdb=" N VAL a 229 " --> pdb=" O ASP a 225 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS a 230 " --> pdb=" O GLN a 226 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS a 231 " --> pdb=" O GLU a 227 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE a 232 " --> pdb=" O GLU a 228 " (cutoff:3.500A) Processing helix chain 'b' and resid 21 through 33 Processing helix chain 'b' and resid 81 through 104 Processing helix chain 'b' and resid 108 through 126 removed outlier: 3.737A pdb=" N LEU b 112 " --> pdb=" O ASN b 108 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR b 123 " --> pdb=" O GLN b 119 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 180 Processing helix chain 'b' and resid 185 through 202 removed outlier: 3.533A pdb=" N SER b 200 " --> pdb=" O ALA b 196 " (cutoff:3.500A) Processing helix chain 'b' and resid 225 through 233 removed outlier: 3.704A pdb=" N VAL b 229 " --> pdb=" O ASP b 225 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS b 230 " --> pdb=" O GLN b 226 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS b 231 " --> pdb=" O GLU b 227 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE b 232 " --> pdb=" O GLU b 228 " (cutoff:3.500A) Processing helix chain 'c' and resid 21 through 33 Processing helix chain 'c' and resid 81 through 104 Processing helix chain 'c' and resid 108 through 126 removed outlier: 3.744A pdb=" N LEU c 112 " --> pdb=" O ASN c 108 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR c 123 " --> pdb=" O GLN c 119 " (cutoff:3.500A) Processing helix chain 'c' and resid 169 through 180 Processing helix chain 'c' and resid 185 through 202 removed outlier: 3.537A pdb=" N SER c 200 " --> pdb=" O ALA c 196 " (cutoff:3.500A) Processing helix chain 'c' and resid 225 through 233 removed outlier: 3.702A pdb=" N VAL c 229 " --> pdb=" O ASP c 225 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS c 230 " --> pdb=" O GLN c 226 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS c 231 " --> pdb=" O GLU c 227 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE c 232 " --> pdb=" O GLU c 228 " (cutoff:3.500A) Processing helix chain 'd' and resid 21 through 33 Processing helix chain 'd' and resid 81 through 104 Processing helix chain 'd' and resid 108 through 126 removed outlier: 3.737A pdb=" N LEU d 112 " --> pdb=" O ASN d 108 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR d 123 " --> pdb=" O GLN d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 169 through 180 Processing helix chain 'd' and resid 185 through 202 removed outlier: 3.531A pdb=" N SER d 200 " --> pdb=" O ALA d 196 " (cutoff:3.500A) Processing helix chain 'd' and resid 225 through 233 removed outlier: 3.695A pdb=" N VAL d 229 " --> pdb=" O ASP d 225 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS d 230 " --> pdb=" O GLN d 226 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS d 231 " --> pdb=" O GLU d 227 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE d 232 " --> pdb=" O GLU d 228 " (cutoff:3.500A) Processing helix chain 'e' and resid 21 through 33 Processing helix chain 'e' and resid 81 through 104 Processing helix chain 'e' and resid 108 through 126 removed outlier: 3.742A pdb=" N LEU e 112 " --> pdb=" O ASN e 108 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR e 123 " --> pdb=" O GLN e 119 " (cutoff:3.500A) Processing helix chain 'e' and resid 169 through 180 Processing helix chain 'e' and resid 185 through 202 removed outlier: 3.531A pdb=" N SER e 200 " --> pdb=" O ALA e 196 " (cutoff:3.500A) Processing helix chain 'e' and resid 225 through 233 removed outlier: 3.694A pdb=" N VAL e 229 " --> pdb=" O ASP e 225 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS e 230 " --> pdb=" O GLN e 226 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS e 231 " --> pdb=" O GLU e 227 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE e 232 " --> pdb=" O GLU e 228 " (cutoff:3.500A) Processing helix chain 'f' and resid 21 through 33 Processing helix chain 'f' and resid 81 through 104 Processing helix chain 'f' and resid 108 through 126 removed outlier: 3.741A pdb=" N LEU f 112 " --> pdb=" O ASN f 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR f 123 " --> pdb=" O GLN f 119 " (cutoff:3.500A) Processing helix chain 'f' and resid 169 through 180 Processing helix chain 'f' and resid 185 through 202 removed outlier: 3.538A pdb=" N SER f 200 " --> pdb=" O ALA f 196 " (cutoff:3.500A) Processing helix chain 'f' and resid 225 through 233 removed outlier: 3.697A pdb=" N VAL f 229 " --> pdb=" O ASP f 225 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS f 230 " --> pdb=" O GLN f 226 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS f 231 " --> pdb=" O GLU f 227 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE f 232 " --> pdb=" O GLU f 228 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 33 Processing helix chain 'g' and resid 81 through 104 Processing helix chain 'g' and resid 108 through 126 removed outlier: 3.731A pdb=" N LEU g 112 " --> pdb=" O ASN g 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR g 123 " --> pdb=" O GLN g 119 " (cutoff:3.500A) Processing helix chain 'g' and resid 169 through 180 Processing helix chain 'g' and resid 185 through 202 removed outlier: 3.537A pdb=" N SER g 200 " --> pdb=" O ALA g 196 " (cutoff:3.500A) Processing helix chain 'g' and resid 225 through 233 removed outlier: 3.701A pdb=" N VAL g 229 " --> pdb=" O ASP g 225 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS g 230 " --> pdb=" O GLN g 226 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS g 231 " --> pdb=" O GLU g 227 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE g 232 " --> pdb=" O GLU g 228 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 124 through 125 Processing sheet with id=AA2, first strand: chain '1' and resid 34 through 38 removed outlier: 6.509A pdb=" N THR 1 41 " --> pdb=" O ILE 1 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 124 through 125 Processing sheet with id=AA4, first strand: chain '2' and resid 34 through 38 removed outlier: 6.509A pdb=" N THR 2 41 " --> pdb=" O ILE 2 37 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 162 through 165 removed outlier: 3.616A pdb=" N ARG A 222 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 67 through 69 Processing sheet with id=AA7, first strand: chain 'A' and resid 67 through 69 removed outlier: 3.777A pdb=" N GLY A 80 " --> pdb=" O SER R 231 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 162 through 165 removed outlier: 3.609A pdb=" N ARG B 222 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AB1, first strand: chain 'B' and resid 67 through 69 removed outlier: 3.936A pdb=" N GLY B 80 " --> pdb=" O SER S 231 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER S 231 " --> pdb=" O GLY B 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 162 through 165 Processing sheet with id=AB3, first strand: chain 'C' and resid 67 through 69 Processing sheet with id=AB4, first strand: chain 'C' and resid 67 through 69 removed outlier: 3.709A pdb=" N GLY C 80 " --> pdb=" O SER T 231 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 162 through 165 Processing sheet with id=AB6, first strand: chain 'D' and resid 67 through 71 removed outlier: 5.961A pdb=" N VAL D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 67 through 71 removed outlier: 5.961A pdb=" N VAL D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY D 80 " --> pdb=" O SER U 231 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 162 through 165 removed outlier: 3.593A pdb=" N ARG E 222 " --> pdb=" O SER E 214 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 67 through 69 Processing sheet with id=AC1, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.528A pdb=" N GLY E 80 " --> pdb=" O SER O 231 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 162 through 165 Processing sheet with id=AC3, first strand: chain 'F' and resid 67 through 69 Processing sheet with id=AC4, first strand: chain 'F' and resid 67 through 69 removed outlier: 3.749A pdb=" N GLY F 80 " --> pdb=" O SER P 231 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 162 through 165 Processing sheet with id=AC6, first strand: chain 'G' and resid 67 through 69 Processing sheet with id=AC7, first strand: chain 'G' and resid 67 through 69 removed outlier: 3.875A pdb=" N GLY G 80 " --> pdb=" O SER Q 231 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER Q 231 " --> pdb=" O GLY G 80 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 124 through 125 Processing sheet with id=AC9, first strand: chain 'H' and resid 34 through 38 removed outlier: 6.509A pdb=" N THR H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 124 through 125 Processing sheet with id=AD2, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.508A pdb=" N THR I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 124 through 125 Processing sheet with id=AD4, first strand: chain 'J' and resid 34 through 38 removed outlier: 6.508A pdb=" N THR J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 124 through 125 Processing sheet with id=AD6, first strand: chain 'K' and resid 34 through 38 removed outlier: 6.508A pdb=" N THR K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 124 through 125 Processing sheet with id=AD8, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.509A pdb=" N THR L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 124 through 125 Processing sheet with id=AE1, first strand: chain 'M' and resid 34 through 38 removed outlier: 6.508A pdb=" N THR M 41 " --> pdb=" O ILE M 37 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 124 through 125 Processing sheet with id=AE3, first strand: chain 'N' and resid 34 through 38 removed outlier: 6.509A pdb=" N THR N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 124 through 125 Processing sheet with id=AE5, first strand: chain 'V' and resid 34 through 38 removed outlier: 6.508A pdb=" N THR V 41 " --> pdb=" O ILE V 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 124 through 125 Processing sheet with id=AE7, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.509A pdb=" N THR W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'X' and resid 124 through 125 Processing sheet with id=AE9, first strand: chain 'X' and resid 34 through 38 removed outlier: 6.509A pdb=" N THR X 41 " --> pdb=" O ILE X 37 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Y' and resid 124 through 125 Processing sheet with id=AF2, first strand: chain 'Y' and resid 34 through 38 removed outlier: 6.509A pdb=" N THR Y 41 " --> pdb=" O ILE Y 37 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Z' and resid 124 through 125 Processing sheet with id=AF4, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.509A pdb=" N THR Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 162 through 165 removed outlier: 3.504A pdb=" N ARG a 222 " --> pdb=" O SER a 214 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 67 through 71 removed outlier: 6.119A pdb=" N VAL a 74 " --> pdb=" O ILE a 70 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN a 158 " --> pdb=" O ASP a 150 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'b' and resid 162 through 165 removed outlier: 3.513A pdb=" N ARG b 222 " --> pdb=" O SER b 214 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'b' and resid 67 through 71 removed outlier: 6.083A pdb=" N VAL b 74 " --> pdb=" O ILE b 70 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU b 148 " --> pdb=" O TYR b 160 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN b 158 " --> pdb=" O ASP b 150 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'c' and resid 162 through 165 removed outlier: 3.507A pdb=" N ARG c 222 " --> pdb=" O SER c 214 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'c' and resid 67 through 71 removed outlier: 6.140A pdb=" N VAL c 74 " --> pdb=" O ILE c 70 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU c 148 " --> pdb=" O TYR c 160 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN c 158 " --> pdb=" O ASP c 150 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'd' and resid 162 through 165 removed outlier: 3.508A pdb=" N ARG d 222 " --> pdb=" O SER d 214 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'd' and resid 67 through 71 removed outlier: 6.128A pdb=" N VAL d 74 " --> pdb=" O ILE d 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN d 158 " --> pdb=" O ASP d 150 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'e' and resid 162 through 165 removed outlier: 3.511A pdb=" N ARG e 222 " --> pdb=" O SER e 214 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'e' and resid 67 through 71 removed outlier: 6.134A pdb=" N VAL e 74 " --> pdb=" O ILE e 70 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU e 148 " --> pdb=" O TYR e 160 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN e 158 " --> pdb=" O ASP e 150 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'f' and resid 162 through 165 removed outlier: 3.511A pdb=" N ARG f 222 " --> pdb=" O SER f 214 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'f' and resid 67 through 71 removed outlier: 6.144A pdb=" N VAL f 74 " --> pdb=" O ILE f 70 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN f 158 " --> pdb=" O ASP f 150 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'g' and resid 162 through 165 removed outlier: 3.506A pdb=" N ARG g 222 " --> pdb=" O SER g 214 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'g' and resid 67 through 71 removed outlier: 6.116A pdb=" N VAL g 74 " --> pdb=" O ILE g 70 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN g 158 " --> pdb=" O ASP g 150 " (cutoff:3.500A) 3550 hydrogen bonds defined for protein. 10290 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: 21.52 Time building geometry restraints manager: 19.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 9999 1.31 - 1.43: 14050 1.43 - 1.56: 34397 1.56 - 1.69: 18 1.69 - 1.81: 448 Bond restraints: 58912 Sorted by residual: bond pdb=" CA LEU B 21 " pdb=" CB LEU B 21 " ideal model delta sigma weight residual 1.526 1.415 0.111 1.53e-02 4.27e+03 5.29e+01 bond pdb=" C VAL C 129 " pdb=" N ARG C 130 " ideal model delta sigma weight residual 1.327 1.244 0.083 1.71e-02 3.42e+03 2.33e+01 bond pdb=" CA LYS f 53 " pdb=" CB LYS f 53 " ideal model delta sigma weight residual 1.525 1.583 -0.058 1.47e-02 4.63e+03 1.58e+01 bond pdb=" CA LYS c 53 " pdb=" CB LYS c 53 " ideal model delta sigma weight residual 1.525 1.583 -0.058 1.47e-02 4.63e+03 1.56e+01 bond pdb=" CA LYS a 53 " pdb=" CB LYS a 53 " ideal model delta sigma weight residual 1.525 1.582 -0.058 1.47e-02 4.63e+03 1.54e+01 ... (remaining 58907 not shown) Histogram of bond angle deviations from ideal: 97.88 - 106.35: 1186 106.35 - 114.81: 35589 114.81 - 123.28: 40146 123.28 - 131.74: 2578 131.74 - 140.21: 42 Bond angle restraints: 79541 Sorted by residual: angle pdb=" C THR 2 21 " pdb=" N MET 2 22 " pdb=" CA MET 2 22 " ideal model delta sigma weight residual 121.70 140.21 -18.51 1.80e+00 3.09e-01 1.06e+02 angle pdb=" C THR K 21 " pdb=" N MET K 22 " pdb=" CA MET K 22 " ideal model delta sigma weight residual 121.70 140.17 -18.47 1.80e+00 3.09e-01 1.05e+02 angle pdb=" C THR N 21 " pdb=" N MET N 22 " pdb=" CA MET N 22 " ideal model delta sigma weight residual 121.70 140.17 -18.47 1.80e+00 3.09e-01 1.05e+02 angle pdb=" C THR 1 21 " pdb=" N MET 1 22 " pdb=" CA MET 1 22 " ideal model delta sigma weight residual 121.70 140.17 -18.47 1.80e+00 3.09e-01 1.05e+02 angle pdb=" C THR Y 21 " pdb=" N MET Y 22 " pdb=" CA MET Y 22 " ideal model delta sigma weight residual 121.70 140.16 -18.46 1.80e+00 3.09e-01 1.05e+02 ... (remaining 79536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.43: 34270 15.43 - 30.86: 1295 30.86 - 46.30: 382 46.30 - 61.73: 47 61.73 - 77.16: 35 Dihedral angle restraints: 36029 sinusoidal: 14350 harmonic: 21679 Sorted by residual: dihedral pdb=" CA ASN J 24 " pdb=" C ASN J 24 " pdb=" N PHE J 25 " pdb=" CA PHE J 25 " ideal model delta harmonic sigma weight residual 180.00 120.02 59.98 0 5.00e+00 4.00e-02 1.44e+02 dihedral pdb=" CA ASN W 24 " pdb=" C ASN W 24 " pdb=" N PHE W 25 " pdb=" CA PHE W 25 " ideal model delta harmonic sigma weight residual 180.00 120.03 59.97 0 5.00e+00 4.00e-02 1.44e+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 180.00 120.04 59.96 0 5.00e+00 4.00e-02 1.44e+02 ... (remaining 36026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 8206 0.095 - 0.190: 987 0.190 - 0.285: 88 0.285 - 0.380: 15 0.380 - 0.475: 14 Chirality restraints: 9310 Sorted by residual: chirality pdb=" CB ILE W 178 " pdb=" CA ILE W 178 " pdb=" CG1 ILE W 178 " pdb=" CG2 ILE W 178 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" CB ILE L 178 " pdb=" CA ILE L 178 " pdb=" CG1 ILE L 178 " pdb=" CG2 ILE L 178 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" CB ILE M 178 " pdb=" CA ILE M 178 " pdb=" CG1 ILE M 178 " pdb=" CG2 ILE M 178 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.60e+00 ... (remaining 9307 not shown) Planarity restraints: 10206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 63 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C SER D 63 " 0.062 2.00e-02 2.50e+03 pdb=" O SER D 63 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE D 64 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 63 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C SER B 63 " -0.062 2.00e-02 2.50e+03 pdb=" O SER B 63 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE B 64 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 63 " -0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C SER E 63 " 0.062 2.00e-02 2.50e+03 pdb=" O SER E 63 " -0.023 2.00e-02 2.50e+03 pdb=" N ILE E 64 " -0.021 2.00e-02 2.50e+03 ... (remaining 10203 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 14073 2.79 - 3.32: 53747 3.32 - 3.84: 97557 3.84 - 4.37: 114962 4.37 - 4.90: 199233 Nonbonded interactions: 479572 Sorted by model distance: nonbonded pdb=" NH2 ARG H 70 " pdb=" OD1 ASN a 111 " model vdw 2.260 2.520 nonbonded pdb=" OG SER T 63 " pdb=" OG SER U 178 " model vdw 2.262 2.440 nonbonded pdb=" O GLY C 155 " pdb=" NH2 ARG D 86 " model vdw 2.272 2.520 nonbonded pdb=" NH2 ARG N 70 " pdb=" OD1 ASN g 111 " model vdw 2.273 2.520 nonbonded pdb=" NH2 ARG M 70 " pdb=" OD1 ASN f 111 " model vdw 2.273 2.520 ... (remaining 479567 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 10 through 65 or resid 67 through 233)) selection = (chain 'B' and (resid 10 through 65 or resid 67 through 233)) selection = (chain 'C' and (resid 10 through 65 or resid 67 through 233)) selection = (chain 'D' and (resid 10 through 65 or resid 67 through 233)) selection = (chain 'E' and (resid 10 through 65 or resid 67 through 233)) selection = (chain 'F' and (resid 10 through 65 or resid 67 through 233)) selection = (chain 'G' and (resid 10 through 65 or resid 67 through 233)) selection = (chain 'a' and (resid 10 through 65 or resid 67 through 232 or (resid 233 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD1 or name C \ D2)))) selection = (chain 'b' and (resid 10 through 65 or resid 67 through 232 or (resid 233 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD1 or name C \ D2)))) selection = (chain 'c' and (resid 10 through 65 or resid 67 through 232 or (resid 233 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD1 or name C \ D2)))) selection = (chain 'd' and (resid 10 through 65 or resid 67 through 232 or (resid 233 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD1 or name C \ D2)))) selection = (chain 'e' and (resid 10 through 65 or resid 67 through 232 or (resid 233 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD1 or name C \ D2)))) selection = (chain 'f' and (resid 10 through 65 or resid 67 through 232 or (resid 233 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD1 or name C \ D2)))) selection = (chain 'g' and (resid 10 through 65 or resid 67 through 232 or (resid 233 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD1 or name C \ D2)))) } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.520 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: 9.090 Check model and map are aligned: 0.660 Set scattering table: 0.400 Process input model: 117.230 Find NCS groups from input model: 3.560 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 0.111 58912 Z= 0.608 Angle : 1.217 18.506 79541 Z= 0.698 Chirality : 0.066 0.475 9310 Planarity : 0.007 0.061 10206 Dihedral : 10.038 77.161 22155 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.05 % Favored : 94.57 % Rotamer: Outliers : 0.78 % Allowed : 4.84 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.48 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.08), residues: 7441 helix: -1.56 (0.07), residues: 3346 sheet: -1.17 (0.12), residues: 1379 loop : -2.71 (0.10), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP S 28 HIS 0.011 0.004 HIS T 111 PHE 0.028 0.003 PHE b 42 TYR 0.035 0.004 TYR D 221 ARG 0.013 0.001 ARG E 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2521 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 2472 time to evaluate : 5.087 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: 1 8 LEU cc_start: 0.8316 (pp) cc_final: 0.8088 (pp) REVERT: 1 86 MET cc_start: 0.8092 (ttt) cc_final: 0.7650 (ttt) REVERT: 2 8 LEU cc_start: 0.8176 (pp) cc_final: 0.7928 (pp) REVERT: 2 153 ASP cc_start: 0.8001 (m-30) cc_final: 0.7550 (m-30) REVERT: A 156 THR cc_start: 0.8810 (m) cc_final: 0.8573 (m) REVERT: B 135 SER cc_start: 0.9156 (m) cc_final: 0.8716 (p) REVERT: B 174 SER cc_start: 0.8524 (m) cc_final: 0.8187 (p) REVERT: B 211 GLU cc_start: 0.6522 (mt-10) cc_final: 0.6305 (mp0) REVERT: D 135 SER cc_start: 0.9016 (m) cc_final: 0.8564 (p) REVERT: D 174 SER cc_start: 0.8778 (m) cc_final: 0.8321 (p) REVERT: D 227 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8550 (pp20) REVERT: E 120 MET cc_start: 0.9195 (mtp) cc_final: 0.8936 (mtp) REVERT: E 156 THR cc_start: 0.8354 (m) cc_final: 0.8099 (m) REVERT: E 174 SER cc_start: 0.8664 (m) cc_final: 0.8033 (p) REVERT: F 13 THR cc_start: 0.9305 (p) cc_final: 0.9104 (p) REVERT: F 33 LYS cc_start: 0.8673 (mttm) cc_final: 0.8458 (mmtt) REVERT: F 226 GLN cc_start: 0.8140 (pm20) cc_final: 0.7896 (pm20) REVERT: G 224 TYR cc_start: 0.8526 (m-10) cc_final: 0.8306 (m-80) REVERT: H 18 ARG cc_start: 0.8761 (mtm180) cc_final: 0.8531 (mtp180) REVERT: H 88 ASN cc_start: 0.9113 (t0) cc_final: 0.8877 (t0) REVERT: I 27 MET cc_start: 0.8227 (ttt) cc_final: 0.7747 (ttt) REVERT: I 58 TYR cc_start: 0.7868 (t80) cc_final: 0.7404 (t80) REVERT: I 96 MET cc_start: 0.7396 (mpt) cc_final: 0.6929 (mtt) REVERT: I 153 ASP cc_start: 0.7998 (m-30) cc_final: 0.7729 (m-30) REVERT: J 22 MET cc_start: 0.4508 (ttt) cc_final: 0.4021 (ttt) REVERT: J 58 TYR cc_start: 0.7900 (t80) cc_final: 0.7648 (t80) REVERT: J 88 ASN cc_start: 0.8961 (t0) cc_final: 0.8569 (t0) REVERT: J 96 MET cc_start: 0.7237 (mpt) cc_final: 0.6735 (mtt) REVERT: J 98 GLN cc_start: 0.8176 (mt0) cc_final: 0.7885 (mp10) REVERT: J 164 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7720 (mm-40) REVERT: K 58 TYR cc_start: 0.8014 (t80) cc_final: 0.7744 (t80) REVERT: K 98 GLN cc_start: 0.8290 (mt0) cc_final: 0.7936 (mp10) REVERT: L 58 TYR cc_start: 0.7869 (t80) cc_final: 0.7532 (t80) REVERT: L 59 MET cc_start: 0.8067 (mmt) cc_final: 0.7839 (mmm) REVERT: L 67 ARG cc_start: 0.7881 (ttp-110) cc_final: 0.7453 (ttp-110) REVERT: L 86 MET cc_start: 0.8127 (ttt) cc_final: 0.7876 (ttm) REVERT: L 96 MET cc_start: 0.7191 (mpt) cc_final: 0.6279 (mtp) REVERT: M 33 LYS cc_start: 0.8496 (mttm) cc_final: 0.8175 (mttt) REVERT: M 58 TYR cc_start: 0.7936 (t80) cc_final: 0.7731 (t80) REVERT: M 96 MET cc_start: 0.7211 (mpt) cc_final: 0.6991 (mtt) REVERT: M 127 THR cc_start: 0.8138 (p) cc_final: 0.7854 (p) REVERT: N 96 MET cc_start: 0.6769 (mpt) cc_final: 0.6540 (mtt) REVERT: N 98 GLN cc_start: 0.8225 (mt0) cc_final: 0.7936 (mp10) REVERT: N 153 ASP cc_start: 0.8068 (m-30) cc_final: 0.7845 (m-30) REVERT: O 72 GLN cc_start: 0.7744 (tp40) cc_final: 0.7406 (tp40) REVERT: O 86 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7765 (mm-30) REVERT: O 121 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6522 (mt-10) REVERT: O 122 ILE cc_start: 0.7912 (mt) cc_final: 0.7609 (mt) REVERT: O 142 MET cc_start: 0.8403 (tpt) cc_final: 0.8103 (tpt) REVERT: O 193 LYS cc_start: 0.9101 (mttt) cc_final: 0.8873 (mttm) REVERT: P 22 PHE cc_start: 0.8876 (t80) cc_final: 0.8601 (t80) REVERT: P 121 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7236 (mt-10) REVERT: P 142 MET cc_start: 0.8313 (tpt) cc_final: 0.8085 (tpp) REVERT: Q 116 ILE cc_start: 0.8938 (pt) cc_final: 0.8481 (mt) REVERT: Q 122 ILE cc_start: 0.8229 (mt) cc_final: 0.7869 (mt) REVERT: Q 142 MET cc_start: 0.8345 (tpt) cc_final: 0.8124 (tpp) REVERT: Q 148 TYR cc_start: 0.7863 (t80) cc_final: 0.7569 (t80) REVERT: R 148 TYR cc_start: 0.8215 (t80) cc_final: 0.7932 (t80) REVERT: R 204 MET cc_start: 0.8731 (mmm) cc_final: 0.7684 (mmt) REVERT: R 210 ASN cc_start: 0.8821 (t0) cc_final: 0.8616 (t0) REVERT: S 204 MET cc_start: 0.8516 (mmm) cc_final: 0.7057 (mmt) REVERT: T 11 ASN cc_start: 0.7769 (m-40) cc_final: 0.7548 (m-40) REVERT: T 121 GLU cc_start: 0.7637 (mt-10) cc_final: 0.6775 (mt-10) REVERT: T 142 MET cc_start: 0.8364 (tpt) cc_final: 0.7996 (tpp) REVERT: U 27 GLU cc_start: 0.8072 (tp30) cc_final: 0.7811 (tp30) REVERT: U 204 MET cc_start: 0.8681 (mmm) cc_final: 0.8476 (mmt) REVERT: W 27 MET cc_start: 0.8321 (ttt) cc_final: 0.8020 (ttt) REVERT: X 66 TYR cc_start: 0.7571 (t80) cc_final: 0.7206 (t80) REVERT: X 86 MET cc_start: 0.8323 (ttt) cc_final: 0.8052 (ttt) REVERT: Y 8 LEU cc_start: 0.8118 (pp) cc_final: 0.7834 (pp) REVERT: Y 66 TYR cc_start: 0.7322 (t80) cc_final: 0.7070 (t80) REVERT: Y 86 MET cc_start: 0.8238 (ttt) cc_final: 0.7829 (ttt) REVERT: Y 124 TYR cc_start: 0.8449 (p90) cc_final: 0.8053 (p90) REVERT: Z 119 SER cc_start: 0.8590 (t) cc_final: 0.8355 (p) REVERT: Z 164 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8048 (mm-40) REVERT: a 18 ASP cc_start: 0.8764 (p0) cc_final: 0.8455 (p0) REVERT: a 40 MET cc_start: 0.8337 (ptp) cc_final: 0.8010 (ptp) REVERT: a 114 LYS cc_start: 0.8421 (mtpt) cc_final: 0.8195 (mttm) REVERT: a 175 PHE cc_start: 0.8314 (t80) cc_final: 0.7702 (t80) REVERT: a 191 THR cc_start: 0.9171 (m) cc_final: 0.8885 (m) REVERT: b 40 MET cc_start: 0.8258 (ptp) cc_final: 0.7853 (ptm) REVERT: b 42 PHE cc_start: 0.8199 (p90) cc_final: 0.7339 (p90) REVERT: b 175 PHE cc_start: 0.8314 (t80) cc_final: 0.7647 (t80) REVERT: b 191 THR cc_start: 0.9198 (m) cc_final: 0.8937 (m) REVERT: c 114 LYS cc_start: 0.8349 (mtpt) cc_final: 0.8094 (mttp) REVERT: c 175 PHE cc_start: 0.8342 (t80) cc_final: 0.7658 (t80) REVERT: d 42 PHE cc_start: 0.8123 (p90) cc_final: 0.7441 (p90) REVERT: d 111 ASN cc_start: 0.7544 (t160) cc_final: 0.7291 (t160) REVERT: d 191 THR cc_start: 0.9153 (m) cc_final: 0.8900 (m) REVERT: e 18 ASP cc_start: 0.8796 (p0) cc_final: 0.8513 (p0) REVERT: e 42 PHE cc_start: 0.8168 (p90) cc_final: 0.7662 (p90) REVERT: e 175 PHE cc_start: 0.8216 (t80) cc_final: 0.7825 (t80) REVERT: f 42 PHE cc_start: 0.8004 (p90) cc_final: 0.7190 (p90) REVERT: f 70 ILE cc_start: 0.9341 (mm) cc_final: 0.9133 (mt) REVERT: f 110 GLU cc_start: 0.7768 (tt0) cc_final: 0.7417 (tm-30) REVERT: f 175 PHE cc_start: 0.8275 (t80) cc_final: 0.7939 (t80) REVERT: f 191 THR cc_start: 0.9122 (m) cc_final: 0.8851 (m) REVERT: g 40 MET cc_start: 0.8281 (ptp) cc_final: 0.8010 (ptp) REVERT: g 42 PHE cc_start: 0.8133 (p90) cc_final: 0.7539 (p90) REVERT: g 157 ILE cc_start: 0.8527 (pt) cc_final: 0.8191 (pt) REVERT: g 175 PHE cc_start: 0.8342 (t80) cc_final: 0.8088 (t80) REVERT: g 194 ILE cc_start: 0.8875 (mt) cc_final: 0.8595 (mt) outliers start: 49 outliers final: 32 residues processed: 2500 average time/residue: 0.5891 time to fit residues: 2390.6517 Evaluate side-chains 1400 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1368 time to evaluate : 5.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain a residue 212 ILE Chi-restraints excluded: chain d residue 212 ILE Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain f residue 212 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 620 optimal weight: 0.9990 chunk 557 optimal weight: 3.9990 chunk 309 optimal weight: 0.7980 chunk 190 optimal weight: 1.9990 chunk 375 optimal weight: 2.9990 chunk 297 optimal weight: 4.9990 chunk 576 optimal weight: 0.9980 chunk 222 optimal weight: 0.7980 chunk 350 optimal weight: 6.9990 chunk 428 optimal weight: 0.9980 chunk 667 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 36 GLN ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 85 ASN ** 2 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 186 GLN D 219 ASN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN I 88 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 ASN K 88 ASN L 88 ASN M 30 ASN M 88 ASN N 88 ASN ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 GLN O 111 HIS ** P 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 HIS Q 111 HIS R 11 ASN R 72 GLN R 75 GLN R 111 HIS ** S 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 111 HIS T 111 HIS U 111 HIS V 36 GLN V 85 ASN ** V 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 GLN ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 36 GLN ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 23 GLN a 108 ASN b 23 GLN c 23 GLN c 44 ASN c 108 ASN c 122 GLN d 23 GLN d 122 GLN e 23 GLN e 44 ASN f 23 GLN f 44 ASN f 122 GLN g 23 GLN g 44 ASN g 108 ASN g 122 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 58912 Z= 0.225 Angle : 0.708 12.726 79541 Z= 0.385 Chirality : 0.046 0.409 9310 Planarity : 0.005 0.059 10206 Dihedral : 6.549 53.616 8278 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.75 % Favored : 96.16 % Rotamer: Outliers : 4.74 % Allowed : 14.13 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: -1.13 (0.09), residues: 7441 helix: 0.50 (0.08), residues: 3416 sheet: -0.75 (0.12), residues: 1344 loop : -2.38 (0.10), residues: 2681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP T 28 HIS 0.005 0.002 HIS K 28 PHE 0.027 0.002 PHE G 175 TYR 0.025 0.002 TYR T 143 ARG 0.010 0.001 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1912 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 1616 time to evaluate : 5.128 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: 2 2 THR cc_start: 0.8698 (t) cc_final: 0.7594 (p) REVERT: 2 146 MET cc_start: 0.8691 (mtp) cc_final: 0.8438 (mtp) REVERT: A 9 ASP cc_start: 0.8309 (t0) cc_final: 0.7874 (t0) REVERT: A 119 GLN cc_start: 0.8386 (tp40) cc_final: 0.8160 (tp40) REVERT: C 73 TYR cc_start: 0.8037 (m-80) cc_final: 0.7555 (m-10) REVERT: D 73 TYR cc_start: 0.8202 (m-80) cc_final: 0.7976 (m-10) REVERT: D 160 TYR cc_start: 0.8138 (m-10) cc_final: 0.7841 (m-10) REVERT: D 224 TYR cc_start: 0.7953 (m-10) cc_final: 0.7695 (m-10) REVERT: E 28 ARG cc_start: 0.8559 (ttm-80) cc_final: 0.8251 (ttm-80) REVERT: F 9 ASP cc_start: 0.8267 (t0) cc_final: 0.7948 (t0) REVERT: G 9 ASP cc_start: 0.7855 (t0) cc_final: 0.7099 (t0) REVERT: G 227 GLU cc_start: 0.7941 (pp20) cc_final: 0.7644 (pm20) REVERT: H 123 ILE cc_start: 0.8841 (tt) cc_final: 0.8624 (mp) REVERT: H 149 ASP cc_start: 0.7360 (t0) cc_final: 0.6992 (t0) REVERT: H 153 ASP cc_start: 0.8051 (m-30) cc_final: 0.7671 (m-30) REVERT: I 7 THR cc_start: 0.8920 (m) cc_final: 0.8649 (t) REVERT: I 40 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.8480 (m-10) REVERT: I 96 MET cc_start: 0.7084 (mpt) cc_final: 0.6814 (mtt) REVERT: I 111 PHE cc_start: 0.7914 (m-10) cc_final: 0.7626 (m-80) REVERT: I 122 ASP cc_start: 0.7462 (t0) cc_final: 0.7217 (t0) REVERT: I 149 ASP cc_start: 0.7591 (t0) cc_final: 0.7178 (t0) REVERT: I 153 ASP cc_start: 0.8225 (m-30) cc_final: 0.7845 (m-30) REVERT: I 191 GLN cc_start: 0.7005 (tm-30) cc_final: 0.6505 (tm-30) REVERT: J 22 MET cc_start: 0.4361 (ttt) cc_final: 0.3980 (ttt) REVERT: J 96 MET cc_start: 0.7357 (mpt) cc_final: 0.6663 (mtt) REVERT: J 98 GLN cc_start: 0.8253 (mt0) cc_final: 0.7906 (mp10) REVERT: K 98 GLN cc_start: 0.8339 (mt0) cc_final: 0.7911 (mp10) REVERT: K 111 PHE cc_start: 0.7951 (m-10) cc_final: 0.7705 (m-10) REVERT: L 96 MET cc_start: 0.7106 (mpt) cc_final: 0.6369 (mtt) REVERT: L 123 ILE cc_start: 0.8789 (mp) cc_final: 0.8552 (mp) REVERT: M 96 MET cc_start: 0.7039 (mpt) cc_final: 0.6669 (mtt) REVERT: N 59 MET cc_start: 0.8212 (mmt) cc_final: 0.7896 (tpp) REVERT: N 96 MET cc_start: 0.6557 (mpt) cc_final: 0.6328 (mtm) REVERT: N 98 GLN cc_start: 0.8246 (mt0) cc_final: 0.7880 (mp10) REVERT: N 111 PHE cc_start: 0.8356 (m-80) cc_final: 0.8098 (m-80) REVERT: N 149 ASP cc_start: 0.7527 (t0) cc_final: 0.7019 (t0) REVERT: N 153 ASP cc_start: 0.8141 (m-30) cc_final: 0.7914 (m-30) REVERT: O 121 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7107 (mt-10) REVERT: O 122 ILE cc_start: 0.7955 (mt) cc_final: 0.7624 (mt) REVERT: P 14 ASP cc_start: 0.8248 (m-30) cc_final: 0.8035 (m-30) REVERT: P 22 PHE cc_start: 0.8681 (t80) cc_final: 0.8207 (t80) REVERT: P 115 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8539 (ttmt) REVERT: P 121 GLU cc_start: 0.7340 (mt-10) cc_final: 0.7017 (mt-10) REVERT: P 142 MET cc_start: 0.8272 (tpt) cc_final: 0.7914 (tpp) REVERT: P 230 PHE cc_start: 0.8949 (m-80) cc_final: 0.8662 (m-80) REVERT: Q 116 ILE cc_start: 0.8950 (pt) cc_final: 0.8707 (mt) REVERT: Q 122 ILE cc_start: 0.8003 (mt) cc_final: 0.7703 (mt) REVERT: Q 148 TYR cc_start: 0.8197 (t80) cc_final: 0.7693 (t80) REVERT: S 22 PHE cc_start: 0.8722 (t80) cc_final: 0.8495 (t80) REVERT: S 122 ILE cc_start: 0.7904 (mt) cc_final: 0.7695 (mt) REVERT: S 210 ASN cc_start: 0.8728 (t0) cc_final: 0.8372 (t0) REVERT: T 22 PHE cc_start: 0.8872 (t80) cc_final: 0.8360 (t80) REVERT: T 121 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6678 (mt-10) REVERT: T 142 MET cc_start: 0.8271 (tpt) cc_final: 0.7570 (tpp) REVERT: U 22 PHE cc_start: 0.8812 (t80) cc_final: 0.8454 (t80) REVERT: V 2 THR cc_start: 0.8620 (t) cc_final: 0.7769 (p) REVERT: V 58 TYR cc_start: 0.7996 (t80) cc_final: 0.7710 (t80) REVERT: W 93 MET cc_start: 0.6362 (mpp) cc_final: 0.5902 (ttm) REVERT: X 2 THR cc_start: 0.8853 (t) cc_final: 0.8007 (p) REVERT: X 195 ARG cc_start: 0.6695 (mmm-85) cc_final: 0.6265 (mmt180) REVERT: Y 2 THR cc_start: 0.8631 (t) cc_final: 0.7733 (p) REVERT: Y 58 TYR cc_start: 0.8166 (t80) cc_final: 0.7921 (t80) REVERT: Y 93 MET cc_start: 0.6281 (mpp) cc_final: 0.6032 (ttm) REVERT: Y 127 THR cc_start: 0.8750 (p) cc_final: 0.8496 (p) REVERT: Z 164 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8153 (mm-40) REVERT: Z 195 ARG cc_start: 0.6991 (tpp80) cc_final: 0.6693 (tpp-160) REVERT: a 40 MET cc_start: 0.8286 (ptp) cc_final: 0.7838 (ptp) REVERT: a 94 ILE cc_start: 0.9030 (pt) cc_final: 0.8643 (mt) REVERT: a 114 LYS cc_start: 0.8595 (mtpt) cc_final: 0.8306 (mttp) REVERT: a 119 GLN cc_start: 0.8415 (tm-30) cc_final: 0.7979 (tm-30) REVERT: a 175 PHE cc_start: 0.8359 (t80) cc_final: 0.7780 (t80) REVERT: b 40 MET cc_start: 0.8108 (ptp) cc_final: 0.7772 (ptm) REVERT: c 121 GLN cc_start: 0.8109 (tm130) cc_final: 0.7786 (tm-30) REVERT: c 175 PHE cc_start: 0.8586 (t80) cc_final: 0.8349 (t80) REVERT: e 90 ASP cc_start: 0.8389 (t70) cc_final: 0.8070 (t0) REVERT: e 114 LYS cc_start: 0.8502 (mtpt) cc_final: 0.8260 (mttp) REVERT: e 119 GLN cc_start: 0.8890 (tp40) cc_final: 0.8663 (tp40) REVERT: e 143 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7863 (tm-30) REVERT: f 51 ASP cc_start: 0.8011 (t0) cc_final: 0.7725 (t0) REVERT: f 109 ILE cc_start: 0.9006 (tt) cc_final: 0.8708 (mp) REVERT: f 110 GLU cc_start: 0.7618 (tt0) cc_final: 0.7314 (tm-30) REVERT: f 119 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8207 (tm-30) REVERT: f 175 PHE cc_start: 0.8395 (t80) cc_final: 0.8174 (t80) REVERT: f 211 GLU cc_start: 0.7565 (tp30) cc_final: 0.7354 (tp30) REVERT: g 119 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8154 (tm-30) REVERT: g 175 PHE cc_start: 0.8407 (t80) cc_final: 0.8150 (t80) outliers start: 296 outliers final: 176 residues processed: 1804 average time/residue: 0.5483 time to fit residues: 1661.0611 Evaluate side-chains 1487 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1310 time to evaluate : 5.