Starting phenix.real_space_refine on Tue Aug 26 10:15:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wlh_37619/08_2025/8wlh_37619.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wlh_37619/08_2025/8wlh_37619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wlh_37619/08_2025/8wlh_37619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wlh_37619/08_2025/8wlh_37619.map" model { file = "/net/cci-nas-00/data/ceres_data/8wlh_37619/08_2025/8wlh_37619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wlh_37619/08_2025/8wlh_37619.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.006 sd= 0.133 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 235 5.16 5 C 23017 2.51 5 N 6157 2.21 5 O 6821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36230 Number of models: 1 Model: "" Number of chains: 43 Chain: "A" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "B" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "C" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "D" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "E" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1945 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 15, 'TRANS': 237} Chain: "F" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1605 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 15, 'TRANS': 191} Chain: "G" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1626 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 15, 'TRANS': 193} Chain: "H" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1614 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "I" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1614 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "J" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1623 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 15, 'TRANS': 193} Chain: "K" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 300 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "L" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 543 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 557 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 557 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "O" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 557 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "P" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 550 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "Q" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 922 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain breaks: 1 Chain: "R" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 848 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain breaks: 1 Chain: "S" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 848 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain breaks: 1 Chain: "T" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 863 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain breaks: 1 Chain: "U" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 832 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 1 Chain: "V" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 969 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain: "W" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 964 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain: "X" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 969 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain: "Y" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 969 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain: "Z" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 956 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "a" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 969 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain: "b" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 81 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 3, 'TRANS': 9} Chain: "c" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 103 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 4, 'TRANS': 11} Chain: "d" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 133 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 5, 'TRANS': 14} Chain: "e" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 103 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 4, 'TRANS': 11} Chain: "f" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 140 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 6, 'TRANS': 14} Chain: "g" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 103 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 4, 'TRANS': 11} Chain: "h" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 140 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 6, 'TRANS': 14} Chain: "i" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 103 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 4, 'TRANS': 11} Chain: "j" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 133 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 5, 'TRANS': 14} Chain: "k" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 103 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 4, 'TRANS': 11} Chain: "l" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 140 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 6, 'TRANS': 14} Chain: "m" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1804 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 15, 'TRANS': 232} Chain: "n" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1812 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 15, 'TRANS': 233} Chain: "o" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1820 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 15, 'TRANS': 234} Chain: "p" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1820 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 15, 'TRANS': 234} Chain: "q" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1812 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 15, 'TRANS': 233} Time building chain proxies: 9.72, per 1000 atoms: 0.27 Number of scatterers: 36230 At special positions: 0 Unit cell: (133.2, 129.204, 249.084, 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 235 16.00 O 6821 8.00 N 6157 7.00 C 23017 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 - 3.00 Amino acid : True - 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: 3.71 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 953.7 nanoseconds 9498 Ramachandran restraints generated. 4749 Oldfield, 0 Emsley, 4749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8988 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 57 sheets defined 61.1% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 2 through 43 Proline residue: A 23 - end of helix removed outlier: 3.688A pdb=" N VAL A 27 " --> pdb=" O PRO A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 88 Proline residue: A 67 - end of helix removed outlier: 3.899A pdb=" N THR A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Proline residue: A 85 - end of helix Processing helix chain 'B' and resid 2 through 43 Proline residue: B 23 - end of helix removed outlier: 4.054A pdb=" N VAL B 27 " --> pdb=" O PRO B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.752A pdb=" N LEU B 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 50 through 83 removed outlier: 3.984A pdb=" N LYS B 54 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL B 56 " --> pdb=" O ILE B 52 " (cutoff:3.500A) Proline residue: B 67 - end of helix removed outlier: 3.868A pdb=" N LEU B 73 " --> pdb=" O MET B 69 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 88 removed outlier: 4.219A pdb=" N ILE B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 42 removed outlier: 4.483A pdb=" N MET C 9 " --> pdb=" O SER C 5 " (cutoff:3.500A) Proline residue: C 23 - end of helix Processing helix chain 'C' and resid 50 through 88 Proline residue: C 67 - end of helix Proline residue: C 85 - end of helix removed outlier: 3.914A pdb=" N ILE C 88 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 43 Proline residue: D 23 - end of helix Processing helix chain 'D' and resid 50 through 84 removed outlier: 4.148A pdb=" N LYS D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE D 55 " --> pdb=" O PHE D 51 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL D 56 " --> pdb=" O ILE D 52 " (cutoff:3.500A) Proline residue: D 67 - end of helix Processing helix chain 'D' and resid 85 through 87 No H-bonds generated for 'chain 'D' and resid 85 through 87' Processing helix chain 'E' and resid 8 through 28 removed outlier: 3.731A pdb=" N TRP E 12 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TRP E 18 " --> pdb=" O HIS E 14 " (cutoff:3.500A) Proline residue: E 19 - end of helix Processing helix chain 'E' and resid 39 through 55 Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 67 through 106 removed outlier: 4.396A pdb=" N ALA E 91 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE E 92 " --> pdb=" O MET E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 115 removed outlier: 4.010A pdb=" N VAL E 114 " --> pdb=" O PHE E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 140 Processing helix chain 'E' and resid 141 through 157 removed outlier: 4.282A pdb=" N PHE E 154 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N HIS E 155 " --> pdb=" O VAL E 151 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR E 156 " --> pdb=" O ASP E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 175 removed outlier: 3.913A pdb=" N MET E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 206 removed outlier: 3.715A pdb=" N ILE E 179 " --> pdb=" O ALA E 175 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Proline residue: E 189 - end of helix Processing helix chain 'E' and resid 216 through 233 removed outlier: 3.652A pdb=" N LEU E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 256 removed outlier: 3.755A pdb=" N PHE E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER E 256 " --> pdb=" O ALA E 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 53 removed outlier: 3.597A pdb=" N THR F 52 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE F 53 " --> pdb=" O THR F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 61 Processing helix chain 'F' and resid 63 through 79 removed outlier: 3.710A pdb=" N GLY F 79 " --> pdb=" O ARG F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 112 Proline residue: F 103 - end of helix Processing helix chain 'F' and resid 112 through 119 removed outlier: 3.900A pdb=" N SER F 117 " --> pdb=" O TYR F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 142 Proline residue: F 133 - end of helix Processing helix chain 'F' and resid 143 through 153 removed outlier: 3.647A pdb=" N LEU F 147 " --> pdb=" O ARG F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 207 Proline residue: F 172 - end of helix Proline residue: F 192 - end of helix Processing helix chain 'F' and resid 213 through 229 removed outlier: 4.114A pdb=" N ILE F 217 " --> pdb=" O PRO F 213 " (cutoff:3.500A) Proline residue: F 220 - end of helix Processing helix chain 'F' and resid 230 through 242 removed outlier: 3.772A pdb=" N LEU F 234 " --> pdb=" O ASP F 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 51 Processing helix chain 'G' and resid 53 through 62 Processing helix chain 'G' and resid 63 through 78 removed outlier: 3.550A pdb=" N ILE G 69 " --> pdb=" O THR G 65 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN G 76 " --> pdb=" O GLY G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 112 Proline residue: G 103 - end of helix Processing helix chain 'G' and resid 112 through 118 Processing helix chain 'G' and resid 122 through 141 removed outlier: 3.749A pdb=" N ALA G 131 " --> pdb=" O LEU G 127 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLN G 132 " --> pdb=" O ASP G 128 " (cutoff:3.500A) Proline residue: G 133 - end of helix removed outlier: 3.661A pdb=" N GLN G 141 " --> pdb=" O PHE G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 154 Processing helix chain 'G' and resid 161 through 165 Processing helix chain 'G' and resid 166 through 190 Proline residue: G 172 - end of helix Processing helix chain 'G' and resid 190 through 207 Processing helix chain 'G' and resid 213 through 229 removed outlier: 4.143A pdb=" N ILE G 217 " --> pdb=" O PRO G 213 " (cutoff:3.500A) Proline residue: G 220 - end of helix Processing helix chain 'G' and resid 230 through 244 removed outlier: 3.534A pdb=" N TYR G 244 " --> pdb=" O ALA G 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 53 removed outlier: 3.634A pdb=" N PHE H 53 " --> pdb=" O THR H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 62 removed outlier: 3.663A pdb=" N THR H 62 " --> pdb=" O LEU H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 78 Processing helix chain 'H' and resid 85 through 112 Proline residue: H 103 - end of helix Processing helix chain 'H' and resid 112 through 118 Processing helix chain 'H' and resid 122 through 141 removed outlier: 3.774A pdb=" N GLN H 132 " --> pdb=" O ASP H 128 " (cutoff:3.500A) Proline residue: H 133 - end of helix Processing helix chain 'H' and resid 143 through 154 Processing helix chain 'H' and resid 166 through 190 Proline residue: H 172 - end of helix Processing helix chain 'H' and resid 190 through 207 removed outlier: 3.559A pdb=" N LEU H 207 " --> pdb=" O VAL H 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 229 removed outlier: 4.398A pdb=" N ILE H 217 " --> pdb=" O PRO H 213 " (cutoff:3.500A) Proline residue: H 220 - end of helix Processing helix chain 'H' and resid 230 through 242 Processing helix chain 'I' and resid 39 through 51 removed outlier: 3.569A pdb=" N LEU I 51 " --> pdb=" O PHE I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 62 removed outlier: 3.647A pdb=" N THR I 62 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 79 removed outlier: 3.844A pdb=" N GLY I 79 " --> pdb=" O ARG I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 112 Proline residue: I 103 - end of helix Processing helix chain 'I' and resid 112 through 118 Processing helix chain 'I' and resid 122 through 141 