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 119 SER Chi-restraints excluded: chain 1 residue 140 SER Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 110 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 140 SER Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 140 SER Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain M residue 140 SER Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain N residue 140 SER Chi-restraints excluded: chain N residue 164 GLN Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 158 LYS Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 62 LYS Chi-restraints excluded: chain T residue 116 ILE Chi-restraints excluded: chain U residue 17 THR Chi-restraints excluded: chain U residue 116 ILE Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 26 ILE 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 140 SER Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain W residue 26 ILE 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 140 SER Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 96 MET Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 110 VAL Chi-restraints excluded: chain X residue 119 SER Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 26 ILE 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 Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 165 ILE Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain a residue 212 ILE Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 78 THR Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 165 ILE Chi-restraints excluded: chain b residue 173 VAL Chi-restraints excluded: chain b residue 201 LEU Chi-restraints excluded: chain b residue 223 ILE Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain c residue 74 VAL Chi-restraints excluded: chain c residue 77 VAL Chi-restraints excluded: chain c residue 78 THR Chi-restraints excluded: chain c residue 165 ILE Chi-restraints excluded: chain c residue 173 VAL Chi-restraints excluded: chain c residue 216 THR Chi-restraints excluded: chain d residue 32 LYS Chi-restraints excluded: chain d residue 74 VAL Chi-restraints excluded: chain d residue 78 THR Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 165 ILE Chi-restraints excluded: chain d residue 233 LEU Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 151 CYS Chi-restraints excluded: chain e residue 165 ILE Chi-restraints excluded: chain e residue 173 VAL Chi-restraints excluded: chain e residue 216 THR Chi-restraints excluded: chain f residue 78 THR Chi-restraints excluded: chain f residue 151 CYS Chi-restraints excluded: chain f residue 216 THR Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 67 ILE Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 78 THR Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 173 VAL Chi-restraints excluded: chain g residue 191 THR Chi-restraints excluded: chain g residue 223 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 370 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 555 optimal weight: 2.9990 chunk 454 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 668 optimal weight: 1.9990 chunk 722 optimal weight: 8.9990 chunk 595 optimal weight: 8.9990 chunk 663 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 536 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 36 GLN ** 2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 141 GLN A 23 GLN A 61 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN H 88 ASN H 89 GLN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN I 88 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 ASN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 ASN ** L 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 ASN ** M 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 47 HIS O 79 HIS P 11 ASN P 47 HIS P 72 GLN P 75 GLN P 79 HIS P 200 HIS Q 79 HIS ** R 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 47 HIS S 79 HIS T 47 HIS T 79 HIS U 47 HIS ** V 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 73 ASN ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 68 GLN c 44 ASN c 68 GLN ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 68 GLN d 122 GLN e 122 GLN g 68 GLN g 219 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 58912 Z= 0.281 Angle : 0.696 13.699 79541 Z= 0.376 Chirality : 0.046 0.408 9310 Planarity : 0.004 0.054 10206 Dihedral : 6.128 53.881 8270 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.30 % Favored : 95.59 % Rotamer: Outliers : 5.89 % Allowed : 14.99 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: -0.45 (0.09), residues: 7441 helix: 1.20 (0.08), residues: 3416 sheet: -0.65 (0.12), residues: 1358 loop : -2.12 (0.10), residues: 2667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP O 28 HIS 0.010 0.002 HIS I 28 PHE 0.028 0.002 PHE d 42 TYR 0.038 0.002 TYR Z 66 ARG 0.009 0.001 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1792 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 368 poor density : 1424 time to evaluate : 5.184 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: 1 2 THR cc_start: 0.8109 (t) cc_final: 0.7252 (m) REVERT: 1 139 GLU cc_start: 0.8078 (tp30) cc_final: 0.7857 (tp30) REVERT: 2 58 TYR cc_start: 0.8334 (t80) cc_final: 0.7897 (t80) REVERT: 2 66 TYR cc_start: 0.8604 (t80) cc_final: 0.8370 (t80) REVERT: A 98 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7681 (mm-40) REVERT: B 13 THR cc_start: 0.9191 (p) cc_final: 0.8977 (p) REVERT: B 73 TYR cc_start: 0.8459 (m-80) cc_final: 0.8205 (m-80) REVERT: B 123 TYR cc_start: 0.9020 (m-10) cc_final: 0.8813 (m-80) REVERT: C 119 GLN cc_start: 0.8559 (tp40) cc_final: 0.8323 (tp40) REVERT: C 187 LYS cc_start: 0.8301 (mmtm) cc_final: 0.8017 (ptpt) REVERT: D 26 TYR cc_start: 0.8708 (m-10) cc_final: 0.8507 (m-10) REVERT: D 108 ASN cc_start: 0.7886 (t0) cc_final: 0.7645 (t0) REVERT: D 221 TYR cc_start: 0.8837 (OUTLIER) cc_final: 0.7637 (t80) REVERT: F 73 TYR cc_start: 0.8453 (m-10) cc_final: 0.8056 (m-10) REVERT: F 119 GLN cc_start: 0.8636 (tp40) cc_final: 0.8373 (tp40) REVERT: G 9 ASP cc_start: 0.8182 (t0) cc_final: 0.7933 (t0) REVERT: G 68 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7675 (mp10) REVERT: H 40 TYR cc_start: 0.8718 (m-80) cc_final: 0.8454 (m-10) REVERT: H 57 ARG cc_start: 0.8692 (mtm-85) cc_final: 0.8454 (mtm-85) REVERT: H 88 ASN cc_start: 0.8928 (OUTLIER) cc_final: 0.8618 (t0) REVERT: H 149 ASP cc_start: 0.7241 (t0) cc_final: 0.6886 (t0) REVERT: H 153 ASP cc_start: 0.7984 (m-30) cc_final: 0.7633 (m-30) REVERT: I 40 TYR cc_start: 0.8741 (m-10) cc_final: 0.8502 (m-10) REVERT: I 59 MET cc_start: 0.7939 (tpp) cc_final: 0.7651 (tpp) REVERT: I 96 MET cc_start: 0.7227 (mpt) cc_final: 0.6861 (mtt) REVERT: I 153 ASP cc_start: 0.8275 (m-30) cc_final: 0.7836 (m-30) REVERT: J 22 MET cc_start: 0.4492 (ttt) cc_final: 0.3916 (ttt) REVERT: J 64 GLU cc_start: 0.7891 (tp30) cc_final: 0.7280 (tp30) REVERT: J 96 MET cc_start: 0.7217 (mpt) cc_final: 0.6930 (mtm) REVERT: J 98 GLN cc_start: 0.8211 (mt0) cc_final: 0.7868 (mp10) REVERT: J 146 MET cc_start: 0.7889 (mtt) cc_final: 0.7540 (mtp) REVERT: J 164 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7996 (tp40) REVERT: K 86 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7765 (ttm) REVERT: K 98 GLN cc_start: 0.8420 (mt0) cc_final: 0.7914 (mp10) REVERT: L 8 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8251 (pp) REVERT: L 67 ARG cc_start: 0.8142 (ttp-110) cc_final: 0.7898 (ttp-110) REVERT: L 74 MET cc_start: 0.7750 (ttm) cc_final: 0.7439 (ttp) REVERT: L 95 TYR cc_start: 0.8677 (m-80) cc_final: 0.8438 (m-80) REVERT: L 96 MET cc_start: 0.7183 (mpt) cc_final: 0.6311 (mtt) REVERT: L 98 GLN cc_start: 0.8321 (tt0) cc_final: 0.7898 (mp-120) REVERT: L 149 ASP cc_start: 0.7863 (m-30) cc_final: 0.7618 (t0) REVERT: L 153 ASP cc_start: 0.7888 (m-30) cc_final: 0.7644 (m-30) REVERT: M 96 MET cc_start: 0.6944 (mpt) cc_final: 0.6517 (mtt) REVERT: N 96 MET cc_start: 0.6846 (mpt) cc_final: 0.6427 (mtm) REVERT: N 98 GLN cc_start: 0.8294 (mt0) cc_final: 0.7949 (mp10) REVERT: N 111 PHE cc_start: 0.8572 (m-10) cc_final: 0.8343 (m-80) REVERT: N 123 ILE cc_start: 0.8881 (mp) cc_final: 0.8604 (mp) REVERT: N 149 ASP cc_start: 0.7371 (t0) cc_final: 0.6959 (t0) REVERT: N 153 ASP cc_start: 0.8206 (m-30) cc_final: 0.7901 (m-30) REVERT: O 122 ILE cc_start: 0.8120 (mt) cc_final: 0.7864 (mt) REVERT: P 22 PHE cc_start: 0.8713 (t80) cc_final: 0.8312 (t80) REVERT: P 115 LYS cc_start: 0.8837 (ttmt) cc_final: 0.8585 (ttmt) REVERT: P 230 PHE cc_start: 0.8962 (m-80) cc_final: 0.8733 (m-80) REVERT: Q 16 TYR cc_start: 0.8112 (m-80) cc_final: 0.7740 (m-10) REVERT: Q 116 ILE cc_start: 0.8944 (pt) cc_final: 0.8727 (mt) REVERT: Q 122 ILE cc_start: 0.8103 (mt) cc_final: 0.7826 (mt) REVERT: Q 148 TYR cc_start: 0.8397 (t80) cc_final: 0.8054 (t80) REVERT: R 204 MET cc_start: 0.8910 (mmm) cc_final: 0.7745 (mmt) REVERT: S 122 ILE cc_start: 0.7947 (mt) cc_final: 0.7637 (mt) REVERT: S 210 ASN cc_start: 0.8809 (t0) cc_final: 0.8482 (t0) REVERT: T 11 ASN cc_start: 0.7430 (m-40) cc_final: 0.7211 (m-40) REVERT: T 22 PHE cc_start: 0.8864 (t80) cc_final: 0.8565 (t80) REVERT: U 22 PHE cc_start: 0.8883 (t80) cc_final: 0.8634 (t80) REVERT: U 230 PHE cc_start: 0.8990 (m-80) cc_final: 0.8699 (m-80) REVERT: V 203 LEU cc_start: 0.2469 (OUTLIER) cc_final: 0.1897 (tm) REVERT: W 203 LEU cc_start: 0.2687 (OUTLIER) cc_final: 0.2109 (tm) REVERT: X 96 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6945 (mtt) REVERT: X 195 ARG cc_start: 0.6486 (mmm-85) cc_final: 0.6251 (mmt180) REVERT: Z 164 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8163 (mm-40) REVERT: a 119 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7652 (tm-30) REVERT: a 121 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8235 (tm-30) REVERT: a 143 GLN cc_start: 0.8240 (tm-30) cc_final: 0.7976 (tm-30) REVERT: b 40 MET cc_start: 0.8257 (ptp) cc_final: 0.7896 (ptm) REVERT: b 194 ILE cc_start: 0.9161 (tp) cc_final: 0.8935 (mt) REVERT: c 72 ASP cc_start: 0.7027 (m-30) cc_final: 0.6795 (t0) REVERT: c 175 PHE cc_start: 0.8683 (t80) cc_final: 0.8157 (t80) REVERT: c 219 ASN cc_start: 0.8988 (OUTLIER) cc_final: 0.8329 (p0) REVERT: d 32 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8506 (ptmm) REVERT: d 102 THR cc_start: 0.9376 (m) cc_final: 0.9158 (m) REVERT: d 194 ILE cc_start: 0.9190 (tp) cc_final: 0.8949 (mt) REVERT: e 72 ASP cc_start: 0.7338 (t0) cc_final: 0.6689 (t0) REVERT: e 90 ASP cc_start: 0.8327 (t70) cc_final: 0.8096 (t0) REVERT: e 121 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8029 (tm-30) REVERT: e 143 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7842 (tm-30) REVERT: e 152 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6927 (t0) REVERT: f 44 ASN cc_start: 0.7343 (p0) cc_final: 0.7075 (p0) REVERT: f 70 ILE cc_start: 0.9356 (mm) cc_final: 0.9096 (mt) REVERT: f 99 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: f 119 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8110 (tm-30) REVERT: f 175 PHE cc_start: 0.8449 (t80) cc_final: 0.7812 (t80) REVERT: f 194 ILE cc_start: 0.9211 (tp) cc_final: 0.8927 (mt) REVERT: g 44 ASN cc_start: 0.7541 (p0) cc_final: 0.7234 (p0) REVERT: g 110 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7412 (tm-30) REVERT: g 114 LYS cc_start: 0.8834 (mttt) cc_final: 0.8313 (mttm) REVERT: g 219 ASN cc_start: 0.8896 (OUTLIER) cc_final: 0.8365 (p0) outliers start: 368 outliers final: 252 residues processed: 1650 average time/residue: 0.5353 time to fit residues: 1492.1781 Evaluate side-chains 1506 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1242 time to evaluate : 5.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 68 LEU Chi-restraints excluded: chain 1 residue 85 ASN Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 112 SER Chi-restraints excluded: chain 1 residue 119 SER Chi-restraints excluded: chain 1 residue 146 MET Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 110 VAL Chi-restraints excluded: chain 2 residue 140 SER Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 10 ASP Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 198 LYS Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 86 MET Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 41 THR 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 129 SER Chi-restraints excluded: chain L residue 140 SER Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 10 ASP Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain N residue 135 TYR Chi-restraints excluded: chain N residue 164 GLN Chi-restraints excluded: chain N residue 169 SER Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain Q residue 158 LYS Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 62 LYS Chi-restraints excluded: chain T residue 116 ILE Chi-restraints excluded: chain T residue 149 LEU Chi-restraints excluded: chain U residue 17 THR Chi-restraints excluded: chain U residue 115 LYS Chi-restraints excluded: chain U residue 116 ILE Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 23 GLU Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 41 THR 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 112 SER Chi-restraints excluded: chain V residue 140 SER Chi-restraints excluded: chain V residue 147 THR Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 203 LEU Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 169 SER Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 203 LEU Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 86 MET Chi-restraints excluded: chain X residue 96 MET Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 110 VAL Chi-restraints excluded: chain X residue 119 SER Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain Y residue 26 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 119 SER Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain Z residue 8 LEU Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 141 ILE Chi-restraints excluded: chain a residue 142 ASP Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain a residue 179 GLU Chi-restraints excluded: chain a residue 219 ASN Chi-restraints excluded: chain a residue 223 ILE Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 173 VAL Chi-restraints excluded: chain b residue 201 LEU Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain c residue 74 VAL Chi-restraints excluded: chain c residue 77 VAL Chi-restraints excluded: chain c residue 113 VAL Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 141 ILE Chi-restraints excluded: chain c residue 173 VAL Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 216 THR Chi-restraints excluded: chain c residue 219 ASN Chi-restraints excluded: chain c residue 223 ILE Chi-restraints excluded: chain d residue 32 LYS Chi-restraints excluded: chain d residue 74 VAL Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 141 ILE Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 212 ILE Chi-restraints excluded: chain d residue 219 ASN Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain d residue 233 LEU Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 115 ARG Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 152 ASP Chi-restraints excluded: chain e residue 173 VAL Chi-restraints excluded: chain e residue 191 THR Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain e residue 216 THR Chi-restraints excluded: chain e residue 223 ILE Chi-restraints excluded: chain f residue 36 THR Chi-restraints excluded: chain f residue 99 GLU Chi-restraints excluded: chain f residue 124 THR Chi-restraints excluded: chain f residue 151 CYS Chi-restraints excluded: chain f residue 212 ILE Chi-restraints excluded: chain f residue 216 THR Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain f residue 233 LEU Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 78 THR Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 173 VAL Chi-restraints excluded: chain g residue 179 GLU Chi-restraints excluded: chain g residue 219 ASN Chi-restraints excluded: chain g residue 223 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 660 optimal weight: 10.0000 chunk 502 optimal weight: 5.9990 chunk 347 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 319 optimal weight: 6.9990 chunk 449 optimal weight: 2.9990 chunk 671 optimal weight: 7.9990 chunk 710 optimal weight: 3.9990 chunk 350 optimal weight: 10.0000 chunk 636 optimal weight: 6.9990 chunk 191 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 36 GLN ** 2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN G 61 GLN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN I 88 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 ASN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 ASN ** L 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 ASN ** M 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 ASN P 200 HIS R 11 ASN R 79 HIS ** U 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 79 HIS ** V 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 68 GLN a 122 GLN ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 68 GLN b 219 ASN c 44 ASN c 68 GLN ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 68 GLN ** d 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 68 GLN e 122 GLN ** e 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN ** f 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.079 58912 Z= 0.656 Angle : 0.893 14.666 79541 Z= 0.475 Chirality : 0.052 0.464 9310 Planarity : 0.005 0.058 10206 Dihedral : 6.555 55.269 8268 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.09 % Favored : 94.80 % Rotamer: Outliers : 7.72 % Allowed : 17.14 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.66 (0.09), residues: 7441 helix: 1.00 (0.08), residues: 3402 sheet: -0.85 (0.12), residues: 1372 loop : -2.10 (0.10), residues: 2667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 216 HIS 0.008 0.003 HIS X 28 PHE 0.038 0.003 PHE Q 190 TYR 0.051 0.003 TYR g 221 ARG 0.012 0.001 ARG Y 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1661 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 482 poor density : 1179 time to evaluate : 5.130 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: 2 58 TYR cc_start: 0.8450 (t80) cc_final: 0.8188 (t80) REVERT: 2 70 ARG cc_start: 0.7776 (mpt180) cc_final: 0.7360 (mpt180) REVERT: B 13 THR cc_start: 0.9425 (p) cc_final: 0.9217 (p) REVERT: B 221 TYR cc_start: 0.9089 (OUTLIER) cc_final: 0.6334 (t80) REVERT: C 221 TYR cc_start: 0.9086 (OUTLIER) cc_final: 0.6951 (t80) REVERT: D 125 GLN cc_start: 0.8690 (tt0) cc_final: 0.8255 (tt0) REVERT: F 13 THR cc_start: 0.9420 (p) cc_final: 0.9143 (p) REVERT: F 44 ASN cc_start: 0.8164 (m-40) cc_final: 0.7923 (t0) REVERT: G 132 TYR cc_start: 0.8948 (m-80) cc_final: 0.8704 (m-80) REVERT: G 150 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.6515 (p0) REVERT: G 160 TYR cc_start: 0.8413 (m-10) cc_final: 0.7617 (m-10) REVERT: H 123 ILE cc_start: 0.8783 (mp) cc_final: 0.8511 (mm) REVERT: H 153 ASP cc_start: 0.8170 (m-30) cc_final: 0.7840 (m-30) REVERT: H 184 TYR cc_start: 0.8808 (t80) cc_final: 0.8408 (t80) REVERT: I 17 GLU cc_start: 0.7459 (pp20) cc_final: 0.7101 (pp20) REVERT: I 96 MET cc_start: 0.7359 (mpt) cc_final: 0.6940 (mtt) REVERT: J 88 ASN cc_start: 0.8941 (OUTLIER) cc_final: 0.8560 (t0) REVERT: J 90 VAL cc_start: 0.7302 (OUTLIER) cc_final: 0.7085 (p) REVERT: J 96 MET cc_start: 0.7405 (mpt) cc_final: 0.6968 (mtm) REVERT: J 180 ARG cc_start: 0.8436 (tpp-160) cc_final: 0.8164 (tpp-160) REVERT: K 98 GLN cc_start: 0.8578 (mt0) cc_final: 0.8193 (mp-120) REVERT: L 17 GLU cc_start: 0.7543 (pp20) cc_final: 0.7071 (pp20) REVERT: L 29 LYS cc_start: 0.8571 (mtpp) cc_final: 0.8301 (mtmm) REVERT: L 64 GLU cc_start: 0.7973 (tp30) cc_final: 0.7714 (tp30) REVERT: L 96 MET cc_start: 0.7350 (mpt) cc_final: 0.6807 (mtm) REVERT: M 96 MET cc_start: 0.7466 (mpt) cc_final: 0.6949 (mtm) REVERT: M 164 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7917 (mm-40) REVERT: N 96 MET cc_start: 0.7752 (mpt) cc_final: 0.7342 (mtm) REVERT: N 98 GLN cc_start: 0.8460 (mt0) cc_final: 0.8111 (mp10) REVERT: N 113 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8453 (mp) REVERT: N 193 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7164 (mt-10) REVERT: O 142 MET cc_start: 0.8883 (tpp) cc_final: 0.8140 (tpp) REVERT: P 142 MET cc_start: 0.8908 (tpp) cc_final: 0.8207 (tpp) REVERT: P 204 MET cc_start: 0.8473 (mmm) cc_final: 0.7846 (mtt) REVERT: R 116 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8676 (mt) REVERT: R 119 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7676 (tt0) REVERT: S 210 ASN cc_start: 0.8857 (t0) cc_final: 0.8647 (t0) REVERT: T 11 ASN cc_start: 0.7492 (m-40) cc_final: 0.7237 (m-40) REVERT: T 68 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9017 (mm) REVERT: T 142 MET cc_start: 0.8984 (tpp) cc_final: 0.7977 (tpp) REVERT: V 203 LEU cc_start: 0.2781 (OUTLIER) cc_final: 0.2240 (tm) REVERT: W 203 LEU cc_start: 0.2757 (OUTLIER) cc_final: 0.2242 (tm) REVERT: X 58 TYR cc_start: 0.8483 (t80) cc_final: 0.8085 (t80) REVERT: X 62 GLU cc_start: 0.7996 (tp30) cc_final: 0.7792 (tp30) REVERT: X 96 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7247 (mtt) REVERT: Y 62 GLU cc_start: 0.7911 (tp30) cc_final: 0.7709 (mm-30) REVERT: Z 62 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7405 (mt-10) REVERT: a 40 MET cc_start: 0.8263 (ptp) cc_final: 0.8060 (ptp) REVERT: a 44 ASN cc_start: 0.7755 (p0) cc_final: 0.7415 (p0) REVERT: a 114 LYS cc_start: 0.8665 (mtpt) cc_final: 0.8330 (mttp) REVERT: a 119 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8074 (tm-30) REVERT: a 143 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7995 (tm-30) REVERT: a 151 CYS cc_start: 0.7486 (m) cc_final: 0.7107 (m) REVERT: a 212 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8629 (mp) REVERT: b 40 MET cc_start: 0.8609 (ptp) cc_final: 0.8250 (ptm) REVERT: b 152 ASP cc_start: 0.7483 (t0) cc_final: 0.7251 (t70) REVERT: c 40 MET cc_start: 0.8381 (ptp) cc_final: 0.8178 (ptm) REVERT: c 175 PHE cc_start: 0.8624 (t80) cc_final: 0.8293 (t80) REVERT: d 44 ASN cc_start: 0.7882 (p0) cc_final: 0.7626 (p0) REVERT: e 121 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8539 (tm-30) REVERT: e 143 GLN cc_start: 0.8119 (tm-30) cc_final: 0.7857 (tm-30) REVERT: e 175 PHE cc_start: 0.8547 (t80) cc_final: 0.8062 (t80) REVERT: e 219 ASN cc_start: 0.8632 (p0) cc_final: 0.8261 (p0) REVERT: f 44 ASN cc_start: 0.7365 (p0) cc_final: 0.7050 (p0) REVERT: f 119 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8131 (tm-30) REVERT: f 175 PHE cc_start: 0.8450 (t80) cc_final: 0.7970 (t80) REVERT: f 179 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7257 (tt0) REVERT: f 194 ILE cc_start: 0.9288 (tp) cc_final: 0.9076 (mt) REVERT: g 44 ASN cc_start: 0.7575 (p0) cc_final: 0.7161 (p0) REVERT: g 68 GLN cc_start: 0.8585 (pm20) cc_final: 0.8378 (pm20) REVERT: g 119 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8104 (tm-30) REVERT: g 175 PHE cc_start: 0.8767 (t80) cc_final: 0.8451 (t80) REVERT: g 219 ASN cc_start: 0.9303 (OUTLIER) cc_final: 0.9010 (p0) outliers start: 482 outliers final: 366 residues processed: 1490 average time/residue: 0.5240 time to fit residues: 1328.5313 Evaluate side-chains 1463 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 380 poor density : 1083 time to evaluate : 5.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 45 ILE Chi-restraints excluded: chain 1 residue 68 LEU Chi-restraints excluded: chain 1 residue 85 ASN Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 112 SER Chi-restraints excluded: chain 1 residue 119 SER Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 140 SER Chi-restraints excluded: chain 1 residue 146 MET Chi-restraints excluded: chain 1 residue 177 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 37 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 86 MET Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 110 VAL Chi-restraints excluded: chain 2 residue 140 SER Chi-restraints excluded: chain 2 residue 164 GLN Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 44 ASN Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 10 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 88 ASN Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 198 LYS Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 131 SER Chi-restraints excluded: chain K residue 140 SER Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 10 ASP Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 77 GLU 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 129 SER Chi-restraints excluded: chain L residue 140 SER Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain M residue 10 ASP Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 77 GLU Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain M residue 140 SER Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 104 ILE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain N residue 140 SER Chi-restraints excluded: chain N residue 169 SER Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 62 LYS Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 76 ASP Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain Q residue 158 LYS Chi-restraints excluded: chain Q residue 186 ILE Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 76 ASP Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 76 ASP Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain S residue 149 LEU Chi-restraints excluded: chain T residue 62 LYS Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain T residue 76 ASP Chi-restraints excluded: chain T residue 116 ILE Chi-restraints excluded: chain T residue 149 LEU Chi-restraints excluded: chain U residue 17 THR Chi-restraints excluded: chain U residue 116 ILE Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 23 GLU Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 41 THR 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 112 SER Chi-restraints excluded: chain V residue 119 SER Chi-restraints excluded: chain V residue 140 SER Chi-restraints excluded: chain V residue 147 THR Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 203 LEU Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 177 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 203 LEU Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 86 MET Chi-restraints excluded: chain X residue 96 MET Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 104 ILE Chi-restraints excluded: chain X residue 110 VAL Chi-restraints excluded: chain X residue 140 SER Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 45 ILE 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 112 SER Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 147 THR Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain Z residue 8 LEU Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 45 ILE Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 96 MET 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 140 SER Chi-restraints excluded: chain Z residue 146 MET Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 142 ASP Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain a residue 179 GLU Chi-restraints excluded: chain a residue 212 ILE Chi-restraints excluded: chain a residue 219 ASN Chi-restraints excluded: chain a residue 223 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 78 THR Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 141 ILE Chi-restraints excluded: chain b residue 173 VAL Chi-restraints excluded: chain b residue 201 LEU Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 74 VAL Chi-restraints excluded: chain c residue 77 VAL Chi-restraints excluded: chain c residue 78 THR Chi-restraints excluded: chain c residue 109 ILE Chi-restraints excluded: chain c residue 113 VAL Chi-restraints excluded: chain c residue 120 MET Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 141 ILE Chi-restraints excluded: chain c residue 163 THR Chi-restraints excluded: chain c residue 173 VAL Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 216 THR Chi-restraints excluded: chain c residue 219 ASN Chi-restraints excluded: chain c residue 223 ILE Chi-restraints excluded: chain d residue 74 VAL Chi-restraints excluded: chain d residue 78 THR Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 141 ILE Chi-restraints excluded: chain d residue 151 CYS Chi-restraints excluded: chain d residue 163 THR Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain d residue 177 GLU Chi-restraints excluded: chain d residue 179 GLU Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 212 ILE Chi-restraints excluded: chain d residue 219 ASN Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain d residue 233 LEU Chi-restraints excluded: chain e residue 47 LEU Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 115 ARG Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 163 THR Chi-restraints excluded: chain e residue 165 ILE Chi-restraints excluded: chain e residue 173 VAL Chi-restraints excluded: chain e residue 191 THR Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain e residue 216 THR Chi-restraints excluded: chain e residue 223 ILE Chi-restraints excluded: chain f residue 74 VAL Chi-restraints excluded: chain f residue 77 VAL Chi-restraints excluded: chain f residue 78 THR Chi-restraints excluded: chain f residue 113 VAL Chi-restraints excluded: chain f residue 124 THR Chi-restraints excluded: chain f residue 141 ILE Chi-restraints excluded: chain f residue 151 CYS Chi-restraints excluded: chain f residue 179 GLU Chi-restraints excluded: chain f residue 191 THR Chi-restraints excluded: chain f residue 212 ILE Chi-restraints excluded: chain f residue 216 THR Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain f residue 233 LEU Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 78 THR Chi-restraints excluded: chain g residue 81 LEU Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 141 ILE Chi-restraints excluded: chain g residue 163 THR Chi-restraints excluded: chain g residue 173 VAL Chi-restraints excluded: chain g residue 179 GLU Chi-restraints excluded: chain g residue 191 THR Chi-restraints excluded: chain g residue 219 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 591 optimal weight: 0.9990 chunk 403 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 528 optimal weight: 0.9990 chunk 293 optimal weight: 0.9990 chunk 606 optimal weight: 0.9980 chunk 491 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 362 optimal weight: 3.9990 chunk 637 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN D 61 GLN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 GLN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 GLN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 ASN ** M 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 ASN ** R 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 68 GLN b 44 ASN b 219 ASN c 68 GLN ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 68 GLN ** e 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 219 ASN f 68 GLN g 219 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 58912 Z= 0.213 Angle : 0.675 13.929 79541 Z= 0.364 Chirality : 0.044 0.324 9310 Planarity : 0.004 0.050 10206 Dihedral : 5.973 54.623 8268 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.39 % Favored : 95.51 % Rotamer: Outliers : 5.49 % Allowed : 19.70 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -0.02 (0.09), residues: 7441 helix: 1.62 (0.09), residues: 3430 sheet: -0.56 (0.13), residues: 1260 loop : -1.90 (0.11), residues: 2751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP O 216 HIS 0.007 0.001 HIS K 28 PHE 0.022 0.002 PHE U 190 TYR 0.032 0.002 TYR 1 66 ARG 0.005 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1669 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 343 poor density : 1326 time to evaluate : 5.161 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: 2 70 ARG cc_start: 0.7661 (mpt180) cc_final: 0.7292 (mpt180) REVERT: 2 180 ARG cc_start: 0.8148 (tpp80) cc_final: 0.7898 (ttm-80) REVERT: B 123 TYR cc_start: 0.9033 (m-10) cc_final: 0.8814 (m-80) REVERT: B 221 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.6528 (t80) REVERT: D 125 GLN cc_start: 0.8468 (tt0) cc_final: 0.8144 (tt0) REVERT: E 47 LEU cc_start: 0.8861 (pp) cc_final: 0.8493 (pt) REVERT: E 68 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7555 (mp10) REVERT: E 119 GLN cc_start: 0.8921 (tp40) cc_final: 0.8465 (tp40) REVERT: E 183 ASN cc_start: 0.8683 (m-40) cc_final: 0.8300 (t0) REVERT: F 119 GLN cc_start: 0.8696 (tp40) cc_final: 0.8428 (tp40) REVERT: G 68 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7782 (mp10) REVERT: G 132 TYR cc_start: 0.8677 (m-80) cc_final: 0.8390 (m-80) REVERT: G 221 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7821 (t80) REVERT: H 57 ARG cc_start: 0.8642 (mtm-85) cc_final: 0.8435 (mtm-85) REVERT: H 64 GLU cc_start: 0.8128 (tp30) cc_final: 0.7892 (tp30) REVERT: H 123 ILE cc_start: 0.8723 (mp) cc_final: 0.8472 (mm) REVERT: H 153 ASP cc_start: 0.8068 (m-30) cc_final: 0.7708 (m-30) REVERT: H 184 TYR cc_start: 0.8513 (t80) cc_final: 0.8216 (t80) REVERT: I 69 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8449 (mt0) REVERT: I 96 MET cc_start: 0.7346 (mpt) cc_final: 0.6824 (mtt) REVERT: I 153 ASP cc_start: 0.8256 (m-30) cc_final: 0.7926 (m-30) REVERT: J 55 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8172 (mm) REVERT: J 69 GLN cc_start: 0.8906 (mt0) cc_final: 0.8611 (mt0) REVERT: J 71 ARG cc_start: 0.8166 (mtm-85) cc_final: 0.7960 (mtt-85) REVERT: J 96 MET cc_start: 0.7099 (mpt) cc_final: 0.6690 (mtm) REVERT: K 53 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6876 (mt0) REVERT: K 98 GLN cc_start: 0.8415 (mt0) cc_final: 0.7972 (mp10) REVERT: L 64 GLU cc_start: 0.7697 (tp30) cc_final: 0.7405 (tp30) REVERT: L 95 TYR cc_start: 0.8561 (m-80) cc_final: 0.8155 (m-80) REVERT: L 96 MET cc_start: 0.6993 (mpt) cc_final: 0.6501 (mtm) REVERT: L 98 GLN cc_start: 0.8419 (tt0) cc_final: 0.8010 (mp-120) REVERT: M 71 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7613 (mtt-85) REVERT: M 96 MET cc_start: 0.6975 (mpt) cc_final: 0.6622 (mtm) REVERT: M 164 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7777 (mm-40) REVERT: N 17 GLU cc_start: 0.7450 (pp20) cc_final: 0.7171 (pp20) REVERT: N 96 MET cc_start: 0.7357 (mpt) cc_final: 0.6852 (mtm) REVERT: N 98 GLN cc_start: 0.8393 (mt0) cc_final: 0.8026 (mp10) REVERT: O 122 ILE cc_start: 0.8249 (mt) cc_final: 0.8031 (mt) REVERT: O 142 MET cc_start: 0.8727 (tpp) cc_final: 0.8062 (tpp) REVERT: P 142 MET cc_start: 0.8862 (tpp) cc_final: 0.8304 (tpp) REVERT: P 204 MET cc_start: 0.8545 (mmm) cc_final: 0.7764 (mtt) REVERT: Q 16 TYR cc_start: 0.7971 (m-80) cc_final: 0.7757 (m-80) REVERT: R 102 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7204 (pt0) REVERT: R 116 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8688 (mt) REVERT: R 119 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7768 (tm-30) REVERT: S 92 ILE cc_start: 0.9198 (mt) cc_final: 0.8995 (mp) REVERT: T 11 ASN cc_start: 0.7336 (m-40) cc_final: 0.7087 (m-40) REVERT: T 22 PHE cc_start: 0.8774 (t80) cc_final: 0.8511 (t80) REVERT: T 116 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8796 (mt) REVERT: T 119 GLU cc_start: 0.7936 (tt0) cc_final: 0.7719 (tt0) REVERT: T 142 MET cc_start: 0.8831 (tpp) cc_final: 0.7851 (tpp) REVERT: U 102 GLU cc_start: 0.7201 (pt0) cc_final: 0.6668 (pt0) REVERT: U 204 MET cc_start: 0.8564 (mmt) cc_final: 0.7832 (mmt) REVERT: V 203 LEU cc_start: 0.2618 (OUTLIER) cc_final: 0.2154 (tm) REVERT: W 93 MET cc_start: 0.6869 (mpp) cc_final: 0.6214 (ttt) REVERT: W 96 MET cc_start: 0.7271 (mpt) cc_final: 0.6911 (mpt) REVERT: W 203 LEU cc_start: 0.2369 (OUTLIER) cc_final: 0.1838 (tm) REVERT: X 17 GLU cc_start: 0.8178 (pm20) cc_final: 0.7820 (pm20) REVERT: X 66 TYR cc_start: 0.8473 (t80) cc_final: 0.7564 (t80) REVERT: X 96 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6761 (mpt) REVERT: Z 66 TYR cc_start: 0.8189 (t80) cc_final: 0.7834 (t80) REVERT: Z 96 MET cc_start: 0.7241 (OUTLIER) cc_final: 0.6925 (mtt) REVERT: a 44 ASN cc_start: 0.7569 (p0) cc_final: 0.7196 (p0) REVERT: a 114 LYS cc_start: 0.8607 (mtpt) cc_final: 0.8326 (mttm) REVERT: a 119 GLN cc_start: 0.8615 (tm-30) cc_final: 0.7559 (tm-30) REVERT: a 121 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8477 (tm-30) REVERT: a 143 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7818 (tm-30) REVERT: a 151 CYS cc_start: 0.7453 (m) cc_final: 0.7065 (m) REVERT: a 175 PHE cc_start: 0.8589 (t80) cc_final: 0.8072 (t80) REVERT: a 201 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7670 (tt) REVERT: a 219 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8300 (p0) REVERT: b 40 MET cc_start: 0.8333 (ptp) cc_final: 0.7996 (ptm) REVERT: b 61 GLN cc_start: 0.6614 (mp10) cc_final: 0.6186 (mp10) REVERT: c 175 PHE cc_start: 0.8524 (t80) cc_final: 0.7972 (t80) REVERT: c 219 ASN cc_start: 0.8951 (m-40) cc_final: 0.8698 (p0) REVERT: d 32 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8441 (ptmm) REVERT: f 44 ASN cc_start: 0.7336 (p0) cc_final: 0.6927 (p0) REVERT: f 99 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7868 (tm-30) REVERT: f 113 VAL cc_start: 0.8915 (p) cc_final: 0.8612 (p) REVERT: f 175 PHE cc_start: 0.8434 (t80) cc_final: 0.7930 (t80) REVERT: f 201 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6860 (tp) REVERT: g 44 ASN cc_start: 0.7541 (p0) cc_final: 0.7040 (p0) REVERT: g 68 GLN cc_start: 0.8325 (pm20) cc_final: 0.8079 (pm20) REVERT: g 114 LYS cc_start: 0.8717 (mttt) cc_final: 0.8246 (mttm) REVERT: g 121 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8435 (tm-30) REVERT: g 219 ASN cc_start: 0.8953 (m110) cc_final: 0.8464 (p0) outliers start: 343 outliers final: 245 residues processed: 1539 average time/residue: 0.5259 time to fit residues: 1377.2313 Evaluate side-chains 1433 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1171 time to evaluate : 5.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 68 LEU Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 146 MET Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 37 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 110 VAL Chi-restraints excluded: chain 2 residue 164 GLN Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 10 ASP Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 140 SER Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain L residue 10 ASP Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 10 ASP Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 77 GLU Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 104 ILE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain N residue 140 SER Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain O residue 62 LYS Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 76 ASP Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain Q residue 186 ILE Chi-restraints excluded: chain Q residue 229 MET Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 76 ASP Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain S residue 76 ASP Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain S residue 149 LEU Chi-restraints excluded: chain T residue 62 LYS Chi-restraints excluded: chain T residue 76 ASP Chi-restraints excluded: chain T residue 116 ILE Chi-restraints excluded: chain T residue 149 LEU Chi-restraints excluded: chain U residue 116 ILE Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 23 GLU Chi-restraints excluded: chain V residue 26 ILE 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 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 203 LEU Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 203 LEU Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 86 MET Chi-restraints excluded: chain X residue 96 MET Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 104 ILE Chi-restraints excluded: chain X residue 110 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 45 ILE Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 147 THR Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain Z residue 8 LEU Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 45 ILE Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 96 MET Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 141 ILE Chi-restraints excluded: chain a residue 142 ASP Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain a residue 201 LEU Chi-restraints excluded: chain a residue 219 ASN Chi-restraints excluded: chain a residue 223 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 141 ILE Chi-restraints excluded: chain b residue 170 ASP Chi-restraints excluded: chain b residue 173 VAL Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain c residue 74 VAL Chi-restraints excluded: chain c residue 77 VAL Chi-restraints excluded: chain c residue 113 VAL Chi-restraints excluded: chain c residue 120 MET Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 141 ILE Chi-restraints excluded: chain c residue 173 VAL Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 216 THR Chi-restraints excluded: chain c residue 223 ILE Chi-restraints excluded: chain d residue 32 LYS Chi-restraints excluded: chain d residue 74 VAL Chi-restraints excluded: chain d residue 141 ILE Chi-restraints excluded: chain d residue 179 GLU Chi-restraints excluded: chain d residue 219 ASN Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 165 ILE Chi-restraints excluded: chain e residue 173 VAL Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain e residue 216 THR Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 74 VAL Chi-restraints excluded: chain f residue 77 VAL Chi-restraints excluded: chain f residue 99 GLU Chi-restraints excluded: chain f residue 124 THR Chi-restraints excluded: chain f residue 141 ILE Chi-restraints excluded: chain f residue 151 CYS Chi-restraints excluded: chain f residue 201 LEU Chi-restraints excluded: chain f residue 212 ILE Chi-restraints excluded: chain f residue 216 THR Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 141 ILE Chi-restraints excluded: chain g residue 173 VAL Chi-restraints excluded: chain g residue 179 GLU Chi-restraints excluded: chain g residue 191 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 239 optimal weight: 3.9990 chunk 639 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 417 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 711 optimal weight: 5.9990 chunk 590 optimal weight: 7.9990 chunk 329 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 235 optimal weight: 0.9980 chunk 373 optimal weight: 0.7980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN I 88 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 GLN J 30 ASN J 88 ASN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 ASN ** M 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN N 88 ASN ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 ASN ** R 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 200 HIS ** V 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 68 GLN b 44 ASN c 68 GLN ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 GLN ** d 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 125 GLN f 68 GLN f 125 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 58912 Z= 0.295 Angle : 0.689 13.822 79541 Z= 0.370 Chirality : 0.045 0.356 9310 Planarity : 0.004 0.049 10206 Dihedral : 5.900 54.504 8266 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.20 % Rotamer: Outliers : 5.78 % Allowed : 20.24 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 0.13 (0.09), residues: 7441 helix: 1.74 (0.09), residues: 3430 sheet: -0.58 (0.12), residues: 1372 loop : -1.80 (0.11), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 216 HIS 0.007 0.002 HIS L 28 PHE 0.025 0.002 PHE G 175 TYR 0.037 0.002 TYR Y 66 ARG 0.008 0.000 ARG J 195 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1588 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 361 poor density : 1227 time to evaluate : 5.175 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: A 221 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.7652 (t80) REVERT: B 123 TYR cc_start: 0.8942 (m-10) cc_final: 0.8722 (m-80) REVERT: B 221 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.6336 (t80) REVERT: C 221 TYR cc_start: 0.9072 (OUTLIER) cc_final: 0.6734 (t80) REVERT: D 125 GLN cc_start: 0.8547 (tt0) cc_final: 0.8223 (tt0) REVERT: E 47 LEU cc_start: 0.8887 (pp) cc_final: 0.8529 (pt) REVERT: E 68 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7618 (mp10) REVERT: E 119 GLN cc_start: 0.8970 (tp40) cc_final: 0.8520 (tp40) REVERT: E 183 ASN cc_start: 0.8678 (m-40) cc_final: 0.8315 (t0) REVERT: E 221 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.7767 (t80) REVERT: F 119 GLN cc_start: 0.8762 (tp40) cc_final: 0.8494 (tp40) REVERT: F 221 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.7944 (t80) REVERT: G 68 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7784 (mp10) REVERT: G 221 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.8136 (t80) REVERT: H 17 GLU cc_start: 0.7402 (pp20) cc_final: 0.7187 (pp20) REVERT: H 153 ASP cc_start: 0.8008 (m-30) cc_final: 0.7672 (m-30) REVERT: H 184 TYR cc_start: 0.8527 (t80) cc_final: 0.8311 (t80) REVERT: I 59 MET cc_start: 0.7800 (tpp) cc_final: 0.7587 (tpp) REVERT: I 69 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8503 (mt0) REVERT: I 96 MET cc_start: 0.7353 (mpt) cc_final: 0.7132 (mtm) REVERT: I 153 ASP cc_start: 0.8214 (m-30) cc_final: 0.7867 (m-30) REVERT: J 69 GLN cc_start: 0.8902 (mt0) cc_final: 0.8633 (mt0) REVERT: J 96 MET cc_start: 0.6919 (mpt) cc_final: 0.6539 (mtm) REVERT: J 180 ARG cc_start: 0.8475 (tpp-160) cc_final: 0.8258 (tpp-160) REVERT: K 53 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.6743 (mt0) REVERT: K 98 GLN cc_start: 0.8414 (mt0) cc_final: 0.8026 (mp-120) REVERT: K 180 ARG cc_start: 0.8418 (tpp-160) cc_final: 0.8215 (tpm170) REVERT: L 64 GLU cc_start: 0.7744 (tp30) cc_final: 0.7516 (tp30) REVERT: L 95 TYR cc_start: 0.8546 (m-80) cc_final: 0.8210 (m-80) REVERT: L 96 MET cc_start: 0.7120 (mpt) cc_final: 0.6493 (mtm) REVERT: L 98 GLN cc_start: 0.8463 (tt0) cc_final: 0.8046 (mp-120) REVERT: M 59 MET cc_start: 0.8328 (mmm) cc_final: 0.8101 (tpt) REVERT: M 86 MET cc_start: 0.8708 (ttp) cc_final: 0.8339 (ttp) REVERT: N 17 GLU cc_start: 0.7451 (pp20) cc_final: 0.7154 (pp20) REVERT: N 96 MET cc_start: 0.7347 (mpt) cc_final: 0.7097 (mtm) REVERT: N 98 GLN cc_start: 0.8365 (mt0) cc_final: 0.8004 (mp10) REVERT: O 122 ILE cc_start: 0.8249 (mt) cc_final: 0.8033 (mt) REVERT: O 187 ASP cc_start: 0.8447 (m-30) cc_final: 0.8127 (m-30) REVERT: P 116 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8748 (mt) REVERT: P 142 MET cc_start: 0.8818 (tpp) cc_final: 0.8229 (tpp) REVERT: R 86 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8290 (mm-30) REVERT: R 102 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7307 (pt0) REVERT: R 119 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7751 (tm-30) REVERT: S 5 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6605 (mpt-90) REVERT: S 92 ILE cc_start: 0.9192 (mt) cc_final: 0.8972 (mp) REVERT: S 142 MET cc_start: 0.8784 (tpp) cc_final: 0.8183 (tpp) REVERT: T 11 ASN cc_start: 0.7382 (m-40) cc_final: 0.7137 (m-40) REVERT: T 22 PHE cc_start: 0.8845 (t80) cc_final: 0.8535 (t80) REVERT: T 92 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.8958 (mp) REVERT: T 142 MET cc_start: 0.8868 (tpp) cc_final: 0.7995 (tpp) REVERT: U 16 TYR cc_start: 0.7706 (m-80) cc_final: 0.7469 (m-80) REVERT: V 66 TYR cc_start: 0.8328 (t80) cc_final: 0.8035 (t80) REVERT: W 96 MET cc_start: 0.7316 (mpt) cc_final: 0.6926 (mpt) REVERT: W 203 LEU cc_start: 0.2261 (OUTLIER) cc_final: 0.1601 (tm) REVERT: X 93 MET cc_start: 0.6769 (mpp) cc_final: 0.6300 (ttt) REVERT: Y 96 MET cc_start: 0.7251 (mpt) cc_final: 0.6904 (mtt) REVERT: Y 191 GLN cc_start: 0.6725 (tm-30) cc_final: 0.6433 (tm-30) REVERT: Z 66 TYR cc_start: 0.8340 (t80) cc_final: 0.8049 (t80) REVERT: a 114 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8367 (mttm) REVERT: a 119 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8100 (tm-30) REVERT: a 121 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8458 (tm-30) REVERT: a 143 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7815 (tm-30) REVERT: a 151 CYS cc_start: 0.7427 (m) cc_final: 0.6998 (m) REVERT: a 201 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7354 (tt) REVERT: a 219 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8342 (p0) REVERT: b 40 MET cc_start: 0.8400 (ptp) cc_final: 0.8011 (ptm) REVERT: b 61 GLN cc_start: 0.6608 (mp10) cc_final: 0.6193 (mp10) REVERT: b 121 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8420 (tm-30) REVERT: b 170 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.7067 (p0) REVERT: d 32 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8492 (ptmm) REVERT: d 44 ASN cc_start: 0.7806 (p0) cc_final: 0.7465 (p0) REVERT: d 119 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8063 (tm-30) REVERT: e 68 GLN cc_start: 0.8194 (pm20) cc_final: 0.7870 (pm20) REVERT: e 121 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8487 (tm-30) REVERT: e 219 ASN cc_start: 0.8789 (p0) cc_final: 0.8274 (p0) REVERT: f 44 ASN cc_start: 0.7383 (p0) cc_final: 0.6885 (p0) REVERT: f 113 VAL cc_start: 0.8929 (p) cc_final: 0.8553 (p) REVERT: f 201 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7129 (tt) REVERT: g 61 GLN cc_start: 0.6390 (mp10) cc_final: 0.5986 (mp10) REVERT: g 68 GLN cc_start: 0.8373 (pm20) cc_final: 0.8057 (pm20) REVERT: g 119 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8117 (tm-30) REVERT: g 121 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8578 (tm-30) REVERT: g 219 ASN cc_start: 0.9020 (m110) cc_final: 0.8536 (p0) REVERT: g 221 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.7299 (t80) outliers start: 361 outliers final: 273 residues processed: 1446 average time/residue: 0.5335 time to fit residues: 1304.1678 Evaluate side-chains 1440 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1148 time to evaluate : 5.