removed outlier: 4.044A pdb=" N GLN I 132 " --> pdb=" O ASP I 128 " (cutoff:3.500A) Proline residue: I 133 - end of helix removed outlier: 3.717A pdb=" N GLN I 141 " --> pdb=" O PHE I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 154 Processing helix chain 'I' and resid 161 through 165 removed outlier: 4.056A pdb=" N VAL I 165 " --> pdb=" O PRO I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 190 Proline residue: I 172 - end of helix removed outlier: 3.703A pdb=" N THR I 188 " --> pdb=" O GLN I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 190 through 208 Processing helix chain 'I' and resid 213 through 229 removed outlier: 3.652A pdb=" N ILE I 217 " --> pdb=" O PRO I 213 " (cutoff:3.500A) Proline residue: I 220 - end of helix Processing helix chain 'I' and resid 230 through 242 Processing helix chain 'J' and resid 39 through 51 Processing helix chain 'J' and resid 53 through 61 Processing helix chain 'J' and resid 64 through 79 removed outlier: 4.475A pdb=" N VAL J 70 " --> pdb=" O ARG J 66 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE J 71 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY J 79 " --> pdb=" O ARG J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 101 removed outlier: 3.889A pdb=" N LEU J 89 " --> pdb=" O PRO J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 112 Processing helix chain 'J' and resid 112 through 118 Processing helix chain 'J' and resid 122 through 141 removed outlier: 3.795A pdb=" N LEU J 127 " --> pdb=" O MET J 123 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP J 128 " --> pdb=" O GLN J 124 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN J 132 " --> pdb=" O ASP J 128 " (cutoff:3.500A) Proline residue: J 133 - end of helix Processing helix chain 'J' and resid 143 through 154 removed outlier: 3.884A pdb=" N LEU J 147 " --> pdb=" O ARG J 143 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA J 154 " --> pdb=" O PHE J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 165 Processing helix chain 'J' and resid 166 through 207 Proline residue: J 172 - end of helix removed outlier: 3.883A pdb=" N ILE J 191 " --> pdb=" O PHE J 187 " (cutoff:3.500A) Proline residue: J 192 - end of helix removed outlier: 3.749A pdb=" N ASP J 197 " --> pdb=" O PHE J 193 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU J 207 " --> pdb=" O VAL J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 229 removed outlier: 4.057A pdb=" N ILE J 217 " --> pdb=" O PRO J 213 " (cutoff:3.500A) Proline residue: J 220 - end of helix Processing helix chain 'J' and resid 230 through 244 removed outlier: 3.643A pdb=" N LEU J 235 " --> pdb=" O GLY J 231 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 101 Processing helix chain 'L' and resid 34 through 61 Processing helix chain 'L' and resid 67 through 101 Processing helix chain 'M' and resid 33 through 61 Processing helix chain 'M' and resid 67 through 100 Processing helix chain 'N' and resid 33 through 61 Processing helix chain 'N' and resid 67 through 101 Processing helix chain 'O' and resid 33 through 62 Processing helix chain 'O' and resid 67 through 101 Processing helix chain 'P' and resid 33 through 62 Processing helix chain 'P' and resid 67 through 101 Processing helix chain 'Q' and resid 4 through 9 Processing helix chain 'Q' and resid 9 through 32 Processing helix chain 'Q' and resid 44 through 55 Processing helix chain 'Q' and resid 101 through 132 Processing helix chain 'R' and resid 4 through 32 removed outlier: 3.612A pdb=" N LEU R 9 " --> pdb=" O LEU R 5 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N PHE R 11 " --> pdb=" O ALA R 7 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN R 12 " --> pdb=" O ALA R 8 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 55 Processing helix chain 'R' and resid 101 through 135 removed outlier: 3.598A pdb=" N LEU R 134 " --> pdb=" O MET R 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 9 Processing helix chain 'S' and resid 9 through 32 Processing helix chain 'S' and resid 44 through 55 Processing helix chain 'S' and resid 101 through 135 removed outlier: 3.516A pdb=" N LEU S 134 " --> pdb=" O MET S 130 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 32 removed outlier: 3.645A pdb=" N LEU T 9 " --> pdb=" O LEU T 5 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE T 11 " --> pdb=" O ALA T 7 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N GLN T 12 " --> pdb=" O ALA T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 56 Processing helix chain 'T' and resid 101 through 135 Processing helix chain 'U' and resid 4 through 32 removed outlier: 4.771A pdb=" N PHE U 11 " --> pdb=" O ALA U 7 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLN U 12 " --> pdb=" O ALA U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 33 through 35 No H-bonds generated for 'chain 'U' and resid 33 through 35' Processing helix chain 'U' and resid 44 through 54 Processing helix chain 'U' and resid 101 through 135 removed outlier: 3.599A pdb=" N LEU U 134 " --> pdb=" O MET U 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 30 removed outlier: 3.787A pdb=" N ASP V 8 " --> pdb=" O LEU V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 97 through 131 Processing helix chain 'W' and resid 4 through 30 Processing helix chain 'W' and resid 97 through 130 Processing helix chain 'X' and resid 5 through 30 Processing helix chain 'X' and resid 97 through 130 removed outlier: 3.578A pdb=" N LEU X 130 " --> pdb=" O MET X 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 5 through 30 Processing helix chain 'Y' and resid 97 through 130 Processing helix chain 'Z' and resid 5 through 30 Processing helix chain 'Z' and resid 97 through 130 removed outlier: 3.904A pdb=" N LEU Z 130 " --> pdb=" O MET Z 126 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 30 Processing helix chain 'a' and resid 97 through 130 removed outlier: 3.693A pdb=" N GLU a 101 " --> pdb=" O ASP a 97 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER a 124 " --> pdb=" O ASN a 120 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET a 125 " --> pdb=" O THR a 121 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU a 130 " --> pdb=" O MET a 126 " (cutoff:3.500A) Processing helix chain 'c' and resid 315 through 319 removed outlier: 3.883A pdb=" N GLN c 319 " --> pdb=" O LEU c 316 " (cutoff:3.500A) Processing helix chain 'g' and resid 314 through 318 removed outlier: 3.549A pdb=" N ASN g 318 " --> pdb=" O ALA g 315 " (cutoff:3.500A) Processing helix chain 'k' and resid 315 through 319 removed outlier: 3.689A pdb=" N GLN k 319 " --> pdb=" O LEU k 316 " (cutoff:3.500A) Processing helix chain 'm' and resid 3 through 28 removed outlier: 3.635A pdb=" N ASN m 28 " --> pdb=" O SER m 24 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 155 Processing helix chain 'm' and resid 182 through 190 removed outlier: 3.749A pdb=" N GLU m 188 " --> pdb=" O GLU m 184 " (cutoff:3.500A) Processing helix chain 'm' and resid 212 through 249 Processing helix chain 'n' and resid 4 through 28 removed outlier: 3.765A pdb=" N GLY n 10 " --> pdb=" O TYR n 6 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU n 16 " --> pdb=" O ALA n 12 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER n 24 " --> pdb=" O ALA n 20 " (cutoff:3.500A) Processing helix chain 'n' and resid 151 through 155 Processing helix chain 'n' and resid 182 through 190 removed outlier: 3.561A pdb=" N GLU n 188 " --> pdb=" O GLU n 184 " (cutoff:3.500A) Processing helix chain 'n' and resid 212 through 247 removed outlier: 4.413A pdb=" N MET n 229 " --> pdb=" O ARG n 225 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY n 242 " --> pdb=" O ASP n 238 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG n 243 " --> pdb=" O GLU n 239 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA n 244 " --> pdb=" O ASN n 240 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 28 removed outlier: 3.703A pdb=" N GLY o 10 " --> pdb=" O TYR o 6 " (cutoff:3.500A) Processing helix chain 'o' and resid 151 through 155 Processing helix chain 'o' and resid 167 through 169 No H-bonds generated for 'chain 'o' and resid 167 through 169' Processing helix chain 'o' and resid 182 through 190 Processing helix chain 'o' and resid 212 through 245 Processing helix chain 'o' and resid 246 through 249 Processing helix chain 'p' and resid 3 through 28 removed outlier: 3.646A pdb=" N THR p 7 " --> pdb=" O HIS p 3 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN p 28 " --> pdb=" O SER p 24 " (cutoff:3.500A) Processing helix chain 'p' and resid 151 through 155 removed outlier: 3.892A pdb=" N VAL p 155 " --> pdb=" O PRO p 152 " (cutoff:3.500A) Processing helix chain 'p' and resid 167 through 169 No H-bonds generated for 'chain 'p' and resid 167 through 169' Processing helix chain 'p' and resid 182 through 190 Processing helix chain 'p' and resid 212 through 245 Processing helix chain 'p' and resid 246 through 249 Processing helix chain 'q' and resid 3 through 27 removed outlier: 3.691A pdb=" N ALA q 8 " --> pdb=" O ALA q 4 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET q 9 " --> pdb=" O ILE q 5 " (cutoff:3.500A) Processing helix chain 'q' and resid 151 through 155 removed outlier: 3.625A pdb=" N VAL q 155 " --> pdb=" O PRO q 152 " (cutoff:3.500A) Processing helix chain 'q' and resid 167 through 169 No H-bonds generated for 'chain 'q' and resid 167 through 169' Processing helix chain 'q' and resid 182 through 190 Processing helix chain 'q' and resid 212 through 245 Processing helix chain 'q' and resid 246 through 249 Processing sheet with id=AA1, first strand: chain 'Q' and resid 41 through 42 removed outlier: 3.711A pdb=" N TYR Q 87 " --> pdb=" O SER d 317 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER d 317 " --> pdb=" O TYR Q 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 41 through 42 removed outlier: 3.760A pdb=" N TYR R 87 " --> pdb=" O SER f 317 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER f 317 " --> pdb=" O TYR R 87 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 41 through 42 removed outlier: 3.660A pdb=" N TYR S 87 " --> pdb=" O SER h 317 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'T' and resid 41 through 42 Processing sheet with id=AA5, first strand: chain 'U' and resid 41 through 42 Processing sheet with id=AA6, first strand: chain 'V' and resid 45 through 52 removed outlier: 4.338A pdb=" N SER V 66 " --> pdb=" O VAL V 48 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN V 50 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL V 64 " --> pdb=" O GLN V 50 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASP V 52 " --> pdb=" O VAL V 62 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL V 62 " --> pdb=" O ASP V 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'V' and resid 75 through 78 Processing sheet with id=AA8, first strand: chain 'W' and resid 45 through 51 removed outlier: 6.139A pdb=" N GLN W 46 " --> pdb=" O VAL W 67 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL W 67 " --> pdb=" O GLN W 46 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL W 48 " --> pdb=" O ALA W 65 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'W' and resid 75 through 78 Processing sheet with id=AB1, first strand: chain 'X' and resid 33 through 35 removed outlier: 7.493A pdb=" N ALA n 43 " --> pdb=" O VAL X 34 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'X' and resid 45 through 50 removed outlier: 4.226A pdb=" N SER X 66 " --> pdb=" O VAL X 48 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN X 50 " --> pdb=" O VAL X 64 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N VAL X 64 " --> pdb=" O GLN X 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'X' and resid 75 through 78 Processing sheet with id=AB4, first strand: chain 'Y' and resid 45 through 51 removed outlier: 4.245A pdb=" N SER Y 66 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN Y 50 " --> pdb=" O VAL Y 64 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL Y 64 " --> pdb=" O GLN Y 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Y' and resid 75 through 78 Processing sheet with id=AB6, first strand: chain 'Z' and resid 33 through 35 removed outlier: 6.877A pdb=" N ALA p 43 " --> pdb=" O VAL Z 34 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Z' and resid 45 through 52 removed outlier: 6.206A pdb=" N GLN Z 46 " --> pdb=" O VAL Z 67 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL Z 67 " --> pdb=" O GLN Z 46 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL Z 48 " --> pdb=" O ALA Z 65 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Z' and resid 75 through 78 Processing sheet with id=AB9, first strand: chain 'a' and resid 33 through 35 removed outlier: 7.310A pdb=" N ALA q 43 " --> pdb=" O VAL a 34 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'a' and resid 45 through 51 removed outlier: 5.973A pdb=" N GLN a 46 " --> pdb=" O VAL a 67 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL a 67 " --> pdb=" O GLN a 46 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N VAL a 48 " --> pdb=" O ALA a 65 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA a 65 " --> pdb=" O VAL a 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'a' and resid 75 through 78 Processing sheet with id=AC3, first strand: chain 'm' and resid 40 through 45 Processing sheet with id=AC4, first strand: chain 'm' and resid 71 through 73 Processing sheet with id=AC5, first strand: chain 'm' and resid 80 through 81 Processing sheet with id=AC6, first strand: chain 'm' and resid 97 through 100 Processing sheet with id=AC7, first strand: chain 'm' and resid 106 through 107 Processing sheet with id=AC8, first strand: chain 'm' and resid 121 through 122 Processing sheet with id=AC9, first strand: chain 'm' and resid 134 through 137 removed outlier: 6.847A pdb=" N ILE m 143 " --> pdb=" O VAL m 158 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA m 156 " --> pdb=" O ALA m 145 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'm' and resid 171 through 173 Processing sheet with id=AD2, first strand: chain 'n' and resid 71 through 72 Processing sheet with id=AD3, first strand: chain 'n' and resid 80 through 82 Processing sheet with id=AD4, first strand: chain 'n' and resid 97 through 100 Processing sheet with id=AD5, first strand: chain 'n' and resid 106 through 107 Processing sheet with id=AD6, first strand: chain 'n' and resid 121 through 122 Processing sheet with id=AD7, first strand: chain 'n' and resid 134 through 137 removed outlier: 3.806A pdb=" N GLY n 159 " --> pdb=" O ILE n 143 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA n 145 " --> pdb=" O PRO n 157 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'n' and resid 171 through 173 Processing sheet with id=AD9, first strand: chain 'o' and resid 42 through 45 Processing sheet with id=AE1, first strand: chain 'o' and resid 71 through 73 Processing sheet with id=AE2, first strand: chain 'o' and resid 80 through 82 Processing sheet with id=AE3, first strand: chain 'o' and resid 97 through 100 Processing sheet with id=AE4, first strand: chain 'o' and resid 105 through 107 Processing sheet with id=AE5, first strand: chain 'o' and resid 121 through 122 Processing sheet with id=AE6, first strand: chain 'o' and resid 134 through 137 removed outlier: 6.733A pdb=" N ILE o 143 " --> pdb=" O VAL o 158 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA o 156 " --> pdb=" O ALA o 145 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'o' and resid 171 through 173 Processing sheet with id=AE8, first strand: chain 'p' and resid 71 through 73 Processing sheet with id=AE9, first strand: chain 'p' and resid 80 through 82 Processing sheet with id=AF1, first strand: chain 'p' and resid 97 through 100 Processing sheet with id=AF2, first strand: chain 'p' and resid 106 through 107 Processing sheet with id=AF3, first strand: chain 'p' and resid 121 through 122 Processing sheet with id=AF4, first strand: chain 'p' and resid 134 through 137 removed outlier: 3.895A pdb=" N GLY p 159 " --> pdb=" O ILE p 143 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA p 145 " --> pdb=" O PRO p 157 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'p' and resid 171 through 173 Processing sheet with id=AF6, first strand: chain 'q' and resid 71 through 72 Processing sheet with id=AF7, first strand: chain 'q' and resid 80 through 82 Processing sheet with id=AF8, first strand: chain 'q' and resid 97 through 100 Processing sheet with id=AF9, first strand: chain 'q' and resid 105 through 107 Processing sheet with id=AG1, first strand: chain 'q' and resid 121 through 122 removed outlier: 3.509A pdb=" N GLY q 125 " --> pdb=" O GLY q 122 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'q' and resid 134 through 137 removed outlier: 6.663A pdb=" N ILE q 143 " --> pdb=" O VAL q 158 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA q 156 " --> pdb=" O ALA q 145 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'q' and resid 171 through 173 2382 hydrogen bonds defined for protein. 6978 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: 7.95 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6348 1.32 - 1.45: 8454 1.45 - 1.58: 21535 1.58 - 1.71: 2 1.71 - 1.83: 469 Bond restraints: 36808 Sorted by residual: bond pdb=" N PRO a 37 " pdb=" CA PRO a 37 " ideal model delta sigma weight residual 1.473 1.408 0.065 1.32e-02 5.74e+03 2.42e+01 bond pdb=" N PRO F 162 " pdb=" CD PRO F 162 " ideal model delta sigma weight residual 1.473 1.540 -0.067 1.40e-02 5.10e+03 2.29e+01 bond pdb=" C ARG A 78 " pdb=" O ARG A 78 " ideal model delta sigma weight residual 1.237 1.291 -0.054 1.19e-02 7.06e+03 2.08e+01 bond pdb=" CG PRO F 162 " pdb=" CD PRO F 162 " ideal model delta sigma weight residual 1.503 1.350 0.153 3.40e-02 8.65e+02 2.01e+01 bond pdb=" CA SER o 50 " pdb=" CB SER o 50 " ideal model delta sigma weight residual 1.530 1.456 0.075 1.69e-02 3.50e+03 1.95e+01 ... (remaining 36803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 49493 3.46 - 6.91: 494 6.91 - 10.37: 45 10.37 - 13.82: 4 13.82 - 17.28: 1 Bond angle restraints: 50037 Sorted by residual: angle pdb=" CA PRO F 162 " pdb=" N PRO F 162 " pdb=" CD PRO F 162 " ideal model delta sigma weight residual 112.00 94.72 17.28 1.40e+00 5.10e-01 1.52e+02 angle pdb=" N PRO b 320 " pdb=" CA PRO b 320 " pdb=" C PRO b 320 " ideal model delta sigma weight residual 113.65 101.21 12.44 1.35e+00 5.49e-01 8.49e+01 angle pdb=" C THR n 53 " pdb=" CA THR n 53 " pdb=" CB THR n 53 " ideal model delta sigma weight residual 109.80 96.43 13.37 1.61e+00 3.86e-01 6.90e+01 angle pdb=" O GLY A 66 " pdb=" C GLY A 66 " pdb=" N PRO A 67 " ideal model delta sigma weight residual 121.07 118.26 2.81 3.60e-01 7.72e+00 6.08e+01 angle pdb=" N LYS C 15 " pdb=" CA LYS C 15 " pdb=" C LYS C 15 " ideal model delta sigma weight residual 111.03 102.85 8.18 1.11e+00 8.12e-01 5.43e+01 ... (remaining 50032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 19389 18.08 - 36.16: 2457 36.16 - 54.24: 550 54.24 - 72.32: 154 72.32 - 90.40: 23 Dihedral angle restraints: 22573 sinusoidal: 8701 harmonic: 13872 Sorted by residual: dihedral pdb=" CD ARG J 140 " pdb=" NE ARG J 140 " pdb=" CZ ARG J 140 " pdb=" NH1 ARG J 140 " ideal model delta sinusoidal sigma weight residual 0.00 -82.21 82.21 1 1.00e+01 1.00e-02 8.30e+01 dihedral pdb=" CD ARG a 110 " pdb=" NE ARG a 110 " pdb=" CZ ARG a 110 " pdb=" NH1 ARG a 110 " ideal model delta sinusoidal sigma weight residual 0.00 -64.31 64.31 1 1.00e+01 1.00e-02 5.44e+01 dihedral pdb=" CD ARG H 135 " pdb=" NE ARG H 135 " pdb=" CZ ARG H 135 " pdb=" NH1 ARG H 135 " ideal model delta sinusoidal sigma weight residual 0.00 61.07 -61.07 1 1.00e+01 1.00e-02 4.96e+01 ... (remaining 22570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 5070 0.064 - 0.128: 794 0.128 - 0.193: 102 0.193 - 0.257: 26 0.257 - 0.321: 6 Chirality restraints: 5998 Sorted by residual: chirality pdb=" CA GLN Y 57 " pdb=" N GLN Y 57 " pdb=" C GLN Y 57 " pdb=" CB GLN Y 57 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA THR o 58 " pdb=" N THR o 58 " pdb=" C THR o 58 " pdb=" CB THR o 58 " both_signs ideal model delta sigma weight residual False 2.53 2.82 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA LYS C 15 " pdb=" N LYS C 15 " pdb=" C LYS C 15 " pdb=" CB LYS C 15 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 5995 not shown) Planarity restraints: 6518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 140 " 1.084 9.50e-02 1.11e+02 4.86e-01 1.42e+02 pdb=" NE ARG J 140 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG J 140 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG J 140 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG J 140 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG a 110 " 0.992 9.50e-02 1.11e+02 4.45e-01 1.20e+02 pdb=" NE ARG a 110 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG a 110 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG a 110 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG a 110 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 135 " -0.951 9.50e-02 1.11e+02 4.26e-01 1.10e+02 pdb=" NE ARG H 135 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG H 135 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG H 135 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG H 135 " -0.023 2.00e-02 2.50e+03 ... (remaining 6515 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 256 2.52 - 3.12: 27514 3.12 - 3.71: 57170 3.71 - 4.31: 75567 4.31 - 4.90: 130528 Nonbonded interactions: 291035 Sorted by model distance: nonbonded pdb=" NE2 GLN N 76 " pdb=" O LEU Y 132 " model vdw 1.926 3.120 nonbonded pdb=" OG SER D 36 " pdb=" O LEU E 211 " model vdw 1.968 3.040 nonbonded pdb=" NZ LYS Z 45 " pdb=" OG1 THR p 55 " model vdw 1.994 3.120 nonbonded pdb=" OD1 ASP U 103 " pdb=" OH TYR a 112 " model vdw 2.001 3.040 nonbonded pdb=" OG1 THR Z 121 " pdb=" O LEU q 248 " model vdw 2.037 3.040 ... (remaining 291030 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 37 through 243) selection = (chain 'H' and resid 37 through 243) selection = (chain 'I' and resid 37 through 243) selection = (chain 'J' and resid 37 through 243) } ncs_group { reference = chain 'L' selection = (chain 'M' and resid 33 through 104) selection = (chain 'N' and resid 33 through 104) selection = (chain 'O' and resid 33 through 104) selection = (chain 'P' and resid 33 through 104) } ncs_group { reference = (chain 'Q' and (resid 3 through 54 or resid 83 through 136)) selection = (chain 'R' and (resid 3 through 54 or resid 83 through 136)) selection = (chain 'S' and (resid 3 through 54 or resid 83 through 136)) selection = (chain 'T' and (resid 3 through 54 or resid 83 through 136)) selection = chain 'U' } ncs_group { reference = (chain 'V' and resid 4 through 134) selection = (chain 'W' and resid 4 through 134) selection = (chain 'X' and resid 4 through 134) selection = (chain 'Y' and resid 4 through 134) selection = chain 'Z' selection = (chain 'a' and resid 4 through 134) } ncs_group { reference = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' } ncs_group { reference = chain 'd' selection = (chain 'f' and resid 311 through 330) selection = (chain 'h' and resid 311 through 330) selection = chain 'j' selection = (chain 'l' and resid 311 through 330) } ncs_group { reference = chain 'm' selection = (chain 'n' and resid 2 through 249) selection = (chain 'o' and resid 2 through 249) selection = (chain 'p' and resid 2 through 249) selection = (chain 'q' and resid 2 through 249) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.220 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: 0.060 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 36.840 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.150 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:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.197 36808 Z= 0.304 Angle : 0.845 17.275 50037 Z= 0.524 Chirality : 0.049 0.321 5998 Planarity : 0.017 0.486 6518 Dihedral : 17.125 90.396 13585 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.46 % Allowed : 3.41 % Favored : 96.13 % Rotamer: Outliers : 1.80 % Allowed : 21.47 % Favored : 76.74 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.12), residues: 4749 helix: 2.14 (0.10), residues: 2802 sheet: -0.75 (0.26), residues: 354 loop : -0.54 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 10 TYR 0.017 0.002 TYR Z 112 PHE 0.035 0.002 PHE E 101 TRP 0.028 0.002 TRP B 68 HIS 0.003 0.001 HIS E 155 Details of bonding type rmsd covalent geometry : bond 0.00501 (36808) covalent geometry : angle 0.84522 (50037) hydrogen bonds : bond 0.12649 ( 2382) hydrogen bonds : angle 5.29597 ( 6978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9498 Ramachandran restraints generated. 4749 Oldfield, 0 Emsley, 4749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9498 Ramachandran restraints generated. 4749 Oldfield, 0 Emsley, 4749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2292 residues out of total 3890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 2222 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 80 LEU cc_start: 0.7961 (tp) cc_final: 0.7501 (tt) REVERT: B 7 MET cc_start: 0.8881 (mmm) cc_final: 0.8415 (mmm) REVERT: D 71 ASN cc_start: 0.7089 (m-40) cc_final: 0.6606 (m110) REVERT: E 153 THR cc_start: 0.6027 (p) cc_final: 0.5679 (p) REVERT: E 240 CYS cc_start: 0.6576 (t) cc_final: 0.3870 (t) REVERT: F 149 LEU cc_start: 0.7226 (tp) cc_final: 0.6766 (tp) REVERT: F 159 LEU cc_start: 0.7703 (tp) cc_final: 0.7362 (pt) REVERT: G 53 PHE cc_start: 0.5830 (m-10) cc_final: 0.5538 (m-10) REVERT: G 234 LEU cc_start: 0.8240 (tp) cc_final: 0.7761 (tp) REVERT: H 107 LYS cc_start: 0.8690 (mmtt) cc_final: 0.8449 (mmtp) REVERT: H 174 TYR cc_start: 0.8380 (t80) cc_final: 0.7866 (t80) REVERT: I 109 TYR cc_start: 0.8290 (t80) cc_final: 0.7957 (t80) REVERT: I 143 ARG cc_start: 0.6288 (mpt90) cc_final: 0.6022 (mmm160) REVERT: I 155 ASN cc_start: 0.8027 (m-40) cc_final: 0.7751 (t0) REVERT: J 152 ARG cc_start: 0.6717 (ttm170) cc_final: 0.6023 (mtt180) REVERT: M 64 PRO cc_start: 0.6461 (Cg_endo) cc_final: 0.6169 (Cg_exo) REVERT: N 71 VAL cc_start: 0.8984 (t) cc_final: 0.8705 (t) REVERT: Q 23 GLN cc_start: 0.8180 (tt0) cc_final: 0.7780 (tt0) REVERT: Q 92 GLN cc_start: 0.8178 (pt0) cc_final: 0.7839 (pt0) REVERT: Q 111 ASP cc_start: 0.7117 (t0) cc_final: 0.6773 (t0) REVERT: R 53 MET cc_start: 0.8026 (mmm) cc_final: 0.7302 (mmm) REVERT: R 131 MET cc_start: 0.8323 (mmm) cc_final: 0.7804 (mmt) REVERT: S 24 GLU cc_start: 0.8360 (tt0) cc_final: 0.8083 (tt0) REVERT: S 96 ASP cc_start: 0.8130 (p0) cc_final: 0.7851 (p0) REVERT: T 16 LEU cc_start: 0.9284 (tp) cc_final: 0.8937 (tp) REVERT: T 52 VAL cc_start: 0.8678 (t) cc_final: 0.8357 (t) REVERT: T 99 THR cc_start: 0.8254 (m) cc_final: 0.7970 (m) REVERT: T 116 TYR cc_start: 0.9094 (t80) cc_final: 0.8828 (t80) REVERT: U 19 ARG cc_start: 0.8286 (mmt180) cc_final: 0.7732 (mmt-90) REVERT: U 22 ARG cc_start: 0.8597 (ttt180) cc_final: 0.8253 (ttt180) REVERT: V 93 MET cc_start: 0.8606 (mmm) cc_final: 0.8387 (mtp) REVERT: V 112 TYR cc_start: 0.8369 (t80) cc_final: 0.8002 (t80) REVERT: W 3 LEU cc_start: 0.6136 (OUTLIER) cc_final: 0.5911 (mp) REVERT: W 5 ASN cc_start: 0.7831 (m-40) cc_final: 0.7331 (m-40) REVERT: W 33 SER cc_start: 0.9014 (m) cc_final: 0.8700 (p) REVERT: X 17 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8149 (mt0) REVERT: X 104 ASN cc_start: 0.8663 (m-40) cc_final: 0.8372 (t0) REVERT: Y 93 MET cc_start: 0.8109 (mmt) cc_final: 0.7867 (tpp) REVERT: Z 95 ASN cc_start: 0.7871 (p0) cc_final: 0.7650 (p0) REVERT: Z 104 ASN cc_start: 0.8828 (m-40) cc_final: 0.8619 (m-40) REVERT: Z 119 LEU cc_start: 0.8913 (mt) cc_final: 0.8645 (tp) REVERT: a 76 LEU cc_start: 0.8076 (mt) cc_final: 0.7702 (mt) REVERT: a 110 ARG cc_start: 0.7648 (mmt-90) cc_final: 0.6505 (mmt180) REVERT: d 325 GLU cc_start: 0.6982 (tp30) cc_final: 0.6572 (mp0) REVERT: m 94 ASP cc_start: 0.7534 (p0) cc_final: 0.7326 (t0) REVERT: m 217 MET cc_start: 0.7446 (mmm) cc_final: 0.7219 (mmm) REVERT: m 225 ARG cc_start: 0.8198 (mmt-90) cc_final: 0.6725 (mmm160) REVERT: m 228 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8319 (tt0) REVERT: m 232 LYS cc_start: 0.8131 (tppt) cc_final: 0.7677 (mttt) REVERT: n 