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 68 LEU Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 119 SER Chi-restraints excluded: chain 1 residue 146 MET Chi-restraints excluded: chain 1 residue 177 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 37 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 110 VAL Chi-restraints excluded: chain 2 residue 164 GLN Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 10 ASP Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 101 VAL 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 K residue 10 ASP Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 131 SER Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain L residue 10 ASP Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain M residue 10 ASP Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain M residue 140 SER Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 104 ILE Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain N residue 140 SER Chi-restraints excluded: chain N residue 169 SER Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain O residue 62 LYS Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain Q residue 186 ILE Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 76 ASP Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain S residue 5 ARG Chi-restraints excluded: chain S residue 76 ASP Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain S residue 149 LEU Chi-restraints excluded: chain T residue 76 ASP Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain T residue 116 ILE Chi-restraints excluded: chain T residue 149 LEU Chi-restraints excluded: chain U residue 116 ILE Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 23 GLU Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 147 THR Chi-restraints excluded: chain V residue 177 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 146 MET Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 164 GLN Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 203 LEU Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 26 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 110 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain Y residue 26 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 120 VAL Chi-restraints excluded: chain Y residue 146 MET Chi-restraints excluded: chain Y residue 147 THR Chi-restraints excluded: chain Y residue 177 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain Z residue 8 LEU Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 96 MET Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 141 ILE Chi-restraints excluded: chain a residue 142 ASP Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain a residue 201 LEU Chi-restraints excluded: chain a residue 219 ASN Chi-restraints excluded: chain a residue 223 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 141 ILE Chi-restraints excluded: chain b residue 170 ASP Chi-restraints excluded: chain b residue 173 VAL Chi-restraints excluded: chain b residue 201 LEU Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 74 VAL Chi-restraints excluded: chain c residue 77 VAL Chi-restraints excluded: chain c residue 113 VAL Chi-restraints excluded: chain c residue 120 MET Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 141 ILE Chi-restraints excluded: chain c residue 173 VAL Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 216 THR Chi-restraints excluded: chain c residue 223 ILE Chi-restraints excluded: chain d residue 32 LYS Chi-restraints excluded: chain d residue 74 VAL Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 132 TYR Chi-restraints excluded: chain d residue 141 ILE Chi-restraints excluded: chain d residue 163 THR Chi-restraints excluded: chain d residue 177 GLU Chi-restraints excluded: chain d residue 179 GLU Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 212 ILE Chi-restraints excluded: chain d residue 219 ASN Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 40 MET Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 115 ARG Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 132 TYR Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 173 VAL Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain e residue 216 THR Chi-restraints excluded: chain e residue 223 ILE Chi-restraints excluded: chain f residue 36 THR Chi-restraints excluded: chain f residue 74 VAL Chi-restraints excluded: chain f residue 77 VAL Chi-restraints excluded: chain f residue 124 THR Chi-restraints excluded: chain f residue 141 ILE Chi-restraints excluded: chain f residue 151 CYS Chi-restraints excluded: chain f residue 191 THR Chi-restraints excluded: chain f residue 201 LEU Chi-restraints excluded: chain f residue 212 ILE Chi-restraints excluded: chain f residue 216 THR Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 67 ILE Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 78 THR Chi-restraints excluded: chain g residue 81 LEU Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 141 ILE Chi-restraints excluded: chain g residue 173 VAL Chi-restraints excluded: chain g residue 191 THR Chi-restraints excluded: chain g residue 221 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 685 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 405 optimal weight: 5.9990 chunk 519 optimal weight: 0.9990 chunk 402 optimal weight: 6.9990 chunk 598 optimal weight: 9.9990 chunk 397 optimal weight: 10.0000 chunk 708 optimal weight: 4.9990 chunk 443 optimal weight: 10.0000 chunk 431 optimal weight: 0.0870 chunk 327 optimal weight: 0.5980 overall best weight: 1.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN I 88 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 GLN J 88 ASN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 ASN ** R 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 88 ASN ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 85 ASN ** Z 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 68 GLN b 125 GLN c 68 GLN ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 58912 Z= 0.273 Angle : 0.684 13.931 79541 Z= 0.366 Chirality : 0.045 0.326 9310 Planarity : 0.004 0.046 10206 Dihedral : 5.816 54.544 8266 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.49 % Favored : 95.42 % Rotamer: Outliers : 5.70 % Allowed : 20.50 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.25 (0.10), residues: 7441 helix: 1.86 (0.09), residues: 3430 sheet: -0.54 (0.12), residues: 1372 loop : -1.75 (0.11), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 216 HIS 0.004 0.001 HIS L 28 PHE 0.025 0.002 PHE a 175 TYR 0.048 0.002 TYR 1 66 ARG 0.007 0.000 ARG M 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1571 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 356 poor density : 1215 time to evaluate : 5.180 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: A 227 GLU cc_start: 0.8081 (mp0) cc_final: 0.7597 (pm20) REVERT: B 221 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.6344 (t80) REVERT: C 221 TYR cc_start: 0.9081 (OUTLIER) cc_final: 0.6834 (t80) REVERT: D 125 GLN cc_start: 0.8543 (tt0) cc_final: 0.8184 (tt0) REVERT: D 231 LYS cc_start: 0.8793 (mtpt) cc_final: 0.8505 (mmmm) REVERT: E 183 ASN cc_start: 0.8669 (m-40) cc_final: 0.8341 (t0) REVERT: F 119 GLN cc_start: 0.8732 (tp40) cc_final: 0.8482 (tp40) REVERT: F 221 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.7822 (t80) REVERT: G 68 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7719 (mp10) REVERT: G 221 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.8059 (t80) REVERT: H 153 ASP cc_start: 0.7966 (m-30) cc_final: 0.7621 (m-30) REVERT: H 184 TYR cc_start: 0.8554 (t80) cc_final: 0.8345 (t80) REVERT: I 59 MET cc_start: 0.7665 (tpp) cc_final: 0.7347 (tpp) REVERT: I 69 GLN cc_start: 0.8812 (mt0) cc_final: 0.8420 (mt0) REVERT: I 96 MET cc_start: 0.7337 (mpt) cc_final: 0.7069 (mtm) REVERT: I 153 ASP cc_start: 0.8244 (m-30) cc_final: 0.7898 (m-30) REVERT: J 69 GLN cc_start: 0.8903 (mt0) cc_final: 0.8648 (mt0) REVERT: J 88 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8377 (t0) REVERT: J 96 MET cc_start: 0.6820 (mpt) cc_final: 0.6437 (mtm) REVERT: K 53 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6848 (mt0) REVERT: K 98 GLN cc_start: 0.8358 (mt0) cc_final: 0.7985 (mp-120) REVERT: L 95 TYR cc_start: 0.8465 (m-80) cc_final: 0.8210 (m-80) REVERT: L 96 MET cc_start: 0.7212 (mpt) cc_final: 0.6495 (mtm) REVERT: L 98 GLN cc_start: 0.8455 (tt0) cc_final: 0.8034 (mp-120) REVERT: L 153 ASP cc_start: 0.7865 (m-30) cc_final: 0.7602 (m-30) REVERT: N 17 GLU cc_start: 0.7435 (pp20) cc_final: 0.7139 (pp20) REVERT: N 96 MET cc_start: 0.7174 (mpt) cc_final: 0.6925 (mtm) REVERT: N 98 GLN cc_start: 0.8407 (mt0) cc_final: 0.7995 (mp10) REVERT: O 122 ILE cc_start: 0.8210 (mt) cc_final: 0.7985 (mt) REVERT: O 187 ASP cc_start: 0.8429 (m-30) cc_final: 0.8156 (m-30) REVERT: P 142 MET cc_start: 0.8784 (tpp) cc_final: 0.8427 (ttm) REVERT: R 86 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8210 (mm-30) REVERT: R 102 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7289 (pt0) REVERT: S 5 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6602 (mpt-90) REVERT: S 116 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8337 (mt) REVERT: T 11 ASN cc_start: 0.7359 (m-40) cc_final: 0.7128 (m-40) REVERT: T 22 PHE cc_start: 0.8830 (t80) cc_final: 0.8569 (t80) REVERT: T 92 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.8979 (mp) REVERT: T 142 MET cc_start: 0.8870 (tpp) cc_final: 0.8012 (tpp) REVERT: U 16 TYR cc_start: 0.7573 (m-80) cc_final: 0.7356 (m-80) REVERT: W 96 MET cc_start: 0.7240 (mpt) cc_final: 0.6911 (mpt) REVERT: W 203 LEU cc_start: 0.2171 (OUTLIER) cc_final: 0.1529 (tm) REVERT: X 17 GLU cc_start: 0.8136 (pm20) cc_final: 0.7610 (pm20) REVERT: X 93 MET cc_start: 0.7115 (mpp) cc_final: 0.6530 (ttm) REVERT: a 114 LYS cc_start: 0.8621 (mtpt) cc_final: 0.8349 (mttm) REVERT: a 119 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8210 (tm-30) REVERT: a 121 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8476 (tm-30) REVERT: a 143 GLN cc_start: 0.8240 (tm-30) cc_final: 0.7812 (tm-30) REVERT: a 151 CYS cc_start: 0.7416 (m) cc_final: 0.6995 (m) REVERT: a 201 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7347 (tt) REVERT: a 219 ASN cc_start: 0.8693 (OUTLIER) cc_final: 0.8318 (p0) REVERT: a 221 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.7418 (t80) REVERT: b 40 MET cc_start: 0.8387 (ptp) cc_final: 0.8034 (ptm) REVERT: b 61 GLN cc_start: 0.6563 (mp10) cc_final: 0.6111 (mp10) REVERT: b 170 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.7073 (p0) REVERT: c 175 PHE cc_start: 0.8780 (t80) cc_final: 0.8550 (t80) REVERT: d 32 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8533 (ptmm) REVERT: d 44 ASN cc_start: 0.7697 (p0) cc_final: 0.7288 (p0) REVERT: d 90 ASP cc_start: 0.8346 (t70) cc_final: 0.8099 (t0) REVERT: d 119 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8066 (tm-30) REVERT: d 175 PHE cc_start: 0.8462 (t80) cc_final: 0.7317 (t80) REVERT: d 221 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.7580 (t80) REVERT: e 68 GLN cc_start: 0.8207 (pm20) cc_final: 0.7765 (pm20) REVERT: e 121 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8496 (tm-30) REVERT: e 219 ASN cc_start: 0.8813 (p0) cc_final: 0.8349 (p0) REVERT: f 44 ASN cc_start: 0.7332 (p0) cc_final: 0.6796 (p0) REVERT: f 113 VAL cc_start: 0.8900 (p) cc_final: 0.8502 (p) REVERT: f 201 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7024 (tt) REVERT: g 61 GLN cc_start: 0.6397 (mp10) cc_final: 0.5992 (mp10) REVERT: g 68 GLN cc_start: 0.8438 (pm20) cc_final: 0.8067 (pm20) REVERT: g 119 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8145 (tm-30) REVERT: g 121 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8551 (tm-30) REVERT: g 219 ASN cc_start: 0.8942 (m110) cc_final: 0.8469 (p0) REVERT: g 221 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.7102 (t80) outliers start: 356 outliers final: 278 residues processed: 1432 average time/residue: 0.5297 time to fit residues: 1285.9133 Evaluate side-chains 1445 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 1148 time to evaluate : 5.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 68 LEU Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 97 VAL Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 119 SER Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 146 MET Chi-restraints excluded: chain 1 residue 177 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 37 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 70 ARG Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 110 VAL Chi-restraints excluded: chain 2 residue 164 GLN Chi-restraints excluded: chain 2 residue 177 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain H residue 10 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 88 ASN Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 131 SER Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain L residue 10 ASP Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain M residue 10 ASP Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 104 ILE Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain N residue 140 SER Chi-restraints excluded: chain N residue 146 MET Chi-restraints excluded: chain N residue 169 SER Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain O residue 62 LYS Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 76 ASP Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain S residue 5 ARG Chi-restraints excluded: chain S residue 76 ASP Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain S residue 149 LEU Chi-restraints excluded: chain T residue 62 LYS Chi-restraints excluded: chain T residue 76 ASP Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain T residue 116 ILE Chi-restraints excluded: chain T residue 149 LEU Chi-restraints excluded: chain U residue 116 ILE Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 23 GLU Chi-restraints excluded: chain V residue 26 ILE 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 147 THR Chi-restraints excluded: chain V residue 177 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 203 LEU Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 26 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 110 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain Y residue 26 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 120 VAL Chi-restraints excluded: chain Y residue 146 MET Chi-restraints excluded: chain Y residue 147 THR Chi-restraints excluded: chain Y residue 177 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain Z residue 8 LEU Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 45 ILE Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 93 MET Chi-restraints excluded: chain Z residue 96 MET 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 155 VAL Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 141 ILE Chi-restraints excluded: chain a residue 142 ASP Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain a residue 201 LEU Chi-restraints excluded: chain a residue 219 ASN Chi-restraints excluded: chain a residue 221 TYR Chi-restraints excluded: chain a residue 223 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 141 ILE Chi-restraints excluded: chain b residue 170 ASP Chi-restraints excluded: chain b residue 201 LEU Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 74 VAL Chi-restraints excluded: chain c residue 77 VAL Chi-restraints excluded: chain c residue 113 VAL Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 141 ILE Chi-restraints excluded: chain c residue 173 VAL Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 216 THR Chi-restraints excluded: chain c residue 223 ILE Chi-restraints excluded: chain d residue 32 LYS Chi-restraints excluded: chain d residue 49 ILE Chi-restraints excluded: chain d residue 74 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 132 TYR Chi-restraints excluded: chain d residue 141 ILE Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 212 ILE Chi-restraints excluded: chain d residue 219 ASN Chi-restraints excluded: chain d residue 221 TYR Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 40 MET Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 132 TYR Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 173 VAL Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain e residue 216 THR Chi-restraints excluded: chain e residue 223 ILE Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 67 ILE Chi-restraints excluded: chain f residue 74 VAL Chi-restraints excluded: chain f residue 77 VAL Chi-restraints excluded: chain f residue 124 THR Chi-restraints excluded: chain f residue 141 ILE Chi-restraints excluded: chain f residue 151 CYS Chi-restraints excluded: chain f residue 201 LEU Chi-restraints excluded: chain f residue 212 ILE Chi-restraints excluded: chain f residue 216 THR Chi-restraints excluded: chain f residue 223 ILE Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 67 ILE Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 78 THR Chi-restraints excluded: chain g residue 81 LEU Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 141 ILE Chi-restraints excluded: chain g residue 173 VAL Chi-restraints excluded: chain g residue 191 THR Chi-restraints excluded: chain g residue 221 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 438 optimal weight: 0.9990 chunk 282 optimal weight: 0.8980 chunk 423 optimal weight: 0.9990 chunk 213 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 450 optimal weight: 0.8980 chunk 482 optimal weight: 3.9990 chunk 350 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 556 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 88 ASN ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 88 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 GLN J 88 ASN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 ASN ** L 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 ASN ** V 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 88 ASN ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 88 ASN ** X 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 88 ASN ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 68 GLN c 68 GLN ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 58912 Z= 0.202 Angle : 0.660 13.286 79541 Z= 0.354 Chirality : 0.044 0.279 9310 Planarity : 0.004 0.051 10206 Dihedral : 5.647 54.648 8266 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.48 % Rotamer: Outliers : 4.72 % Allowed : 21.67 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.42 (0.10), residues: 7441 helix: 1.99 (0.09), residues: 3437 sheet: -0.45 (0.12), residues: 1407 loop : -1.70 (0.12), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 216 HIS 0.005 0.001 HIS 1 28 PHE 0.023 0.001 PHE a 175 TYR 0.047 0.001 TYR 1 66 ARG 0.008 0.000 ARG O 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1590 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 1295 time to evaluate : 5.800 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: 2 180 ARG cc_start: 0.8384 (tpp80) cc_final: 0.8047 (ttm-80) REVERT: A 221 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.7613 (t80) REVERT: A 227 GLU cc_start: 0.8138 (mp0) cc_final: 0.7686 (pm20) REVERT: B 107 VAL cc_start: 0.6650 (OUTLIER) cc_final: 0.6445 (m) REVERT: B 221 TYR cc_start: 0.9030 (OUTLIER) cc_final: 0.6356 (t80) REVERT: C 221 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.6963 (t80) REVERT: D 68 GLN cc_start: 0.8007 (mp10) cc_final: 0.7355 (mp10) REVERT: D 106 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.7757 (tt) REVERT: D 125 GLN cc_start: 0.8523 (tt0) cc_final: 0.8135 (tt0) REVERT: D 231 LYS cc_start: 0.8648 (mtpt) cc_final: 0.8382 (mmmm) REVERT: E 66 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7589 (mttm) REVERT: E 183 ASN cc_start: 0.8633 (m-40) cc_final: 0.8350 (t0) REVERT: F 26 TYR cc_start: 0.8444 (m-10) cc_final: 0.8102 (m-10) REVERT: F 187 LYS cc_start: 0.8116 (mmtm) cc_final: 0.7699 (ptpp) REVERT: F 221 TYR cc_start: 0.8737 (OUTLIER) cc_final: 0.7953 (t80) REVERT: G 68 