94 ASP cc_start: 0.7952 (p0) cc_final: 0.7686 (p0) REVERT: n 193 LEU cc_start: 0.7463 (mt) cc_final: 0.7163 (mt) REVERT: n 220 MET cc_start: 0.7396 (mtm) cc_final: 0.6789 (tmm) REVERT: n 225 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.6465 (ttt180) REVERT: n 228 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6348 (tt0) REVERT: n 245 ASN cc_start: 0.8453 (m-40) cc_final: 0.8233 (m110) REVERT: o 51 LEU cc_start: 0.9032 (mp) cc_final: 0.8804 (mt) REVERT: o 206 LEU cc_start: 0.8918 (tp) cc_final: 0.8710 (tt) REVERT: o 225 ARG cc_start: 0.7133 (mmt180) cc_final: 0.6407 (mtt180) REVERT: o 228 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6589 (tt0) REVERT: o 245 ASN cc_start: 0.8954 (m-40) cc_final: 0.8659 (m-40) REVERT: p 189 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8037 (mtp180) REVERT: p 193 LEU cc_start: 0.8011 (mt) cc_final: 0.7722 (mt) REVERT: p 231 MET cc_start: 0.8132 (mmp) cc_final: 0.7900 (mtt) REVERT: p 236 SER cc_start: 0.8540 (m) cc_final: 0.7844 (t) REVERT: q 18 GLN cc_start: 0.8211 (mt0) cc_final: 0.7811 (mt0) REVERT: q 65 ASP cc_start: 0.6574 (t0) cc_final: 0.5826 (p0) REVERT: q 104 ASN cc_start: 0.7943 (t0) cc_final: 0.7226 (p0) REVERT: q 174 SER cc_start: 0.8612 (t) cc_final: 0.7958 (m) REVERT: q 188 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7380 (tm-30) REVERT: q 202 MET cc_start: 0.4581 (ttm) cc_final: 0.3924 (ttm) REVERT: q 210 ASN cc_start: 0.7613 (p0) cc_final: 0.7175 (p0) REVERT: q 225 ARG cc_start: 0.7209 (mmt-90) cc_final: 0.6038 (mmt180) outliers start: 70 outliers final: 10 residues processed: 2246 average time/residue: 0.2378 time to fit residues: 866.4825 Evaluate side-chains 1367 residues out of total 3890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 1354 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain Q residue 53 MET Chi-restraints excluded: chain W residue 3 LEU Chi-restraints excluded: chain W residue 126 MET Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain a residue 38 ASP Chi-restraints excluded: chain m residue 123 GLU Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 225 ARG Chi-restraints excluded: chain p residue 189 ARG Chi-restraints excluded: chain q residue 155 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.7980 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 0.2980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN E 76 GLN E 162 ASN E 198 ASN ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN F 114 GLN F 119 GLN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 GLN G 141 GLN G 233 GLN H 36 GLN H 184 GLN J 87 GLN J 114 GLN J 132 GLN J 155 ASN ** K 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 GLN L 90 ASN M 103 GLN N 55 GLN O 83 GLN O 87 GLN O 90 ASN P 39 HIS ** P 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 ASN Q 135 GLN R 23 GLN S 23 GLN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN T 17 ASN T 29 ASN T 32 ASN T 108 GLN T 135 GLN U 29 ASN U 39 GLN W 5 ASN W 82 ASN W 134 GLN X 22 ASN X 46 GLN X 50 GLN X 57 GLN X 115 ASN X 134 GLN a 57 GLN a 113 GLN a 115 ASN ** c 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 318 ASN l 324 ASN n 104 ASN ** n 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 210 ASN ** n 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 240 ASN n 246 GLN o 14 GLN o 18 GLN o 39 ASN o 84 GLN o 116 GLN o 223 ASN o 240 ASN p 37 GLN ** p 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 210 ASN ** p 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 246 GLN q 18 GLN q 37 GLN q 153 ASN q 240 ASN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.124615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.110488 restraints weight = 86689.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.113255 restraints weight = 42361.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.115083 restraints weight = 24966.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.116307 restraints weight = 16778.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.117121 restraints weight = 12475.623| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 36808 Z= 0.179 Angle : 0.755 11.301 50037 Z= 0.373 Chirality : 0.045 0.215 5998 Planarity : 0.006 0.088 6518 Dihedral : 4.915 63.305 5109 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.82 % Favored : 97.05 % Rotamer: Outliers : 5.09 % Allowed : 24.22 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.12), residues: 4749 helix: 2.24 (0.10), residues: 2811 sheet: -0.67 (0.26), residues: 346 loop : -0.45 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 110 TYR 0.027 0.002 TYR E 16 PHE 0.030 0.002 PHE E 101 TRP 0.022 0.002 TRP m 87 HIS 0.009 0.001 HIS P 39 Details of bonding type rmsd covalent geometry : bond 0.00418 (36808) covalent geometry : angle 0.75518 (50037) hydrogen bonds : bond 0.04638 ( 2382) hydrogen bonds : angle 4.19429 ( 6978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9498 Ramachandran restraints generated. 4749 Oldfield, 0 Emsley, 4749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9498 Ramachandran restraints generated. 4749 Oldfield, 0 Emsley, 4749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1711 residues out of total 3890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 1513 time to evaluate : 1.462 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: B 4 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7758 (pm20) REVERT: B 7 MET cc_start: 0.9197 (mmm) cc_final: 0.8923 (mmm) REVERT: B 26 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.7038 (mm) REVERT: C 2 THR cc_start: 0.7972 (p) cc_final: 0.7508 (p) REVERT: C 70 LEU cc_start: 0.8835 (mm) cc_final: 0.8493 (tp) REVERT: D 35 ILE cc_start: 0.6909 (mt) cc_final: 0.6640 (mt) REVERT: D 46 GLU cc_start: 0.6376 (tt0) cc_final: 0.5822 (tt0) REVERT: D 71 ASN cc_start: 0.8787 (m-40) cc_final: 0.8510 (m-40) REVERT: E 52 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7280 (mp) REVERT: E 106 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7899 (tpp) REVERT: E 170 MET cc_start: 0.7859 (mmm) cc_final: 0.7297 (tmm) REVERT: E 210 GLN cc_start: 0.8261 (mp10) cc_final: 0.7911 (mp10) REVERT: E 224 VAL cc_start: 0.8924 (m) cc_final: 0.8505 (p) REVERT: E 254 ILE cc_start: 0.6950 (mm) cc_final: 0.6629 (mm) REVERT: F 40 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7687 (tp) REVERT: F 128 ASP cc_start: 0.8743 (m-30) cc_final: 0.8217 (m-30) REVERT: F 129 LYS cc_start: 0.8438 (tptm) cc_final: 0.8208 (tptm) REVERT: F 149 LEU cc_start: 0.8337 (tp) cc_final: 0.7829 (tp) REVERT: F 159 LEU cc_start: 0.7357 (tp) cc_final: 0.7133 (pt) REVERT: F 190 PHE cc_start: 0.7681 (m-10) cc_final: 0.6942 (m-80) REVERT: G 53 PHE cc_start: 0.7529 (m-10) cc_final: 0.7065 (m-10) REVERT: G 101 MET cc_start: 0.8742 (mmp) cc_final: 0.7999 (mmm) REVERT: G 184 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.8090 (tm-30) REVERT: H 36 GLN cc_start: 0.6494 (OUTLIER) cc_final: 0.6136 (tm-30) REVERT: H 118 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7549 (mt-10) REVERT: H 178 GLU cc_start: 0.8837 (tp30) cc_final: 0.8519 (mm-30) REVERT: H 180 LYS cc_start: 0.8065 (mttm) cc_final: 0.7785 (mttm) REVERT: H 205 MET cc_start: 0.7999 (mmp) cc_final: 0.7741 (mmp) REVERT: H 210 MET cc_start: 0.6516 (tpp) cc_final: 0.6230 (tpp) REVERT: H 223 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8886 (mm) REVERT: I 120 LYS cc_start: 0.8633 (tptp) cc_final: 0.8169 (mtmt) REVERT: I 143 ARG cc_start: 0.5940 (mpt90) cc_final: 0.5680 (mmm160) REVERT: I 210 MET cc_start: 0.8269 (tmm) cc_final: 0.8042 (tmm) REVERT: J 190 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7167 (m-80) REVERT: K 82 MET cc_start: 0.8268 (tmm) cc_final: 0.6818 (ppp) REVERT: K 84 MET cc_start: 0.6491 (ttt) cc_final: 0.6045 (ttt) REVERT: K 91 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8670 (tppt) REVERT: K 102 MET cc_start: 0.6784 (tpp) cc_final: 0.6543 (tpp) REVERT: L 63 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6954 (tm-30) REVERT: L 75 MET cc_start: 0.8227 (ttp) cc_final: 0.7950 (ttm) REVERT: L 96 TYR cc_start: 0.8416 (t80) cc_final: 0.8178 (t80) REVERT: M 46 SER cc_start: 0.8831 (t) cc_final: 0.8559 (p) REVERT: M 96 TYR cc_start: 0.8400 (t80) cc_final: 0.8002 (t80) REVERT: N 58 LYS cc_start: 0.8987 (mtmm) cc_final: 0.8527 (mttp) REVERT: N 81 SER cc_start: 0.9172 (OUTLIER) cc_final: 0.8622 (t) REVERT: O 47 ASP cc_start: 0.8636 (p0) cc_final: 0.8391 (p0) REVERT: O 74 ASP cc_start: 0.8291 (m-30) cc_final: 0.8005 (m-30) REVERT: O 86 ILE cc_start: 0.9661 (tt) cc_final: 0.9452 (tt) REVERT: O 90 ASN cc_start: 0.8709 (m-40) cc_final: 0.8497 (m110) REVERT: P 76 GLN cc_start: 0.8567 (tp40) cc_final: 0.8332 (tp40) REVERT: P 82 MET cc_start: 0.8642 (tpp) cc_final: 0.8308 (tpp) REVERT: Q 23 GLN cc_start: 0.8828 (tt0) cc_final: 0.8560 (tt0) REVERT: Q 42 ASP cc_start: 0.7736 (t0) cc_final: 0.7491 (t0) REVERT: Q 135 GLN cc_start: 0.7927 (tp40) cc_final: 0.7622 (tp-100) REVERT: R 4 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8431 (mtt180) REVERT: R 53 MET cc_start: 0.7996 (mmm) cc_final: 0.7736 (mmm) REVERT: R 131 MET cc_start: 0.8258 (mmm) cc_final: 0.7933 (mmt) REVERT: S 29 ASN cc_start: 0.8293 (m-40) cc_final: 0.8032 (t0) REVERT: S 96 ASP cc_start: 0.8225 (p0) cc_final: 0.7854 (p0) REVERT: S 118 MET cc_start: 0.8338 (ttm) cc_final: 0.7718 (ttm) REVERT: T 12 GLN cc_start: 0.8714 (mm110) cc_final: 0.8488 (mm-40) REVERT: T 91 ASP cc_start: 0.8169 (m-30) cc_final: 0.7716 (t0) REVERT: T 103 ASP cc_start: 0.8276 (m-30) cc_final: 0.7750 (m-30) REVERT: U 21 GLN cc_start: 0.8101 (mt0) cc_final: 0.7858 (mt0) REVERT: U 22 ARG cc_start: 0.8493 (ttt180) cc_final: 0.8091 (ttt180) REVERT: U 23 GLN cc_start: 0.8263 (tp-100) cc_final: 0.7830 (tp-100) REVERT: U 45 PHE cc_start: 0.8075 (t80) cc_final: 0.7779 (t80) REVERT: U 102 MET cc_start: 0.7143 (tpp) cc_final: 0.6671 (tpp) REVERT: V 46 GLN cc_start: 0.7645 (mp10) cc_final: 0.7360 (mp10) REVERT: V 112 TYR cc_start: 0.8323 (t80) cc_final: 0.7996 (t80) REVERT: W 7 PHE cc_start: 0.9217 (m-80) cc_final: 0.8873 (m-80) REVERT: W 33 SER cc_start: 0.9173 (m) cc_final: 0.8735 (p) REVERT: W 45 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7699 (mtpp) REVERT: Y 27 ASN cc_start: 0.8764 (m-40) cc_final: 0.8371 (m-40) REVERT: Y 45 LYS cc_start: 0.8951 (ptmt) cc_final: 0.8713 (ptmt) REVERT: Y 97 ASP cc_start: 0.7187 (p0) cc_final: 0.6965 (p0) REVERT: Y 117 GLU cc_start: 0.7168 (tp30) cc_final: 0.6959 (tp30) REVERT: Z 12 SER cc_start: 0.8953 (m) cc_final: 0.8620 (p) REVERT: Z 63 LYS cc_start: 0.9069 (pttt) cc_final: 0.8863 (ptmt) REVERT: Z 104 ASN cc_start: 0.9163 (m-40) cc_final: 0.8913 (m-40) REVERT: Z 119 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8804 (tp) REVERT: a 5 ASN cc_start: 0.8147 (t0) cc_final: 0.7834 (m110) REVERT: a 42 TYR cc_start: 0.8356 (t80) cc_final: 0.8059 (t80) REVERT: a 50 GLN cc_start: 0.7805 (mt0) cc_final: 0.7517 (mp10) REVERT: a 63 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8308 (ttpp) REVERT: a 76 LEU cc_start: 0.8452 (mt) cc_final: 0.8223 (mt) REVERT: c 318 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.7898 (t0) REVERT: d 325 GLU cc_start: 0.7377 (tp30) cc_final: 0.6829 (mp0) REVERT: e 319 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7959 (mm110) REVERT: g 317 SER cc_start: 0.7571 (p) cc_final: 0.7280 (t) REVERT: j 324 ASN cc_start: 0.7218 (OUTLIER) cc_final: 0.6714 (p0) REVERT: m 175 ASP cc_start: 0.6443 (OUTLIER) cc_final: 0.6083 (m-30) REVERT: m 217 MET cc_start: 0.7154 (mmm) cc_final: 0.6892 (mmm) REVERT: m 228 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8024 (tt0) REVERT: m 232 LYS cc_start: 0.8474 (tppt) cc_final: 0.7587 (mttt) REVERT: n 9 MET cc_start: 0.8910 (tmm) cc_final: 0.8685 (tmm) REVERT: n 73 TYR cc_start: 0.8048 (t80) cc_final: 0.7783 (t80) REVERT: n 94 ASP cc_start: 0.8309 (p0) cc_final: 0.8088 (p0) REVERT: n 99 TYR cc_start: 0.8735 (m-80) cc_final: 0.8453 (m-10) REVERT: n 193 LEU cc_start: 0.7841 (mt) cc_final: 0.7502 (mt) REVERT: n 220 MET cc_start: 0.7352 (mtm) cc_final: 0.6787 (tmm) REVERT: n 225 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.6529 (ttt180) REVERT: n 228 GLU cc_start: 0.7495 (mt-10) cc_final: 0.6516 (tt0) REVERT: o 18 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: o 58 THR cc_start: 0.9175 (m) cc_final: 0.8955 (p) REVERT: o 212 LYS cc_start: 0.7501 (tppt) cc_final: 0.7036 (mmtt) REVERT: o 225 ARG cc_start: 0.7459 (mmt180) cc_final: 0.6238 (mtt180) REVERT: o 241 GLU cc_start: 0.8193 (tp30) cc_final: 0.7748 (mm-30) REVERT: o 250 MET cc_start: 0.7611 (mpp) cc_final: 0.7241 (mpp) REVERT: p 236 SER cc_start: 0.8765 (m) cc_final: 0.8403 (t) REVERT: q 9 MET cc_start: 0.8973 (tmm) cc_final: 0.8588 (tmm) REVERT: q 65 ASP cc_start: 0.7189 (t0) cc_final: 0.5646 (p0) REVERT: q 202 MET cc_start: 0.4485 (ttm) cc_final: 0.3814 (ttm) REVERT: q 210 ASN cc_start: 0.7575 (p0) cc_final: 0.6865 (p0) REVERT: q 225 ARG cc_start: 0.7735 (mmt-90) cc_final: 0.5932 (mmm160) REVERT: q 231 MET cc_start: 0.7421 (ptm) cc_final: 0.7018 (ptp) outliers start: 198 outliers final: 97 residues processed: 1621 average time/residue: 0.2216 time to fit residues: 596.9697 Evaluate side-chains 1429 residues out of total 3890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 1314 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain E residue 9 TRP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 60 MET Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 196 ILE Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 190 PHE Chi-restraints excluded: chain J residue 216 THR Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain Q residue 103 ASP Chi-restraints excluded: chain R residue 4 ARG Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 89 VAL Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 SER Chi-restraints excluded: chain T residue 133 VAL Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain W residue 45 LYS Chi-restraints excluded: chain W residue 120 ASN Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain X residue 122 VAL Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 23 VAL Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 91 VAL Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 99 VAL Chi-restraints excluded: chain Z residue 5 ASN Chi-restraints excluded: chain Z residue 18 SER Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 106 MET Chi-restraints excluded: chain Z residue 119 LEU Chi-restraints excluded: chain Z residue 122 VAL Chi-restraints excluded: chain Z residue 124 SER Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 63 LYS Chi-restraints excluded: chain a residue 70 SER Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain c residue 318 ASN Chi-restraints excluded: chain d residue 328 ILE Chi-restraints excluded: chain j residue 312 VAL Chi-restraints excluded: chain j residue 324 ASN Chi-restraints excluded: chain m residue 107 VAL Chi-restraints excluded: chain m residue 123 GLU Chi-restraints excluded: chain m residue 171 VAL Chi-restraints excluded: chain m residue 175 ASP Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 225 ARG Chi-restraints excluded: chain n residue 246 GLN Chi-restraints excluded: chain o residue 18 GLN Chi-restraints excluded: chain o residue 193 LEU Chi-restraints excluded: chain p residue 30 SER Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 120 VAL Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain q residue 49 LEU Chi-restraints excluded: chain q residue 51 LEU Chi-restraints excluded: chain q residue 155 VAL Chi-restraints excluded: chain q residue 238 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 138 optimal weight: 0.3980 chunk 361 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 260 optimal weight: 6.9990 chunk 319 optimal weight: 0.9990 chunk 396 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 362 optimal weight: 6.9990 chunk 315 optimal weight: 0.7980 chunk 341 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 14 HIS E 210 GLN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 GLN J 124 GLN K 90 ASN M 55 GLN ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 GLN U 23 GLN U 29 ASN ** V 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 134 GLN ** a 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 319 GLN e 318 ASN j 318 ASN ** n 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 70 GLN ** n 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 246 GLN o 18 GLN ** o 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 116 GLN o 240 ASN p 37 GLN ** p 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 106 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.123733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.109911 restraints weight = 86768.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.112626 restraints weight = 42550.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.114409 restraints weight = 25092.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.115586 restraints weight = 16864.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.116356 restraints weight = 12563.568| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 36808 Z= 0.150 Angle : 0.708 12.652 50037 Z= 0.346 Chirality : 0.044 0.224 5998 Planarity : 0.005 0.078 6518 Dihedral : 4.459 55.870 5093 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.53 % Favored : 97.39 % Rotamer: Outliers : 5.40 % Allowed : 26.04 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.12), residues: 4749 helix: 2.20 (0.10), residues: 2815 sheet: -0.61 (0.26), residues: 347 loop : -0.44 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 19 TYR 0.018 0.002 TYR T 38 PHE 0.030 0.002 PHE B 51 TRP 0.016 0.001 TRP C 68 HIS 0.007 0.001 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00350 (36808) covalent geometry : angle 0.70801 (50037) hydrogen bonds : bond 0.04181 ( 2382) hydrogen bonds : angle 4.03683 ( 6978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9498 Ramachandran restraints generated. 4749 Oldfield, 0 Emsley, 4749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9498 Ramachandran restraints generated. 4749 Oldfield, 0 Emsley, 4749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1620 residues out of total 3890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 1410 time to evaluate : 1.495 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: A 74 LEU cc_start: 0.8452 (mt) cc_final: 0.8150 (mp) REVERT: A 83 ASN cc_start: 0.8462 (m110) cc_final: 0.8003 (m110) REVERT: A 86 TYR cc_start: 0.7817 (m-80) cc_final: 0.7491 (m-80) REVERT: B 1 MET cc_start: 0.7976 (pmm) cc_final: 0.7769 (pmm) REVERT: B 7 MET cc_start: 0.9171 (mmm) cc_final: 0.8771 (tmm) REVERT: C 53 PRO cc_start: 0.8528 (Cg_exo) cc_final: 0.8113 (Cg_endo) REVERT: C 70 LEU cc_start: 0.8941 (mm) cc_final: 0.8585 (tp) REVERT: D 35 ILE cc_start: 0.6905 (mt) cc_final: 0.6555 (mt) REVERT: D 46 GLU cc_start: 0.6158 (tt0) cc_final: 0.5687 (tt0) REVERT: E 41 ARG cc_start: 0.6315 (OUTLIER) cc_final: 0.5847 (ttm-80) REVERT: E 52 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7025 (mp) REVERT: E 77 GLN cc_start: 0.8084 (mp10) cc_final: 0.7826 (mm110) REVERT: E 106 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.7881 (tpp) REVERT: E 170 MET cc_start: 0.7615 (mmm) cc_final: 0.7235 (tmm) REVERT: E 209 PRO cc_start: 0.6086 (Cg_endo) cc_final: 0.5597 (Cg_exo) REVERT: E 210 GLN cc_start: 0.8260 (mp-120) cc_final: 0.7843 (mp10) REVERT: E 224 VAL cc_start: 0.8767 (m) cc_final: 0.8343 (p) REVERT: E 254 ILE cc_start: 0.7302 (mm) cc_final: 0.6997 (mm) REVERT: F 40 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7612 (tp) REVERT: F 128 ASP cc_start: 0.8748 (m-30) cc_final: 0.8412 (m-30) REVERT: F 190 PHE cc_start: 0.7370 (m-10) cc_final: 0.6833 (m-80) REVERT: F 205 MET cc_start: 0.8366 (mmm) cc_final: 0.7908 (mmm) REVERT: G 184 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8193 (tm-30) REVERT: G 236 MET cc_start: 0.8898 (mmm) cc_final: 0.8524 (mmm) REVERT: H 180 LYS cc_start: 0.8049 (mttm) cc_final: 0.7760 (mttm) REVERT: H 228 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8684 (mt) REVERT: I 120 LYS cc_start: 0.8621 (tptp) cc_final: 0.8149 (mttt) REVERT: I 143 ARG cc_start: 0.5927 (mpt90) cc_final: 0.5489 (mmm160) REVERT: J 190 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7507 (m-80) REVERT: K 84 MET cc_start: 0.6509 (ttt) cc_final: 0.6125 (ttt) REVERT: K 91 LYS cc_start: 0.8960 (mmtm) cc_final: 0.8744 (tppt) REVERT: K 102 MET cc_start: 0.6721 (tpp) cc_final: 0.6473 (tpp) REVERT: L 63 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7097 (tm-30) REVERT: L 75 MET cc_start: 0.8175 (ttp) cc_final: 0.7816 (ttm) REVERT: L 84 MET cc_start: 0.8838 (tpp) cc_final: 0.8546 (mmm) REVERT: M 96 TYR cc_start: 0.8423 (t80) cc_final: 0.8095 (t80) REVERT: N 58 LYS cc_start: 0.9157 (mtmm) cc_final: 0.8952 (mtmm) REVERT: N 66 ILE cc_start: 0.7993 (mt) cc_final: 0.7062 (mt) REVERT: N 81 SER cc_start: 0.9251 (OUTLIER) cc_final: 0.8799 (t) REVERT: O 47 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8376 (p0) REVERT: O 74 ASP cc_start: 0.8391 (m-30) cc_final: 0.7988 (m-30) REVERT: O 83 GLN cc_start: 0.8568 (tp40) cc_final: 0.8317 (tp-100) REVERT: O 86 ILE cc_start: 0.9631 (tt) cc_final: 0.9314 (tt) REVERT: O 90 ASN cc_start: 0.8637 (m-40) cc_final: 0.8274 (m110) REVERT: P 55 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8589 (tm-30) REVERT: P 76 GLN cc_start: 0.8271 (tp40) cc_final: 0.7764 (tp40) REVERT: P 82 MET cc_start: 0.8650 (tpp) cc_final: 0.8248 (tpp) REVERT: Q 135 GLN cc_start: 0.7806 (tp40) cc_final: 0.7602 (tp40) REVERT: R 24 GLU cc_start: 0.7613 (tt0) cc_final: 0.7178 (tt0) REVERT: R 53 MET cc_start: 0.7848 (mmm) cc_final: 0.7378 (mmm) REVERT: R 131 MET cc_start: 0.8446 (mmm) cc_final: 0.7927 (mmt) REVERT: S 24 GLU cc_start: 0.8310 (tt0) cc_final: 0.7943 (tt0) REVERT: S 29 ASN cc_start: 0.8440 (m-40) cc_final: 0.7938 (t0) REVERT: S 96 ASP cc_start: 0.8305 (p0) cc_final: 0.7970 (p0) REVERT: S 105 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7936 (mm-30) REVERT: U 23 GLN cc_start: 0.8367 (tp40) cc_final: 0.7926 (tp-100) REVERT: U 112 ASN cc_start: 0.9262 (m-40) cc_final: 0.9035 (m-40) REVERT: V 46 GLN cc_start: 0.7834 (mp10) cc_final: 0.7409 (mp10) REVERT: V 112 TYR cc_start: 0.8363 (t80) cc_final: 0.7919 (t80) REVERT: W 7 PHE cc_start: 0.8955 (m-80) cc_final: 0.8711 (m-80) REVERT: W 33 SER cc_start: 0.9006 (m) cc_final: 0.8657 (p) REVERT: X 17 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8112 (mt0) REVERT: X 102 MET cc_start: 0.8240 (mmm) cc_final: 0.7915 (mmm) REVERT: Y 27 ASN cc_start: 0.8816 (m-40) cc_final: 0.8404 (m-40) REVERT: Y 38 ASP cc_start: 0.8110 (p0) cc_final: 0.7816 (p0) REVERT: Y 45 LYS cc_start: 0.8837 (ptmt) cc_final: 0.8555 (ptmt) REVERT: Y 97 ASP cc_start: 0.7061 (p0) cc_final: 0.6809 (p0) REVERT: Y 117 GLU cc_start: 0.7278 (tp30) cc_final: 0.7022 (tp30) REVERT: Z 19 LYS cc_start: 0.8761 (mttp) cc_final: 0.7760 (mttp) REVERT: Z 104 ASN cc_start: 0.9105 (m-40) cc_final: 0.8793 (m-40) REVERT: Z 119 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8804 (tp) REVERT: a 5 ASN cc_start: 0.8174 (t0) cc_final: 0.7632 (m110) REVERT: a 7 PHE cc_start: 0.9083 (m-80) cc_final: 0.8846 (m-10) REVERT: a 46 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7850 (tm-30) REVERT: a 63 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8269 (ttpp) REVERT: a 77 VAL cc_start: 0.8479 (OUTLIER) cc_final: 0.8147 (t) REVERT: a 110 ARG cc_start: 0.8077 (mmt180) cc_final: 0.6617 (mmm160) REVERT: a 117 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8078 (mt-10) REVERT: a 132 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8509 (tt) REVERT: c 318 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.7871 (t0) REVERT: d 325 GLU cc_start: 0.7177 (tp30) cc_final: 0.6815 (mp0) REVERT: e 319 GLN cc_start: 0.8227 (mm-40) cc_final: 0.8024 (mm-40) REVERT: g 317 SER cc_start: 0.7572 (p) cc_final: 0.7204 (t) REVERT: m 123 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.5605 (pp20) REVERT: m 217 MET cc_start: 0.7077 (mmm) cc_final: 0.6729 (mmm) REVERT: m 228 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7934 (tt0) REVERT: m 232 LYS cc_start: 0.8508 (tppt) cc_final: 0.7623 (mttt) REVERT: n 9 MET cc_start: 0.8826 (tmm) cc_final: 0.8525 (tmm) REVERT: n 65 ASP cc_start: 0.8222 (t0) cc_final: 0.7964 (t0) REVERT: n 94 ASP cc_start: 0.8203 (p0) cc_final: 0.7960 (p0) REVERT: n 99 TYR cc_start: 0.8791 (m-80) cc_final: 0.8585 (m-10) REVERT: n 176 ASP cc_start: 0.7875 (t0) cc_final: 0.7472 (t0) REVERT: n 202 MET cc_start: 0.6197 (mpp) cc_final: 0.5921 (mmt) REVERT: n 220 MET cc_start: 0.7350 (mtm) cc_final: 0.6909 (tmm) REVERT: n 225 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.6670 (ttt180) REVERT: n 228 GLU cc_start: 0.7514 (mt-10) cc_final: 0.6414 (tt0) REVERT: n 246 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7981 (pp30) REVERT: o 26 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8956 (mm) REVERT: o 58 THR cc_start: 0.9178 (m) cc_final: 0.8841 (p) REVERT: o 225 ARG cc_start: 0.7587 (mmt180) cc_final: 0.6054 (mtt180) REVERT: o 250 MET cc_start: 0.7920 (mpp) cc_final: 0.7574 (mpp) REVERT: q 9 MET cc_start: 0.8775 (tmm) cc_final: 0.8454 (tmm) REVERT: q 65 ASP cc_start: 0.6993 (t0) cc_final: 0.5654 (p0) REVERT: q 102 ASN cc_start: 0.8698 (t0) cc_final: 0.7946 (m-40) REVERT: q 123 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6339 (mp0) REVERT: q 202 MET cc_start: 0.4538 (ttm) cc_final: 0.3801 (ttm) REVERT: q 210 ASN cc_start: 0.7610 (p0) cc_final: 0.7148 (p0) REVERT: q 225 ARG cc_start: 0.7709 (mmt-90) cc_final: 0.5937 (mmt180) REVERT: q 231 MET cc_start: 0.7340 (ptm) cc_final: 0.6877 (ptp) REVERT: q 239 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7380 (tm-30) REVERT: q 250 MET cc_start: 0.7973 (mpp) cc_final: 0.7584 (mpp) outliers start: 210 outliers final: 119 residues processed: 1529 average time/residue: 0.2205 time to fit residues: 560.9980 Evaluate side-chains 1426 residues out of total 3890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 1288 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain E residue 9 TRP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 196 ILE Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 224 MET Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 190 PHE Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 103 ASP Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 89 VAL Chi-restraints excluded: chain T residue 18 LEU Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 SER Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain V residue 34 VAL Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain X residue 111 SER Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 23 VAL Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 91 VAL Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 99 VAL Chi-restraints excluded: chain Z residue 9 ILE Chi-restraints excluded: chain Z residue 18 SER Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 106 MET Chi-restraints excluded: chain Z residue 119 LEU Chi-restraints excluded: chain Z residue 124 SER Chi-restraints excluded: chain a residue 6 ILE Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 63 LYS Chi-restraints excluded: chain a residue 70 SER Chi-restraints excluded: chain a residue 77 VAL Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain c residue 318 ASN Chi-restraints excluded: chain e residue 312 VAL Chi-restraints excluded: chain j residue 312 VAL Chi-restraints excluded: chain m residue 123 GLU Chi-restraints excluded: chain m residue 171 VAL Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 225 ARG Chi-restraints excluded: chain n residue 246 GLN Chi-restraints excluded: chain o residue 26 LEU Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 82 LEU Chi-restraints excluded: chain o residue 110 THR Chi-restraints excluded: chain o residue 129 VAL Chi-restraints excluded: chain o residue 188 GLU Chi-restraints excluded: chain o residue 193 LEU Chi-restraints excluded: chain o residue 199 ILE Chi-restraints excluded: chain o residue 247 LEU Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain p residue 85 ASP Chi-restraints excluded: chain p residue 104 ASN Chi-restraints excluded: chain p residue 120 VAL Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain q residue 49 LEU Chi-restraints excluded: chain q residue 51 LEU Chi-restraints excluded: chain q residue 56 LEU Chi-restraints excluded: chain q residue 60 SER Chi-restraints excluded: chain q residue 123 GLU Chi-restraints excluded: chain q residue 155 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 60 optimal weight: 1.9990 chunk 334 optimal weight: 10.0000 chunk 277 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 247 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 378 optimal weight: 0.0870 chunk 147 optimal weight: 6.9990 chunk 181 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 257 optimal weight: 0.0770 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 ASN E 141 ASN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 GLN ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 119 GLN ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 GLN R 132 ASN S 23 GLN S 39 GLN T 12 GLN U 29 ASN ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 22 ASN ** X 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 134 GLN Z 115 ASN a 113 GLN ** c 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 319 GLN ** n 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 246 GLN ** o 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 230 GLN o 245 ASN ** p 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 240 ASN p 246 GLN q 83 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.124031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.110265 restraints weight = 86663.