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7657 (mp10) REVERT: G 221 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.8008 (t80) REVERT: H 71 ARG cc_start: 0.8415 (mtt-85) cc_final: 0.8137 (ptp-110) REVERT: H 89 GLN cc_start: 0.8109 (pp30) cc_final: 0.7834 (pp30) REVERT: H 153 ASP cc_start: 0.8024 (m-30) cc_final: 0.7690 (m-30) REVERT: I 96 MET cc_start: 0.7188 (mpt) cc_final: 0.6910 (mtm) REVERT: I 111 PHE cc_start: 0.8215 (m-10) cc_final: 0.7998 (m-80) REVERT: I 153 ASP cc_start: 0.8223 (m-30) cc_final: 0.7902 (m-30) REVERT: J 69 GLN cc_start: 0.8911 (mt0) cc_final: 0.8642 (mt0) REVERT: J 88 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.7981 (t160) REVERT: J 96 MET cc_start: 0.6661 (mpt) cc_final: 0.6393 (mtm) REVERT: K 53 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6287 (mt0) REVERT: K 98 GLN cc_start: 0.8269 (mt0) cc_final: 0.7861 (mp10) REVERT: L 64 GLU cc_start: 0.7612 (tp30) cc_final: 0.7224 (tp30) REVERT: L 96 MET cc_start: 0.7220 (mpt) cc_final: 0.6442 (mtm) REVERT: L 98 GLN cc_start: 0.8485 (tt0) cc_final: 0.7957 (mp-120) REVERT: L 153 ASP cc_start: 0.7910 (m-30) cc_final: 0.7615 (m-30) REVERT: N 96 MET cc_start: 0.6945 (mpt) cc_final: 0.6675 (mtm) REVERT: N 98 GLN cc_start: 0.8380 (mt0) cc_final: 0.7825 (mp-120) REVERT: N 153 ASP cc_start: 0.8217 (m-30) cc_final: 0.7934 (m-30) REVERT: O 122 ILE cc_start: 0.8158 (mt) cc_final: 0.7875 (mt) REVERT: O 187 ASP cc_start: 0.8365 (m-30) cc_final: 0.8062 (m-30) REVERT: O 191 MET cc_start: 0.8665 (mmm) cc_final: 0.8350 (mmp) REVERT: P 142 MET cc_start: 0.8717 (tpp) cc_final: 0.8431 (ttm) REVERT: P 204 MET cc_start: 0.8302 (mmm) cc_final: 0.7762 (mtt) REVERT: Q 86 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8192 (mm-30) REVERT: Q 121 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6587 (mt-10) REVERT: R 86 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8150 (mm-30) REVERT: S 5 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6201 (mtt90) REVERT: S 116 ILE cc_start: 0.8765 (pt) cc_final: 0.8384 (mt) REVERT: T 22 PHE cc_start: 0.8698 (t80) cc_final: 0.8477 (t80) REVERT: T 92 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.8975 (mp) REVERT: T 142 MET cc_start: 0.8841 (tpp) cc_final: 0.8005 (tpp) REVERT: W 59 MET cc_start: 0.8372 (mmm) cc_final: 0.8132 (mmm) REVERT: W 96 MET cc_start: 0.7158 (mpt) cc_final: 0.6947 (mpt) REVERT: W 203 LEU cc_start: 0.2348 (OUTLIER) cc_final: 0.1693 (tm) REVERT: X 17 GLU cc_start: 0.8124 (pm20) cc_final: 0.7590 (pm20) REVERT: X 30 ASN cc_start: 0.8277 (t0) cc_final: 0.8037 (m-40) REVERT: X 43 MET cc_start: 0.8277 (ttt) cc_final: 0.8043 (ttt) REVERT: X 66 TYR cc_start: 0.8005 (t80) cc_final: 0.7773 (t80) REVERT: X 93 MET cc_start: 0.7027 (mpp) cc_final: 0.6294 (ttm) REVERT: Y 139 GLU cc_start: 0.7748 (tp30) cc_final: 0.7408 (tp30) REVERT: Y 191 GLN cc_start: 0.6833 (tm-30) cc_final: 0.6589 (tm-30) REVERT: Z 96 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.6941 (mtt) REVERT: a 114 LYS cc_start: 0.8582 (mtpt) cc_final: 0.8321 (mttm) REVERT: a 119 GLN cc_start: 0.8706 (tm-30) cc_final: 0.7556 (tm-30) REVERT: a 121 GLN cc_start: 0.8800 (tm-30) cc_final: 0.8384 (tm-30) REVERT: a 143 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7807 (tm-30) REVERT: a 151 CYS cc_start: 0.7374 (m) cc_final: 0.6881 (m) REVERT: a 219 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8388 (p0) REVERT: a 221 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.7479 (t80) REVERT: b 40 MET cc_start: 0.8330 (ptp) cc_final: 0.8044 (ptm) REVERT: b 61 GLN cc_start: 0.6406 (mp10) cc_final: 0.6020 (mp10) REVERT: b 71 ASP cc_start: 0.8461 (t0) cc_final: 0.8256 (t0) REVERT: b 170 ASP cc_start: 0.7202 (OUTLIER) cc_final: 0.6928 (p0) REVERT: d 32 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8551 (ptmm) REVERT: d 119 GLN cc_start: 0.8392 (tm-30) cc_final: 0.7942 (tm-30) REVERT: d 219 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8374 (p0) REVERT: d 221 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.7432 (t80) REVERT: e 68 GLN cc_start: 0.8282 (pm20) cc_final: 0.7975 (pm20) REVERT: e 120 MET cc_start: 0.9360 (mtm) cc_final: 0.9158 (mtp) REVERT: e 121 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8340 (tm-30) REVERT: e 219 ASN cc_start: 0.8801 (p0) cc_final: 0.8464 (p0) REVERT: f 42 PHE cc_start: 0.8447 (p90) cc_final: 0.8163 (p90) REVERT: f 44 ASN cc_start: 0.7256 (p0) cc_final: 0.6703 (p0) REVERT: f 72 ASP cc_start: 0.7167 (p0) cc_final: 0.6788 (p0) REVERT: f 113 VAL cc_start: 0.8849 (p) cc_final: 0.8540 (p) REVERT: f 143 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7903 (tm-30) REVERT: g 68 GLN cc_start: 0.8392 (pm20) cc_final: 0.8021 (pm20) REVERT: g 99 GLU cc_start: 0.7988 (tt0) cc_final: 0.7692 (tm-30) REVERT: g 119 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8185 (tm-30) REVERT: g 121 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8457 (tm-30) REVERT: g 219 ASN cc_start: 0.8901 (m110) cc_final: 0.8439 (p0) REVERT: g 221 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.7169 (t80) outliers start: 295 outliers final: 231 residues processed: 1474 average time/residue: 0.5276 time to fit residues: 1321.5496 Evaluate side-chains 1448 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1196 time to evaluate : 5.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 97 VAL Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 146 MET Chi-restraints excluded: chain 1 residue 177 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 37 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 70 ARG Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 110 VAL Chi-restraints excluded: chain 2 residue 164 GLN Chi-restraints excluded: chain 2 residue 177 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 179 THR Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain H residue 10 ASP Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 88 ASN Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain L residue 10 ASP Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain M residue 10 ASP Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 104 ILE Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain O residue 62 LYS Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain Q residue 158 LYS Chi-restraints excluded: chain Q residue 186 ILE Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 76 ASP Chi-restraints excluded: chain S residue 5 ARG Chi-restraints excluded: chain S residue 76 ASP Chi-restraints excluded: chain S residue 149 LEU Chi-restraints excluded: chain T residue 62 LYS Chi-restraints excluded: chain T residue 76 ASP Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain T residue 116 ILE Chi-restraints excluded: chain T residue 149 LEU Chi-restraints excluded: chain U residue 116 ILE Chi-restraints excluded: chain U residue 229 MET Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 23 GLU Chi-restraints excluded: chain V residue 26 ILE 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 147 THR Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain W residue 8 LEU Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain W residue 74 MET Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 203 LEU Chi-restraints excluded: chain X residue 8 LEU 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 110 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 146 MET Chi-restraints excluded: chain Y residue 147 THR Chi-restraints excluded: chain Y residue 177 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 93 MET Chi-restraints excluded: chain Z residue 96 MET Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 141 ILE Chi-restraints excluded: chain a residue 142 ASP Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain a residue 219 ASN Chi-restraints excluded: chain a residue 221 TYR Chi-restraints excluded: chain a residue 223 ILE Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 141 ILE Chi-restraints excluded: chain b residue 170 ASP Chi-restraints excluded: chain b residue 201 LEU Chi-restraints excluded: chain b residue 221 TYR Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 74 VAL Chi-restraints excluded: chain c residue 77 VAL Chi-restraints excluded: chain c residue 113 VAL Chi-restraints excluded: chain c residue 141 ILE Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 216 THR Chi-restraints excluded: chain c residue 223 ILE Chi-restraints excluded: chain d residue 32 LYS Chi-restraints excluded: chain d residue 49 ILE Chi-restraints excluded: chain d residue 67 ILE Chi-restraints excluded: chain d residue 74 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 141 ILE Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 219 ASN Chi-restraints excluded: chain d residue 221 TYR Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 40 MET Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 132 TYR Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 173 VAL Chi-restraints excluded: chain e residue 216 THR Chi-restraints excluded: chain e residue 223 ILE Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 67 ILE Chi-restraints excluded: chain f residue 74 VAL Chi-restraints excluded: chain f residue 77 VAL Chi-restraints excluded: chain f residue 216 THR Chi-restraints excluded: chain g residue 67 ILE Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 78 THR Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 141 ILE Chi-restraints excluded: chain g residue 191 THR Chi-restraints excluded: chain g residue 221 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 644 optimal weight: 4.9990 chunk 678 optimal weight: 10.0000 chunk 619 optimal weight: 0.7980 chunk 660 optimal weight: 7.9990 chunk 397 optimal weight: 10.0000 chunk 287 optimal weight: 0.9990 chunk 518 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 chunk 596 optimal weight: 2.9990 chunk 624 optimal weight: 10.0000 chunk 657 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 88 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 GLN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 ASN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN L 88 ASN ** L 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN N 88 ASN ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 200 HIS ** T 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 ASN ** V 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 88 ASN ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 88 ASN ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 68 GLN c 68 GLN ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 58912 Z= 0.238 Angle : 0.680 13.427 79541 Z= 0.362 Chirality : 0.044 0.300 9310 Planarity : 0.004 0.048 10206 Dihedral : 5.650 54.635 8266 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.48 % Rotamer: Outliers : 4.90 % Allowed : 22.04 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.48 (0.10), residues: 7441 helix: 2.02 (0.09), residues: 3430 sheet: -0.42 (0.12), residues: 1407 loop : -1.63 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP O 216 HIS 0.005 0.001 HIS 2 28 PHE 0.036 0.002 PHE A 175 TYR 0.034 0.002 TYR Y 58 ARG 0.011 0.000 ARG T 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1538 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 1232 time to evaluate : 5.921 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: 2 180 ARG cc_start: 0.8414 (tpp80) cc_final: 0.8067 (ttm-80) REVERT: A 221 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.7525 (t80) REVERT: A 222 ARG cc_start: 0.7957 (tmt-80) cc_final: 0.7474 (ttt-90) REVERT: A 227 GLU cc_start: 0.8148 (mp0) cc_final: 0.7683 (pm20) REVERT: B 221 TYR cc_start: 0.9072 (OUTLIER) cc_final: 0.6425 (t80) REVERT: C 221 TYR cc_start: 0.9041 (OUTLIER) cc_final: 0.7042 (t80) REVERT: D 106 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.7892 (tt) REVERT: D 125 GLN cc_start: 0.8580 (tt0) cc_final: 0.8168 (tt0) REVERT: D 231 LYS cc_start: 0.8647 (mtpt) cc_final: 0.8370 (mmmm) REVERT: E 66 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7589 (mttm) REVERT: E 68 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7682 (mp10) REVERT: E 119 GLN cc_start: 0.8961 (tp40) cc_final: 0.8532 (tp40) REVERT: E 160 TYR cc_start: 0.8274 (m-80) cc_final: 0.7467 (m-80) REVERT: E 183 ASN cc_start: 0.8643 (m-40) cc_final: 0.8361 (t0) REVERT: F 161 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7912 (mmtm) REVERT: F 187 LYS cc_start: 0.8119 (mmtm) cc_final: 0.7702 (ptpp) REVERT: F 221 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.7841 (t80) REVERT: G 68 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7688 (mp10) REVERT: H 89 GLN cc_start: 0.8075 (pp30) cc_final: 0.7683 (pp30) REVERT: H 149 ASP cc_start: 0.7307 (t0) cc_final: 0.6806 (t0) REVERT: H 153 ASP cc_start: 0.7968 (m-30) cc_final: 0.7719 (m-30) REVERT: I 96 MET cc_start: 0.7249 (mpt) cc_final: 0.6837 (mtm) REVERT: I 153 ASP cc_start: 0.8202 (m-30) cc_final: 0.7875 (m-30) REVERT: I 182 ASP cc_start: 0.7697 (t0) cc_final: 0.7477 (t0) REVERT: I 191 GLN cc_start: 0.6706 (tm-30) cc_final: 0.6431 (tm-30) REVERT: J 55 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8265 (mm) REVERT: J 69 GLN cc_start: 0.8886 (mt0) cc_final: 0.8626 (mt0) REVERT: J 96 MET cc_start: 0.6626 (mpt) cc_final: 0.6330 (mtm) REVERT: K 53 GLN cc_start: 0.7195 (OUTLIER) cc_final: 0.6352 (mt0) REVERT: K 98 GLN cc_start: 0.8333 (mt0) cc_final: 0.7918 (mp10) REVERT: L 30 ASN cc_start: 0.8721 (m-40) cc_final: 0.8499 (m-40) REVERT: L 64 GLU cc_start: 0.7514 (tp30) cc_final: 0.7159 (tp30) REVERT: L 96 MET cc_start: 0.7225 (mpt) cc_final: 0.6357 (mtm) REVERT: L 98 GLN cc_start: 0.8423 (tt0) cc_final: 0.7939 (mp-120) REVERT: L 153 ASP cc_start: 0.7891 (m-30) cc_final: 0.7601 (m-30) REVERT: M 191 GLN cc_start: 0.6649 (tm-30) cc_final: 0.6409 (tm-30) REVERT: N 96 MET cc_start: 0.6974 (mpt) cc_final: 0.6622 (mtm) REVERT: N 98 GLN cc_start: 0.8272 (mt0) cc_final: 0.7780 (mp-120) REVERT: N 153 ASP cc_start: 0.8203 (m-30) cc_final: 0.7748 (m-30) REVERT: O 122 ILE cc_start: 0.8247 (mt) cc_final: 0.8002 (mt) REVERT: O 187 ASP cc_start: 0.8378 (m-30) cc_final: 0.8032 (m-30) REVERT: P 142 MET cc_start: 0.8735 (tpp) cc_final: 0.8501 (ttm) REVERT: R 86 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8153 (mm-30) REVERT: R 121 GLU cc_start: 0.7483 (mt-10) cc_final: 0.6442 (mt-10) REVERT: S 5 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6428 (mpt-90) REVERT: S 116 ILE cc_start: 0.8759 (pt) cc_final: 0.8408 (mt) REVERT: T 22 PHE cc_start: 0.8717 (t80) cc_final: 0.8410 (t80) REVERT: T 92 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.8964 (mp) REVERT: T 142 MET cc_start: 0.8841 (tpp) cc_final: 0.8018 (tpp) REVERT: W 59 MET cc_start: 0.8394 (mmm) cc_final: 0.8187 (mmm) REVERT: W 203 LEU cc_start: 0.2171 (OUTLIER) cc_final: 0.1533 (tm) REVERT: X 17 GLU cc_start: 0.8096 (pm20) cc_final: 0.7587 (pm20) REVERT: X 66 TYR cc_start: 0.8125 (t80) cc_final: 0.7801 (t80) REVERT: X 93 MET cc_start: 0.6970 (mpp) cc_final: 0.6227 (ttt) REVERT: Y 139 GLU cc_start: 0.7814 (tp30) cc_final: 0.7489 (tp30) REVERT: Y 191 GLN cc_start: 0.6975 (tm-30) cc_final: 0.6693 (tm-30) REVERT: a 114 LYS cc_start: 0.8565 (mtpt) cc_final: 0.8237 (mttp) REVERT: a 119 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8284 (tm-30) REVERT: a 121 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8428 (tm-30) REVERT: a 143 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7798 (tm-30) REVERT: a 151 CYS cc_start: 0.7288 (m) cc_final: 0.6857 (m) REVERT: a 175 PHE cc_start: 0.8631 (t80) cc_final: 0.8249 (t80) REVERT: a 219 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8415 (p0) REVERT: a 221 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7401 (t80) REVERT: b 40 MET cc_start: 0.8283 (ptp) cc_final: 0.7980 (ptm) REVERT: b 170 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.7006 (p0) REVERT: d 32 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8589 (ptmm) REVERT: d 68 GLN cc_start: 0.8592 (pm20) cc_final: 0.8321 (pm20) REVERT: d 119 GLN cc_start: 0.8370 (tm-30) cc_final: 0.7866 (tm-30) REVERT: d 219 ASN cc_start: 0.8640 (OUTLIER) cc_final: 0.8377 (p0) REVERT: d 221 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.7367 (t80) REVERT: e 68 GLN cc_start: 0.8423 (pm20) cc_final: 0.8134 (pm20) REVERT: e 219 ASN cc_start: 0.8846 (p0) cc_final: 0.8437 (p0) REVERT: f 42 PHE cc_start: 0.8464 (p90) cc_final: 0.8155 (p90) REVERT: f 44 ASN cc_start: 0.7225 (p0) cc_final: 0.6652 (p0) REVERT: f 72 ASP cc_start: 0.7142 (p0) cc_final: 0.6808 (p0) REVERT: f 113 VAL cc_start: 0.8866 (p) cc_final: 0.8475 (p) REVERT: f 221 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7190 (t80) REVERT: g 68 GLN cc_start: 0.8404 (pm20) cc_final: 0.8000 (pm20) REVERT: g 99 GLU cc_start: 0.7950 (tt0) cc_final: 0.7665 (tm-30) REVERT: g 119 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8282 (tm-30) REVERT: g 121 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8399 (tm-30) REVERT: g 143 GLN cc_start: 0.8131 (tm-30) cc_final: 0.7899 (tm-30) REVERT: g 219 ASN cc_start: 0.8825 (m110) cc_final: 0.8361 (p0) REVERT: g 221 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7166 (t80) outliers start: 306 outliers final: 245 residues processed: 1413 average time/residue: 0.5364 time to fit residues: 1284.9859 Evaluate side-chains 1456 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1191 time to evaluate : 5.