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.112922 restraints weight = 43132.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.114684 restraints weight = 25608.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.115861 restraints weight = 17306.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.116634 restraints weight = 12943.042| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36808 Z= 0.140 Angle : 0.699 16.134 50037 Z= 0.338 Chirality : 0.043 0.215 5998 Planarity : 0.005 0.076 6518 Dihedral : 4.381 52.889 5093 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.44 % Favored : 97.45 % Rotamer: Outliers : 5.37 % Allowed : 26.97 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.12), residues: 4749 helix: 2.14 (0.10), residues: 2821 sheet: -0.51 (0.27), residues: 345 loop : -0.40 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 104 TYR 0.024 0.002 TYR T 38 PHE 0.029 0.002 PHE B 51 TRP 0.018 0.001 TRP C 68 HIS 0.006 0.001 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00313 (36808) covalent geometry : angle 0.69915 (50037) hydrogen bonds : bond 0.03899 ( 2382) hydrogen bonds : angle 3.93812 ( 6978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9498 Ramachandran restraints generated. 4749 Oldfield, 0 Emsley, 4749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9498 Ramachandran restraints generated. 4749 Oldfield, 0 Emsley, 4749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1588 residues out of total 3890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 1379 time to evaluate : 1.449 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: A 74 LEU cc_start: 0.8425 (mt) cc_final: 0.8140 (mp) REVERT: A 83 ASN cc_start: 0.8464 (m110) cc_final: 0.8047 (m110) REVERT: B 7 MET cc_start: 0.9183 (mmm) cc_final: 0.8738 (tmm) REVERT: B 83 ASN cc_start: 0.7762 (m-40) cc_final: 0.7390 (m-40) REVERT: C 70 LEU cc_start: 0.8868 (mm) cc_final: 0.8424 (tp) REVERT: D 12 GLU cc_start: 0.8403 (tt0) cc_final: 0.7997 (tm-30) REVERT: D 35 ILE cc_start: 0.7003 (mt) cc_final: 0.6575 (mt) REVERT: D 52 ILE cc_start: 0.7991 (mt) cc_final: 0.6921 (mt) REVERT: E 14 HIS cc_start: 0.6617 (m-70) cc_final: 0.6360 (m170) REVERT: E 52 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7153 (mp) REVERT: E 77 GLN cc_start: 0.8114 (mp10) cc_final: 0.7819 (mm110) REVERT: E 100 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7909 (pp20) REVERT: E 106 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7746 (tpp) REVERT: E 170 MET cc_start: 0.7679 (mmm) cc_final: 0.7267 (tmm) REVERT: E 181 LEU cc_start: 0.8379 (tp) cc_final: 0.8154 (tt) REVERT: E 185 MET cc_start: 0.8099 (mmm) cc_final: 0.7265 (mmm) REVERT: E 210 GLN cc_start: 0.8240 (mp-120) cc_final: 0.7769 (mp10) REVERT: E 254 ILE cc_start: 0.7451 (mm) cc_final: 0.7142 (mm) REVERT: F 52 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8012 (p) REVERT: F 107 LYS cc_start: 0.8693 (mmmm) cc_final: 0.8421 (tppt) REVERT: F 128 ASP cc_start: 0.8740 (m-30) cc_final: 0.8405 (m-30) REVERT: F 190 PHE cc_start: 0.7202 (m-10) cc_final: 0.6546 (m-80) REVERT: G 43 GLN cc_start: 0.9155 (mt0) cc_final: 0.8594 (mt0) REVERT: G 184 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8146 (tm-30) REVERT: G 211 MET cc_start: 0.7670 (tpp) cc_final: 0.7458 (tpt) REVERT: G 230 ASP cc_start: 0.8525 (t70) cc_final: 0.8310 (t70) REVERT: G 233 GLN cc_start: 0.7731 (tm130) cc_final: 0.7483 (tm-30) REVERT: H 118 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7604 (mt-10) REVERT: H 180 LYS cc_start: 0.8026 (mttm) cc_final: 0.7748 (mttm) REVERT: H 210 MET cc_start: 0.6125 (tpp) cc_final: 0.5572 (tpp) REVERT: H 223 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8880 (mm) REVERT: I 120 LYS cc_start: 0.8613 (tptp) cc_final: 0.8091 (mttt) REVERT: I 143 ARG cc_start: 0.6085 (mpt90) cc_final: 0.5629 (mmm160) REVERT: I 146 ASP cc_start: 0.8010 (m-30) cc_final: 0.7798 (m-30) REVERT: J 190 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7288 (m-80) REVERT: K 84 MET cc_start: 0.6439 (ttt) cc_final: 0.6231 (ttt) REVERT: L 43 ASP cc_start: 0.8293 (t0) cc_final: 0.8061 (m-30) REVERT: L 58 LYS cc_start: 0.7433 (mmtt) cc_final: 0.7098 (mmtt) REVERT: L 63 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7142 (tm-30) REVERT: L 75 MET cc_start: 0.8062 (ttp) cc_final: 0.7722 (ttm) REVERT: L 84 MET cc_start: 0.8748 (tpp) cc_final: 0.8248 (tpt) REVERT: M 48 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8226 (tpp-160) REVERT: M 96 TYR cc_start: 0.8542 (t80) cc_final: 0.8205 (t80) REVERT: N 63 GLU cc_start: 0.5899 (pp20) cc_final: 0.5668 (pp20) REVERT: N 81 SER cc_start: 0.9326 (OUTLIER) cc_final: 0.8756 (p) REVERT: O 47 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8372 (p0) REVERT: O 74 ASP cc_start: 0.8347 (m-30) cc_final: 0.7936 (m-30) REVERT: O 83 GLN cc_start: 0.8567 (tp40) cc_final: 0.8295 (tp-100) REVERT: O 86 ILE cc_start: 0.9658 (tt) cc_final: 0.9264 (tt) REVERT: O 90 ASN cc_start: 0.8717 (m-40) cc_final: 0.8280 (m110) REVERT: P 55 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8532 (tm-30) REVERT: P 69 ASN cc_start: 0.8005 (m110) cc_final: 0.7697 (m110) REVERT: P 74 ASP cc_start: 0.8078 (m-30) cc_final: 0.7845 (m-30) REVERT: P 82 MET cc_start: 0.8563 (tpp) cc_final: 0.8219 (tpp) REVERT: Q 50 LYS cc_start: 0.8769 (ptmt) cc_final: 0.8075 (pttm) REVERT: R 131 MET cc_start: 0.8609 (mmm) cc_final: 0.7781 (mmt) REVERT: S 6 ASP cc_start: 0.7581 (m-30) cc_final: 0.7364 (m-30) REVERT: S 32 ASN cc_start: 0.8568 (t0) cc_final: 0.7498 (t0) REVERT: S 39 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7913 (mm-40) REVERT: S 96 ASP cc_start: 0.8318 (p0) cc_final: 0.7909 (p0) REVERT: S 105 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7916 (mm-30) REVERT: T 91 ASP cc_start: 0.8264 (t0) cc_final: 0.7933 (t0) REVERT: T 118 MET cc_start: 0.8511 (tmm) cc_final: 0.8078 (tmm) REVERT: U 130 MET cc_start: 0.8184 (tpp) cc_final: 0.7927 (tpp) REVERT: V 46 GLN cc_start: 0.7855 (mp10) cc_final: 0.7268 (mp10) REVERT: V 123 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7727 (tttp) REVERT: W 45 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7863 (mtpp) REVERT: Y 7 PHE cc_start: 0.8189 (m-80) cc_final: 0.7974 (m-80) REVERT: Y 97 ASP cc_start: 0.7095 (p0) cc_final: 0.6762 (p0) REVERT: Z 104 ASN cc_start: 0.9070 (m-40) cc_final: 0.8757 (m-40) REVERT: Z 119 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8816 (tp) REVERT: a 5 ASN cc_start: 0.8135 (t0) cc_final: 0.7532 (m110) REVERT: a 7 PHE cc_start: 0.9081 (m-80) cc_final: 0.8745 (m-10) REVERT: a 28 LEU cc_start: 0.9304 (tp) cc_final: 0.8282 (tp) REVERT: a 46 GLN cc_start: 0.8193 (tm-30) cc_final: 0.7890 (tm-30) REVERT: a 110 ARG cc_start: 0.7904 (mmt180) cc_final: 0.6304 (mmm160) REVERT: a 117 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8074 (mt-10) REVERT: c 318 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.8042 (t0) REVERT: d 325 GLU cc_start: 0.7216 (tp30) cc_final: 0.6593 (mp0) REVERT: g 317 SER cc_start: 0.7575 (p) cc_final: 0.7147 (t) REVERT: m 217 MET cc_start: 0.7085 (mmm) cc_final: 0.6748 (mmm) REVERT: m 228 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7915 (tt0) REVERT: m 232 LYS cc_start: 0.8555 (tppt) cc_final: 0.7587 (mttt) REVERT: n 9 MET cc_start: 0.8703 (tmm) cc_final: 0.8416 (tmm) REVERT: n 65 ASP cc_start: 0.8183 (t0) cc_final: 0.7944 (t0) REVERT: n 176 ASP cc_start: 0.7946 (t0) cc_final: 0.7521 (t0) REVERT: n 202 MET cc_start: 0.6464 (mpp) cc_final: 0.6129 (mmp) REVERT: n 219 ASP cc_start: 0.7601 (p0) cc_final: 0.7354 (p0) REVERT: n 225 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.6639 (ttt180) REVERT: n 228 GLU cc_start: 0.7535 (mt-10) cc_final: 0.6466 (tt0) REVERT: o 9 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7279 (ptm) REVERT: o 225 ARG cc_start: 0.7533 (mmt180) cc_final: 0.5949 (mtt180) REVERT: o 232 LYS cc_start: 0.9439 (tptp) cc_final: 0.9117 (tptp) REVERT: o 239 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6361 (tm-30) REVERT: o 245 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8565 (m-40) REVERT: o 250 MET cc_start: 0.7666 (mpp) cc_final: 0.7285 (mpp) REVERT: q 9 MET cc_start: 0.8722 (tmm) cc_final: 0.8394 (tmm) REVERT: q 44 VAL cc_start: 0.7897 (OUTLIER) cc_final: 0.7543 (p) REVERT: q 51 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7541 (mt) REVERT: q 123 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6221 (mp0) REVERT: q 199 ILE cc_start: 0.7560 (mm) cc_final: 0.6973 (mm) REVERT: q 202 MET cc_start: 0.4555 (ttm) cc_final: 0.3803 (ttm) REVERT: q 225 ARG cc_start: 0.7594 (mmt-90) cc_final: 0.5713 (mmm160) REVERT: q 239 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7432 (tm-30) REVERT: q 250 MET cc_start: 0.7827 (mpp) cc_final: 0.7551 (mpp) outliers start: 209 outliers final: 110 residues processed: 1489 average time/residue: 0.2190 time to fit residues: 544.3452 Evaluate side-chains 1379 residues out of total 3890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 1248 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain E residue 9 TRP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 196 ILE Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 224 MET Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 190 PHE Chi-restraints excluded: chain J residue 200 ILE Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 216 THR Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain M residue 48 ARG Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 53 MET Chi-restraints excluded: chain Q residue 103 ASP Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 89 VAL Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 SER Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain V residue 123 LYS Chi-restraints excluded: chain W residue 45 LYS Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 23 VAL Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 99 VAL Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 106 MET Chi-restraints excluded: chain Z residue 119 LEU Chi-restraints excluded: chain Z residue 124 SER Chi-restraints excluded: chain a residue 6 ILE Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 119 LEU Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain c residue 318 ASN Chi-restraints excluded: chain e residue 312 VAL Chi-restraints excluded: chain f residue 312 VAL Chi-restraints excluded: chain j residue 312 VAL Chi-restraints excluded: chain l residue 317 SER Chi-restraints excluded: chain m residue 107 VAL Chi-restraints excluded: chain m residue 136 THR Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 164 VAL Chi-restraints excluded: chain n residue 225 ARG Chi-restraints excluded: chain o residue 9 MET Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 82 LEU Chi-restraints excluded: chain o residue 129 VAL Chi-restraints excluded: chain o residue 193 LEU Chi-restraints excluded: chain o residue 199 ILE Chi-restraints excluded: chain o residue 245 ASN Chi-restraints excluded: chain o residue 247 LEU Chi-restraints excluded: chain p residue 44 VAL Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 104 ASN Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain p residue 161 LEU Chi-restraints excluded: chain p residue 205 VAL Chi-restraints excluded: chain q residue 44 VAL Chi-restraints excluded: chain q residue 51 LEU Chi-restraints excluded: chain q residue 56 LEU Chi-restraints excluded: chain q residue 123 GLU Chi-restraints excluded: chain q residue 155 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 219 optimal weight: 0.9990 chunk 310 optimal weight: 0.8980 chunk 47 optimal weight: 0.0980 chunk 453 optimal weight: 20.0000 chunk 398 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 343 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 168 optimal weight: 8.9990 chunk 383 optimal weight: 0.9990 chunk 352 optimal weight: 3.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 141 ASN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 GLN ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 184 GLN ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 ASN ** R 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 126 GLN U 21 GLN U 23 GLN U 29 ASN ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 134 GLN Y 30 ASN ** Y 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 113 GLN ** c 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 324 ASN j 318 ASN ** n 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 240 ASN ** p 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 246 GLN q 246 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.123813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.110075 restraints weight = 86307.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.112724 restraints weight = 42888.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.114473 restraints weight = 25510.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.115644 restraints weight = 17284.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.116424 restraints weight = 12937.914| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36808 Z= 0.138 Angle : 0.705 14.587 50037 Z= 0.339 Chirality : 0.043 0.265 5998 Planarity : 0.005 0.076 6518 Dihedral : 4.204 47.147 5090 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.25 % Favored : 97.64 % Rotamer: Outliers : 5.78 % Allowed : 27.17 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.12), residues: 4749 helix: 2.15 (0.10), residues: 2822 sheet: -0.40 (0.27), residues: 356 loop : -0.33 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 66 TYR 0.024 0.002 TYR T 38 PHE 0.023 0.001 PHE B 51 TRP 0.023 0.001 TRP C 68 HIS 0.005 0.001 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00323 (36808) covalent geometry : angle 0.70482 (50037) hydrogen bonds : bond 0.03763 ( 2382) hydrogen bonds : angle 3.91817 ( 6978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9498 Ramachandran restraints generated. 4749 Oldfield, 0 Emsley, 4749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9498 Ramachandran restraints generated. 4749 Oldfield, 0 Emsley, 4749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1548 residues out of total 3890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 1323 time to evaluate : 1.459 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: A 14 MET cc_start: 0.6897 (mtt) cc_final: 0.6587 (mtp) REVERT: A 18 LEU cc_start: 0.9229 (tp) cc_final: 0.8825 (mt) REVERT: A 82 SER cc_start: 0.8170 (m) cc_final: 0.7625 (t) REVERT: A 83 ASN cc_start: 0.8339 (m110) cc_final: 0.7941 (m110) REVERT: A 86 TYR cc_start: 0.7876 (m-80) cc_final: 0.7609 (m-80) REVERT: B 7 MET cc_start: 0.9170 (mmm) cc_final: 0.8761 (tmm) REVERT: B 83 ASN cc_start: 0.7856 (m-40) cc_final: 0.7567 (m-40) REVERT: C 55 ILE cc_start: 0.8523 (tt) cc_final: 0.8296 (pt) REVERT: C 70 LEU cc_start: 0.8912 (mm) cc_final: 0.8432 (tp) REVERT: D 12 GLU cc_start: 0.8449 (tt0) cc_final: 0.7946 (tm-30) REVERT: D 35 ILE cc_start: 0.7034 (mt) cc_final: 0.6651 (mt) REVERT: D 71 ASN cc_start: 0.8289 (m110) cc_final: 0.7933 (m110) REVERT: E 52 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7209 (mp) REVERT: E 77 GLN cc_start: 0.8144 (mp10) cc_final: 0.7791 (mm110) REVERT: E 106 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7710 (tpp) REVERT: E 170 MET cc_start: 0.7682 (mmm) cc_final: 0.7393 (tmm) REVERT: E 210 GLN cc_start: 0.8208 (mp-120) cc_final: 0.7749 (mp10) REVERT: E 254 ILE cc_start: 0.7501 (mm) cc_final: 0.7205 (mm) REVERT: F 52 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.7876 (p) REVERT: F 128 ASP cc_start: 0.8745 (m-30) cc_final: 0.8413 (m-30) REVERT: F 190 PHE cc_start: 0.7282 (m-10) cc_final: 0.6719 (m-80) REVERT: F 205 MET cc_start: 0.7867 (mmm) cc_final: 0.7536 (mmm) REVERT: F 211 MET cc_start: 0.6052 (mmp) cc_final: 0.5692 (mmp) REVERT: G 211 MET cc_start: 0.7738 (tpp) cc_final: 0.7444 (tpt) REVERT: G 236 MET cc_start: 0.8928 (mmm) cc_final: 0.8593 (mmm) REVERT: H 43 GLN cc_start: 0.8311 (mm-40) cc_final: 0.7831 (mm-40) REVERT: H 149 LEU cc_start: 0.8697 (tt) cc_final: 0.8347 (tp) REVERT: H 180 LYS cc_start: 0.8061 (mttm) cc_final: 0.7767 (mttm) REVERT: H 184 GLN cc_start: 0.8287 (mt0) cc_final: 0.7904 (mt0) REVERT: H 210 MET cc_start: 0.6082 (tpp) cc_final: 0.5325 (tpp) REVERT: H 223 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8881 (mm) REVERT: H 228 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8646 (mt) REVERT: I 143 ARG cc_start: 0.6091 (mpt90) cc_final: 0.5619 (mmm160) REVERT: I 211 MET cc_start: 0.7549 (mmm) cc_final: 0.7004 (mmm) REVERT: J 190 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.7450 (m-80) REVERT: J 210 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6597 (tmm) REVERT: J 211 MET cc_start: 0.6587 (mtt) cc_final: 0.6179 (mtt) REVERT: K 84 MET cc_start: 0.6444 (ttt) cc_final: 0.6178 (ttt) REVERT: K 89 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8925 (ttt-90) REVERT: L 43 ASP cc_start: 0.8404 (t0) cc_final: 0.8162 (m-30) REVERT: L 55 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8331 (tm-30) REVERT: L 63 GLU cc_start: 0.7619 (tm-30) cc_final: 0.6686 (tm-30) REVERT: L 75 MET cc_start: 0.8122 (ttp) cc_final: 0.7737 (ttm) REVERT: L 84 MET cc_start: 0.8874 (tpp) cc_final: 0.8559 (mmm) REVERT: M 48 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7855 (tpp-160) REVERT: M 96 TYR cc_start: 0.8571 (t80) cc_final: 0.8220 (t80) REVERT: M 102 MET cc_start: 0.7500 (mmt) cc_final: 0.6949 (mmm) REVERT: N 63 GLU cc_start: 0.6211 (pp20) cc_final: 0.5911 (pp20) REVERT: N 81 SER cc_start: 0.9275 (OUTLIER) cc_final: 0.8730 (p) REVERT: O 47 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8377 (p0) REVERT: O 74 ASP cc_start: 0.8342 (m-30) cc_final: 0.7947 (m-30) REVERT: O 83 GLN cc_start: 0.8547 (tp40) cc_final: 0.8243 (tp-100) REVERT: O 86 ILE cc_start: 0.9656 (tt) cc_final: 0.9311 (tt) REVERT: O 90 ASN cc_start: 0.8707 (m-40) cc_final: 0.8330 (m110) REVERT: P 69 ASN cc_start: 0.7365 (m110) cc_final: 0.6990 (m-40) REVERT: P 74 ASP cc_start: 0.8221 (m-30) cc_final: 0.7963 (m-30) REVERT: P 82 MET cc_start: 0.8615 (tpp) cc_final: 0.8151 (tpp) REVERT: R 24 GLU cc_start: 0.7776 (tt0) cc_final: 0.7497 (tt0) REVERT: R 131 MET cc_start: 0.8622 (mmm) cc_final: 0.7835 (mmt) REVERT: S 32 ASN cc_start: 0.8376 (t0) cc_final: 0.7543 (t0) REVERT: S 50 LYS cc_start: 0.8992 (mtmm) cc_final: 0.8492 (mtmt) REVERT: S 96 ASP cc_start: 0.8309 (p0) cc_final: 0.7836 (p0) REVERT: T 12 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8438 (mm110) REVERT: T 84 ASP cc_start: 0.8053 (p0) cc_final: 0.7850 (p0) REVERT: U 130 MET cc_start: 0.8254 (tpp) cc_final: 0.8042 (tpp) REVERT: V 43 ARG cc_start: 0.8027 (mtp85) cc_final: 0.7753 (mtp180) REVERT: V 46 GLN cc_start: 0.7899 (mp10) cc_final: 0.7226 (mp10) REVERT: V 112 TYR cc_start: 0.8563 (t80) cc_final: 0.8257 (t80) REVERT: W 45 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7847 (mtpp) REVERT: X 17 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8179 (mt0) REVERT: Y 7 PHE cc_start: 0.8151 (m-80) cc_final: 0.7945 (m-80) REVERT: Y 97 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6804 (p0) REVERT: Z 19 LYS cc_start: 0.8696 (mttp) cc_final: 0.8446 (mttp) REVERT: Z 104 ASN cc_start: 0.8945 (m-40) cc_final: 0.8656 (m-40) REVERT: Z 119 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8827 (tp) REVERT: a 5 ASN cc_start: 0.8154 (t0) cc_final: 0.7649 (m-40) REVERT: a 7 PHE cc_start: 0.9071 (m-80) cc_final: 0.8848 (m-10) REVERT: a 28 LEU cc_start: 0.9280 (tp) cc_final: 0.8975 (tt) REVERT: a 46 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7750 (tm-30) REVERT: a 78 TYR cc_start: 0.7977 (t80) cc_final: 0.7573 (t80) REVERT: a 110 ARG cc_start: 0.7866 (mmt180) cc_final: 0.6244 (mmm160) REVERT: a 117 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8136 (mt-10) REVERT: c 318 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.7940 (t0) REVERT: d 325 GLU cc_start: 0.7168 (tp30) cc_final: 0.6584 (mp0) REVERT: e 319 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7779 (mm110) REVERT: e 324 ASN cc_start: 0.6465 (OUTLIER) cc_final: 0.6228 (p0) REVERT: m 160 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7026 (ttm-80) REVERT: m 217 MET cc_start: 0.6985 (mmm) cc_final: 0.6737 (mmm) REVERT: m 232 LYS cc_start: 0.8524 (tppt) cc_final: 0.7628 (mttt) REVERT: n 9 MET cc_start: 0.8712 (tmm) cc_final: 0.8438 (tmm) REVERT: n 89 VAL cc_start: 0.9132 (t) cc_final: 0.8812 (p) REVERT: n 176 ASP cc_start: 0.7942 (t0) cc_final: 0.7619 (t0) REVERT: n 225 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.6669 (ttt-90) REVERT: n 228 GLU cc_start: 0.7525 (mt-10) cc_final: 0.6392 (tt0) REVERT: o 9 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.7154 (ptm) REVERT: o 225 ARG cc_start: 0.7576 (mmt180) cc_final: 0.5914 (mtt180) REVERT: o 250 MET cc_start: 0.7569 (mpp) cc_final: 0.7323 (mpp) REVERT: p 83 GLN cc_start: 0.7945 (tm-30) cc_final: 0.7694 (tm-30) REVERT: q 44 VAL cc_start: 0.7890 (OUTLIER) cc_final: 0.7535 (p) REVERT: q 51 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7595 (mt) REVERT: q 106 GLN cc_start: 0.8197 (mp10) cc_final: 0.7771 (pm20) REVERT: q 123 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6204 (mp0) REVERT: q 202 MET cc_start: 0.4621 (ttm) cc_final: 0.3820 (ttm) REVERT: q 225 ARG cc_start: 0.7751 (mmt-90) cc_final: 0.5995 (mmt180) REVERT: q 231 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6905 (ptm) REVERT: q 239 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7490 (tm-30) REVERT: q 250 MET cc_start: 0.7789 (mpp) cc_final: 0.7427 (mpp) outliers start: 225 outliers final: 139 residues processed: 1441 average time/residue: 0.2211 time to fit residues: 531.5044 Evaluate side-chains 1395 residues out of total 3890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 1233 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain E residue 9 TRP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 196 ILE Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 224 MET Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 233 GLN Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 190 PHE Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 216 THR Chi-restraints excluded: chain K residue 89 ARG Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain M residue 48 ARG Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 102 MET Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 53 MET Chi-restraints excluded: chain Q residue 103 ASP Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 89 VAL Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain T residue 18 LEU Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 SER Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain U residue 21 GLN Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain V residue 34 VAL Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain W residue 45 LYS Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 124 SER Chi-restraints excluded: chain X residue 111 SER Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain X residue 122 VAL Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 23 VAL Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 97 ASP Chi-restraints excluded: chain Y residue 99 VAL Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 46 GLN Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 106 MET Chi-restraints excluded: chain Z residue 119 LEU Chi-restraints excluded: chain Z residue 124 SER Chi-restraints excluded: chain a residue 6 ILE Chi-restraints excluded: chain a residue 14 LEU Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain c residue 318 ASN Chi-restraints excluded: chain e residue 312 VAL Chi-restraints excluded: chain e residue 324 ASN Chi-restraints excluded: chain h residue 330 THR Chi-restraints excluded: chain j residue 312 VAL Chi-restraints excluded: chain m residue 136 THR Chi-restraints excluded: chain m residue 160 ARG Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 225 ARG Chi-restraints excluded: chain o residue 9 MET Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 82 LEU Chi-restraints excluded: chain o residue 110 THR Chi-restraints excluded: chain o residue 129 VAL Chi-restraints excluded: chain o residue 193 LEU Chi-restraints excluded: chain o residue 199 ILE Chi-restraints excluded: chain o residue 247 LEU Chi-restraints excluded: chain p residue 16 LEU Chi-restraints excluded: chain p residue 30 SER Chi-restraints excluded: chain p residue 44 VAL Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain p residue 161 LEU Chi-restraints excluded: chain p residue 205 VAL Chi-restraints excluded: chain q residue 44 VAL Chi-restraints excluded: chain q residue 51 LEU Chi-restraints excluded: chain q residue 56 LEU Chi-restraints excluded: chain q residue 123 GLU Chi-restraints excluded: chain q residue 155 VAL Chi-restraints excluded: chain q residue 192 VAL Chi-restraints excluded: chain q residue 231 MET Chi-restraints excluded: chain q residue 238 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 9 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 426 optimal weight: 0.0980 chunk 361 optimal weight: 0.7980 chunk 201 optimal weight: 8.9990 chunk 322 optimal weight: 7.9990 chunk 312 optimal weight: 3.9990 chunk 451 optimal weight: 0.0980 chunk 159 optimal weight: 0.6980 chunk 300 optimal weight: 3.9990 chunk 223 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 GLN ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 108 GLN U 23 GLN U 29 ASN ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 30 ASN ** X 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 134 GLN Y 115 ASN ** a 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 82 ASN a 113 GLN ** n 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 240 ASN ** p 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 240 ASN ** q 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.124535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.110589 restraints weight = 87364.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.113230 restraints weight = 44408.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.114961 restraints weight = 26677.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.116154 restraints weight = 18327.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.116937 restraints weight = 13820.441| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 36808 Z= 0.139 Angle : 0.714 17.206 50037 Z= 0.341 Chirality : 0.043 0.277 5998 Planarity : 0.005 0.077 6518 Dihedral : 4.160 45.354 5090 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.42 % Favored : 97.47 % Rotamer: Outliers : 5.35 % Allowed : 28.33 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.12), residues: 4749 helix: 2.12 (0.10), residues: 2819 sheet: -0.26 (0.28), residues: 349 loop : -0.31 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 127 TYR 0.023 0.002 TYR T 38 PHE 0.022 0.001 PHE B 51 TRP 0.024 0.001 TRP C 68 HIS 0.004 0.001 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00324 (36808) covalent geometry : angle 0.71425 (50037) hydrogen bonds : bond 0.03703 ( 2382) hydrogen bonds : angle 3.92361 ( 6978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9498 Ramachandran restraints generated. 