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 97 VAL Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 146 MET Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 37 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 70 ARG Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 110 VAL Chi-restraints excluded: chain 2 residue 164 GLN Chi-restraints excluded: chain 2 residue 177 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 179 THR Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 161 LYS Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 10 ASP Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 131 SER Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain L residue 10 ASP Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain M residue 10 ASP Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 104 ILE Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain O residue 62 LYS Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain Q residue 186 ILE Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 76 ASP Chi-restraints excluded: chain S residue 5 ARG Chi-restraints excluded: chain S residue 76 ASP Chi-restraints excluded: chain S residue 149 LEU Chi-restraints excluded: chain T residue 62 LYS Chi-restraints excluded: chain T residue 76 ASP Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain T residue 116 ILE Chi-restraints excluded: chain T residue 149 LEU Chi-restraints excluded: chain U residue 62 LYS Chi-restraints excluded: chain U residue 116 ILE Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 23 GLU Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 41 THR 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 147 THR Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 177 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain W residue 8 LEU Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 203 LEU Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 104 ILE Chi-restraints excluded: chain X residue 110 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 26 ILE 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 146 MET Chi-restraints excluded: chain Y residue 147 THR Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 177 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 93 MET 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 177 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 141 ILE Chi-restraints excluded: chain a residue 142 ASP Chi-restraints excluded: chain a residue 219 ASN Chi-restraints excluded: chain a residue 221 TYR Chi-restraints excluded: chain a residue 223 ILE Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 141 ILE Chi-restraints excluded: chain b residue 170 ASP Chi-restraints excluded: chain b residue 201 LEU Chi-restraints excluded: chain b residue 221 TYR Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 74 VAL Chi-restraints excluded: chain c residue 77 VAL Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 216 THR Chi-restraints excluded: chain c residue 223 ILE Chi-restraints excluded: chain d residue 32 LYS Chi-restraints excluded: chain d residue 49 ILE Chi-restraints excluded: chain d residue 67 ILE Chi-restraints excluded: chain d residue 74 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 132 TYR Chi-restraints excluded: chain d residue 141 ILE Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 219 ASN Chi-restraints excluded: chain d residue 221 TYR Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 40 MET Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 115 ARG Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 173 VAL Chi-restraints excluded: chain e residue 216 THR Chi-restraints excluded: chain e residue 223 ILE Chi-restraints excluded: chain f residue 67 ILE Chi-restraints excluded: chain f residue 74 VAL Chi-restraints excluded: chain f residue 77 VAL Chi-restraints excluded: chain f residue 141 ILE Chi-restraints excluded: chain f residue 151 CYS Chi-restraints excluded: chain f residue 212 ILE Chi-restraints excluded: chain f residue 216 THR Chi-restraints excluded: chain f residue 221 TYR Chi-restraints excluded: chain g residue 67 ILE Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 78 THR Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 141 ILE Chi-restraints excluded: chain g residue 191 THR Chi-restraints excluded: chain g residue 221 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 433 optimal weight: 9.9990 chunk 698 optimal weight: 7.9990 chunk 426 optimal weight: 0.8980 chunk 331 optimal weight: 3.9990 chunk 485 optimal weight: 4.9990 chunk 732 optimal weight: 20.0000 chunk 673 optimal weight: 9.9990 chunk 583 optimal weight: 10.0000 chunk 60 optimal weight: 0.0670 chunk 450 optimal weight: 5.9990 chunk 357 optimal weight: 5.9990 overall best weight: 3.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 88 ASN A 97 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 GLN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN I 98 GLN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 ASN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN L 88 ASN M 88 ASN ** M 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 88 ASN ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 ASN ** V 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 88 ASN ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 88 ASN ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 68 GLN c 68 GLN ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN g 183 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 58912 Z= 0.425 Angle : 0.776 14.698 79541 Z= 0.410 Chirality : 0.047 0.358 9310 Planarity : 0.004 0.047 10206 Dihedral : 5.991 56.243 8266 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.03 % Favored : 94.88 % Rotamer: Outliers : 4.88 % Allowed : 22.45 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.51 % Twisted General : 0.23 % 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: 0.21 (0.10), residues: 7441 helix: 1.77 (0.09), residues: 3416 sheet: -0.63 (0.12), residues: 1435 loop : -1.65 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 216 HIS 0.005 0.002 HIS X 28 PHE 0.027 0.002 PHE A 175 TYR 0.044 0.002 TYR Y 58 ARG 0.012 0.001 ARG Y 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14882 Ramachandran restraints generated. 7441 Oldfield, 0 Emsley, 7441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1488 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1183 time to evaluate : 5.172 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: A 221 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.7547 (t80) REVERT: A 227 GLU cc_start: 0.8202 (mp0) cc_final: 0.7818 (pm20) REVERT: B 221 TYR cc_start: 0.9079 (OUTLIER) cc_final: 0.6100 (t80) REVERT: C 221 TYR cc_start: 0.9072 (OUTLIER) cc_final: 0.7150 (t80) REVERT: D 106 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8108 (tt) REVERT: E 183 ASN cc_start: 0.8669 (m-40) cc_final: 0.8351 (t0) REVERT: F 161 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7675 (mmtt) REVERT: G 68 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7838 (mp10) REVERT: H 89 GLN cc_start: 0.8004 (pp30) cc_final: 0.7582 (pp30) REVERT: H 153 ASP cc_start: 0.7972 (m-30) cc_final: 0.7703 (m-30) REVERT: I 59 MET cc_start: 0.7585 (tpp) cc_final: 0.7263 (tpp) REVERT: I 96 MET cc_start: 0.7310 (mpt) cc_final: 0.6852 (mtm) REVERT: I 153 ASP cc_start: 0.8255 (m-30) cc_final: 0.7912 (m-30) REVERT: I 164 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8156 (mm110) REVERT: J 69 GLN cc_start: 0.8920 (mt0) cc_final: 0.8669 (mt0) REVERT: J 96 MET cc_start: 0.6853 (mpt) cc_final: 0.6554 (mtm) REVERT: K 53 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.7044 (mt0) REVERT: K 58 TYR cc_start: 0.7924 (t80) cc_final: 0.7061 (t80) REVERT: K 98 GLN cc_start: 0.8430 (mt0) cc_final: 0.7998 (mp-120) REVERT: L 30 ASN cc_start: 0.8808 (m-40) cc_final: 0.8586 (m-40) REVERT: L 64 GLU cc_start: 0.7755 (tp30) cc_final: 0.7476 (tp30) REVERT: L 96 MET cc_start: 0.7035 (mpt) cc_final: 0.6626 (mtm) REVERT: L 153 ASP cc_start: 0.7868 (m-30) cc_final: 0.7570 (m-30) REVERT: N 53 GLN cc_start: 0.7863 (mp10) cc_final: 0.7655 (mp10) REVERT: N 96 MET cc_start: 0.7280 (mpt) cc_final: 0.6947 (mtm) REVERT: N 98 GLN cc_start: 0.8307 (mt0) cc_final: 0.7949 (mp10) REVERT: O 142 MET cc_start: 0.8827 (tpp) cc_final: 0.8592 (mmm) REVERT: P 115 LYS cc_start: 0.8991 (ttmt) cc_final: 0.8727 (tttt) REVERT: Q 86 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7649 (mm-30) REVERT: Q 121 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6737 (mt-10) REVERT: R 86 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8134 (mm-30) REVERT: S 116 ILE cc_start: 0.8811 (pt) cc_final: 0.8459 (mt) REVERT: T 92 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.8993 (mp) REVERT: T 142 MET cc_start: 0.8886 (tpp) cc_final: 0.8220 (tpp) REVERT: V 29 LYS cc_start: 0.8905 (mtmt) cc_final: 0.8703 (mtmm) REVERT: W 59 MET cc_start: 0.8394 (mmm) cc_final: 0.8179 (mmm) REVERT: W 203 LEU cc_start: 0.2368 (OUTLIER) cc_final: 0.1745 (tm) REVERT: X 66 TYR cc_start: 0.8434 (t80) cc_final: 0.8165 (t80) REVERT: Y 191 GLN cc_start: 0.6991 (tm-30) cc_final: 0.6698 (tm-30) REVERT: a 114 LYS cc_start: 0.8615 (mtpt) cc_final: 0.8307 (mttp) REVERT: a 119 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8199 (tm-30) REVERT: a 121 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8442 (tm-30) REVERT: a 143 GLN cc_start: 0.8282 (tm-30) cc_final: 0.7854 (tm-30) REVERT: a 151 CYS cc_start: 0.7506 (m) cc_final: 0.7025 (m) REVERT: a 175 PHE cc_start: 0.8605 (t80) cc_final: 0.8244 (t80) REVERT: a 221 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.7244 (t80) REVERT: b 40 MET cc_start: 0.8552 (ptp) cc_final: 0.8181 (ptm) REVERT: b 170 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.7081 (p0) REVERT: d 32 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8583 (ptmm) REVERT: d 68 GLN cc_start: 0.8646 (pm20) cc_final: 0.8357 (pm20) REVERT: d 119 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8078 (tm-30) REVERT: d 221 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.7003 (t80) REVERT: e 68 GLN cc_start: 0.8395 (pm20) cc_final: 0.8092 (pm20) REVERT: e 219 ASN cc_start: 0.8844 (p0) cc_final: 0.8498 (p0) REVERT: f 44 ASN cc_start: 0.7249 (p0) cc_final: 0.6685 (p0) REVERT: f 72 ASP cc_start: 0.7214 (p0) cc_final: 0.6983 (p0) REVERT: f 113 VAL cc_start: 0.8953 (p) cc_final: 0.8592 (p) REVERT: f 221 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.7109 (t80) REVERT: g 61 GLN cc_start: 0.6451 (mp10) cc_final: 0.6023 (mp10) REVERT: g 68 GLN cc_start: 0.8394 (pm20) cc_final: 0.7992 (pm20) REVERT: g 99 GLU cc_start: 0.7955 (tt0) cc_final: 0.7636 (tm-30) REVERT: g 119 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8184 (tm-30) REVERT: g 121 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8544 (tm-30) REVERT: g 143 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7858 (tm-30) REVERT: g 221 TYR cc_start: 0.8840 (OUTLIER) cc_final: 0.7411 (t80) outliers start: 305 outliers final: 266 residues processed: 1374 average time/residue: 0.5402 time to fit residues: 1266.2101 Evaluate side-chains 1414 residues out of total 6244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 1134 time to evaluate : 5.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 86 MET Chi-restraints excluded: chain 1 residue 97 VAL Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 177 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 37 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 70 ARG Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 110 VAL Chi-restraints excluded: chain 2 residue 164 GLN Chi-restraints excluded: chain 2 residue 177 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 179 THR Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 161 LYS Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 131 SER Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain L residue 10 ASP Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain M residue 10 ASP Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 129 SER Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 77 GLU Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 104 ILE Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain O residue 62 LYS Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain Q residue 186 ILE Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 76 ASP Chi-restraints excluded: chain S residue 5 ARG Chi-restraints excluded: chain S residue 76 ASP Chi-restraints excluded: chain S residue 149 LEU Chi-restraints excluded: chain T residue 62 LYS Chi-restraints excluded: chain T residue 76 ASP Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain T residue 116 ILE Chi-restraints excluded: chain T residue 149 LEU Chi-restraints excluded: chain U residue 116 ILE Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 23 GLU Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 41 THR 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 147 THR Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 177 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain W residue 8 LEU Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 164 GLN Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 203 LEU Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 104 ILE Chi-restraints excluded: chain X residue 110 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain Y residue 26 ILE 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 147 THR Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 177 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 93 MET Chi-restraints excluded: chain Z residue 96 MET Chi-restraints excluded: chain Z residue 97 VAL 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 155 VAL Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 141 ILE Chi-restraints excluded: chain a residue 142 ASP Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain a residue 219 ASN Chi-restraints excluded: chain a residue 221 TYR Chi-restraints excluded: chain a residue 223 ILE Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 141 ILE Chi-restraints excluded: chain b residue 170 ASP Chi-restraints excluded: chain b residue 201 LEU Chi-restraints excluded: chain b residue 233 LEU Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 74 VAL Chi-restraints excluded: chain c residue 77 VAL Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 216 THR Chi-restraints excluded: chain c residue 223 ILE Chi-restraints excluded: chain d residue 32 LYS Chi-restraints excluded: chain d residue 49 ILE Chi-restraints excluded: chain d residue 67 ILE Chi-restraints excluded: chain d residue 74 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 132 TYR Chi-restraints excluded: chain d residue 141 ILE Chi-restraints excluded: chain d residue 151 CYS Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 219 ASN Chi-restraints excluded: chain d residue 221 TYR Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain e residue 40 MET Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 115 ARG Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 173 VAL Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain e residue 216 THR Chi-restraints excluded: chain f residue 36 THR Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 67 ILE Chi-restraints excluded: chain f residue 74 VAL Chi-restraints excluded: chain f residue 77 VAL Chi-restraints excluded: chain f residue 141 ILE Chi-restraints excluded: chain f residue 151 CYS Chi-restraints excluded: chain f residue 191 THR Chi-restraints excluded: chain f residue 212 ILE Chi-restraints excluded: chain f residue 216 THR Chi-restraints excluded: chain f residue 221 TYR Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 67 ILE Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 78 THR Chi-restraints excluded: chain g residue 81 LEU Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 141 ILE Chi-restraints excluded: chain g residue 163 THR Chi-restraints excluded: chain g residue 191 THR Chi-restraints excluded: chain g residue 221 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 463 optimal weight: 0.9990 chunk 621 optimal weight: 10.0000 chunk 178 optimal weight: 0.8980 chunk 537 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 162 optimal weight: 0.0570 chunk 584 optimal weight: 4.9990 chunk 244 optimal weight: 0.8980 chunk 599 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 88 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 GLN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 ASN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN L 88 ASN ** L 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN ** N 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 ASN ** V 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 88 ASN ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 85 ASN ** Z 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 68 GLN c 68 GLN ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.123050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.093456 restraints weight = 90376.924| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.11 r_work: 0.3017 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.250 58912 Z= 0.353 Angle : 0.820 58.865 79541 Z= 0.445 Chirality : 0.046 0.564 9310 Planarity : 0.004 0.050 10206 Dihedral : 5.991 56.430 8266 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.93 % Favored : 94.97 % Rotamer: Outliers : 4.63 % Allowed : 22.89 % Favored : 72.49 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.51 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.10), residues: 7441 helix: 1.80 (0.09), residues: 3416 sheet: -0.64 (0.12), residues: 1435 loop : -1.65 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 216 HIS 0.015 0.002 HIS O 47 PHE 0.024 0.002 PHE U 190 TYR 0.050 0.002 TYR K 58 ARG 0.018 0.001 ARG Z 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19728.40 seconds wall clock time: 343 minutes 21.42 seconds (20601.42 seconds total)