4749 Oldfield, 0 Emsley, 4749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9498 Ramachandran restraints generated. 4749 Oldfield, 0 Emsley, 4749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1509 residues out of total 3890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 1301 time to evaluate : 1.390 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 18 LEU cc_start: 0.9223 (tp) cc_final: 0.8839 (mt) REVERT: A 82 SER cc_start: 0.8195 (m) cc_final: 0.7723 (t) REVERT: A 83 ASN cc_start: 0.8342 (m110) cc_final: 0.7914 (m-40) REVERT: A 86 TYR cc_start: 0.7894 (m-80) cc_final: 0.7675 (m-80) REVERT: B 7 MET cc_start: 0.9168 (mmm) cc_final: 0.8777 (tmm) REVERT: B 71 ASN cc_start: 0.8242 (t0) cc_final: 0.8008 (t0) REVERT: B 83 ASN cc_start: 0.7869 (m-40) cc_final: 0.7599 (m-40) REVERT: C 70 LEU cc_start: 0.8892 (mm) cc_final: 0.8426 (tp) REVERT: D 9 MET cc_start: 0.6561 (tmm) cc_final: 0.6300 (ttm) REVERT: D 47 MET cc_start: 0.6345 (ttp) cc_final: 0.5974 (ttp) REVERT: D 71 ASN cc_start: 0.8232 (m110) cc_final: 0.7860 (m-40) REVERT: E 52 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7219 (mp) REVERT: E 110 PHE cc_start: 0.6415 (t80) cc_final: 0.6009 (t80) REVERT: E 170 MET cc_start: 0.7600 (mmm) cc_final: 0.7388 (tmm) REVERT: E 185 MET cc_start: 0.8131 (mmm) cc_final: 0.7267 (ttt) REVERT: E 209 PRO cc_start: 0.5976 (Cg_endo) cc_final: 0.5393 (Cg_exo) REVERT: E 210 GLN cc_start: 0.8381 (mp-120) cc_final: 0.7881 (mp10) REVERT: E 254 ILE cc_start: 0.7504 (mm) cc_final: 0.7204 (mm) REVERT: F 52 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.7755 (p) REVERT: F 128 ASP cc_start: 0.8743 (m-30) cc_final: 0.8409 (m-30) REVERT: F 180 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8983 (pptt) REVERT: F 190 PHE cc_start: 0.7161 (m-10) cc_final: 0.6767 (m-80) REVERT: F 211 MET cc_start: 0.5905 (mmp) cc_final: 0.5658 (mmp) REVERT: G 211 MET cc_start: 0.7657 (tpp) cc_final: 0.7442 (tpt) REVERT: H 43 GLN cc_start: 0.8335 (mm-40) cc_final: 0.7910 (mm-40) REVERT: H 149 LEU cc_start: 0.8614 (tt) cc_final: 0.8315 (tp) REVERT: H 174 TYR cc_start: 0.8807 (t80) cc_final: 0.8578 (t80) REVERT: H 180 LYS cc_start: 0.8062 (mttm) cc_final: 0.7799 (mttm) REVERT: H 223 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8868 (mm) REVERT: H 228 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8492 (mt) REVERT: I 143 ARG cc_start: 0.5973 (mpt90) cc_final: 0.5602 (mmm160) REVERT: I 236 MET cc_start: 0.8297 (mmm) cc_final: 0.8006 (mmt) REVERT: J 190 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.7645 (m-80) REVERT: J 198 LEU cc_start: 0.8914 (tp) cc_final: 0.8701 (tp) REVERT: K 84 MET cc_start: 0.6511 (ttt) cc_final: 0.6257 (ttt) REVERT: L 43 ASP cc_start: 0.8469 (t0) cc_final: 0.8227 (m-30) REVERT: L 55 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8210 (tm-30) REVERT: L 58 LYS cc_start: 0.7402 (mmtt) cc_final: 0.7107 (mmtt) REVERT: L 63 GLU cc_start: 0.7682 (tm-30) cc_final: 0.6733 (tm-30) REVERT: L 75 MET cc_start: 0.8072 (ttp) cc_final: 0.7681 (ttm) REVERT: L 84 MET cc_start: 0.8844 (tpp) cc_final: 0.8578 (mmm) REVERT: L 96 TYR cc_start: 0.8846 (t80) cc_final: 0.8558 (t80) REVERT: L 102 MET cc_start: 0.8315 (mpp) cc_final: 0.8051 (mtt) REVERT: M 96 TYR cc_start: 0.8602 (t80) cc_final: 0.8247 (t80) REVERT: M 102 MET cc_start: 0.7504 (mmt) cc_final: 0.7129 (mmm) REVERT: N 63 GLU cc_start: 0.6196 (pp20) cc_final: 0.5912 (pp20) REVERT: N 81 SER cc_start: 0.9321 (OUTLIER) cc_final: 0.8848 (p) REVERT: N 100 MET cc_start: 0.8369 (mmm) cc_final: 0.8116 (mtp) REVERT: O 47 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8372 (p0) REVERT: O 74 ASP cc_start: 0.8033 (m-30) cc_final: 0.7618 (m-30) REVERT: O 83 GLN cc_start: 0.8576 (tp40) cc_final: 0.8305 (tp-100) REVERT: O 86 ILE cc_start: 0.9646 (tt) cc_final: 0.9302 (tt) REVERT: O 90 ASN cc_start: 0.8699 (m-40) cc_final: 0.8308 (m110) REVERT: P 69 ASN cc_start: 0.7359 (m110) cc_final: 0.6924 (m-40) REVERT: P 74 ASP cc_start: 0.8230 (m-30) cc_final: 0.7928 (m-30) REVERT: P 82 MET cc_start: 0.8623 (tpp) cc_final: 0.8137 (tpp) REVERT: Q 23 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.8864 (tp40) REVERT: Q 112 ASN cc_start: 0.8610 (t0) cc_final: 0.8398 (t0) REVERT: R 50 LYS cc_start: 0.9150 (mtmt) cc_final: 0.8927 (mtmt) REVERT: R 130 MET cc_start: 0.8363 (mmm) cc_final: 0.7683 (tpp) REVERT: R 131 MET cc_start: 0.8532 (mmm) cc_final: 0.8154 (mmt) REVERT: S 32 ASN cc_start: 0.8315 (t0) cc_final: 0.7849 (t0) REVERT: S 50 LYS cc_start: 0.9061 (mtmm) cc_final: 0.8829 (mtmt) REVERT: S 91 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7660 (t0) REVERT: S 96 ASP cc_start: 0.8179 (p0) cc_final: 0.7698 (p0) REVERT: T 12 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8380 (mm110) REVERT: U 130 MET cc_start: 0.8356 (tpp) cc_final: 0.8147 (tpp) REVERT: V 46 GLN cc_start: 0.7918 (mp10) cc_final: 0.7180 (mp10) REVERT: V 112 TYR cc_start: 0.8504 (t80) cc_final: 0.8201 (t80) REVERT: W 7 PHE cc_start: 0.8756 (m-80) cc_final: 0.8468 (m-80) REVERT: W 124 SER cc_start: 0.8554 (t) cc_final: 0.7945 (t) REVERT: X 17 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8149 (mt0) REVERT: X 93 MET cc_start: 0.8734 (mmm) cc_final: 0.8460 (mmt) REVERT: Y 7 PHE cc_start: 0.8106 (m-80) cc_final: 0.7834 (m-80) REVERT: Y 97 ASP cc_start: 0.7133 (OUTLIER) cc_final: 0.6813 (p0) REVERT: Z 104 ASN cc_start: 0.8889 (m-40) cc_final: 0.8651 (m-40) REVERT: Z 119 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8862 (tp) REVERT: a 5 ASN cc_start: 0.8132 (t0) cc_final: 0.7568 (m-40) REVERT: a 7 PHE cc_start: 0.9109 (m-80) cc_final: 0.8764 (m-10) REVERT: a 110 ARG cc_start: 0.8034 (mmt180) cc_final: 0.6350 (mmm160) REVERT: c 318 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.7964 (t0) REVERT: e 319 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7781 (mm110) REVERT: e 324 ASN cc_start: 0.6551 (OUTLIER) cc_final: 0.6266 (p0) REVERT: m 160 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.6990 (ttm-80) REVERT: m 217 MET cc_start: 0.6966 (mmm) cc_final: 0.6713 (mmm) REVERT: m 232 LYS cc_start: 0.8488 (tppt) cc_final: 0.7615 (mttt) REVERT: n 9 MET cc_start: 0.8705 (tmm) cc_final: 0.8422 (tmm) REVERT: n 89 VAL cc_start: 0.9152 (t) cc_final: 0.8810 (p) REVERT: n 165 LYS cc_start: 0.8627 (tppt) cc_final: 0.8288 (tppt) REVERT: n 176 ASP cc_start: 0.8061 (t0) cc_final: 0.7777 (t0) REVERT: n 225 ARG cc_start: 0.7831 (mmt-90) cc_final: 0.6624 (ttt-90) REVERT: n 228 GLU cc_start: 0.7513 (mt-10) cc_final: 0.6342 (tt0) REVERT: o 225 ARG cc_start: 0.7474 (mmt180) cc_final: 0.5806 (mtt180) REVERT: p 83 GLN cc_start: 0.7911 (tm-30) cc_final: 0.7682 (tm-30) REVERT: p 84 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.8033 (mt0) REVERT: q 44 VAL cc_start: 0.7876 (OUTLIER) cc_final: 0.7503 (p) REVERT: q 51 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7322 (mt) REVERT: q 106 GLN cc_start: 0.8141 (mp10) cc_final: 0.7693 (pm20) REVERT: q 123 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6192 (mp0) REVERT: q 225 ARG cc_start: 0.7666 (mmt-90) cc_final: 0.5725 (mmm160) REVERT: q 250 MET cc_start: 0.7728 (mpp) cc_final: 0.7412 (mpp) outliers start: 208 outliers final: 141 residues processed: 1419 average time/residue: 0.2176 time to fit residues: 516.3734 Evaluate side-chains 1386 residues out of total 3890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 1226 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain E residue 9 TRP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 196 ILE Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 233 GLN Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 43 GLN Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 190 PHE Chi-restraints excluded: chain J residue 216 THR Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 23 GLN Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 53 MET Chi-restraints excluded: chain Q residue 103 ASP Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 89 VAL Chi-restraints excluded: chain S residue 91 ASP Chi-restraints excluded: chain T residue 18 LEU Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 SER Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain W residue 33 SER Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 111 SER Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 23 VAL Chi-restraints excluded: chain Y residue 45 LYS Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 91 VAL Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 97 ASP Chi-restraints excluded: chain Y residue 99 VAL Chi-restraints excluded: chain Z residue 18 SER Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 46 GLN Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 119 LEU Chi-restraints excluded: chain Z residue 124 SER Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain a residue 14 LEU Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 82 ASN Chi-restraints excluded: chain c residue 318 ASN Chi-restraints excluded: chain e residue 312 VAL Chi-restraints excluded: chain e residue 324 ASN Chi-restraints excluded: chain j residue 312 VAL Chi-restraints excluded: chain m residue 136 THR Chi-restraints excluded: chain m residue 160 ARG Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 142 THR Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 82 LEU Chi-restraints excluded: chain o residue 110 THR Chi-restraints excluded: chain o residue 129 VAL Chi-restraints excluded: chain o residue 193 LEU Chi-restraints excluded: chain o residue 199 ILE Chi-restraints excluded: chain o residue 247 LEU Chi-restraints excluded: chain p residue 2 ASP Chi-restraints excluded: chain p residue 16 LEU Chi-restraints excluded: chain p residue 44 VAL Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 84 GLN Chi-restraints excluded: chain p residue 104 ASN Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain p residue 161 LEU Chi-restraints excluded: chain p residue 181 LEU Chi-restraints excluded: chain p residue 205 VAL Chi-restraints excluded: chain q residue 44 VAL Chi-restraints excluded: chain q residue 51 LEU Chi-restraints excluded: chain q residue 65 ASP Chi-restraints excluded: chain q residue 123 GLU Chi-restraints excluded: chain q residue 155 VAL Chi-restraints excluded: chain q residue 192 VAL Chi-restraints excluded: chain q residue 238 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 403 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 chunk 346 optimal weight: 6.9990 chunk 435 optimal weight: 8.9990 chunk 283 optimal weight: 5.9990 chunk 244 optimal weight: 0.0570 chunk 145 optimal weight: 7.9990 chunk 319 optimal weight: 5.9990 chunk 220 optimal weight: 7.9990 chunk 426 optimal weight: 4.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 GLN H 184 GLN ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 GLN ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 ASN V 40 GLN X 30 ASN ** X 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 134 GLN ** a 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 319 GLN d 324 ASN e 324 ASN ** m 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 39 ASN n 116 GLN n 223 ASN ** o 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 84 GLN ** p 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 118 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.115399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.101291 restraints weight = 87612.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.103880 restraints weight = 43766.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.105619 restraints weight = 26328.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.106771 restraints weight = 17989.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.107542 restraints weight = 13559.772| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 36808 Z= 0.278 Angle : 0.818 12.680 50037 Z= 0.408 Chirality : 0.048 0.265 5998 Planarity : 0.006 0.077 6518 Dihedral : 4.433 41.120 5086 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.91 % Favored : 96.99 % Rotamer: Outliers : 6.22 % Allowed : 28.02 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.12), residues: 4749 helix: 1.76 (0.10), residues: 2821 sheet: -0.56 (0.26), residues: 372 loop : -0.37 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 41 TYR 0.033 0.002 TYR V 112 PHE 0.024 0.003 PHE H 150 TRP 0.031 0.002 TRP C 68 HIS 0.005 0.002 HIS E 155 Details of bonding type rmsd covalent geometry : bond 0.00625 (36808) covalent geometry : angle 0.81783 (50037) hydrogen bonds : bond 0.04348 ( 2382) hydrogen bonds : angle 4.31552 ( 6978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9498 Ramachandran restraints generated. 4749 Oldfield, 0 Emsley, 4749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9498 Ramachandran restraints generated. 4749 Oldfield, 0 Emsley, 4749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1491 residues out of total 3890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 1249 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 SER cc_start: 0.8553 (m) cc_final: 0.8135 (t) REVERT: A 83 ASN cc_start: 0.8395 (m110) cc_final: 0.7979 (m110) REVERT: B 7 MET cc_start: 0.9223 (mmm) cc_final: 0.8804 (tmm) REVERT: B 71 ASN cc_start: 0.8328 (t0) cc_final: 0.8103 (t0) REVERT: C 70 LEU cc_start: 0.9011 (mm) cc_final: 0.8555 (tp) REVERT: D 43 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.7067 (pm20) REVERT: D 71 ASN cc_start: 0.8404 (m110) cc_final: 0.7984 (m110) REVERT: E 9 TRP cc_start: 0.8034 (m100) cc_final: 0.7752 (m100) REVERT: E 52 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.6985 (mp) REVERT: E 106 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8191 (tmm) REVERT: E 209 PRO cc_start: 0.6340 (Cg_endo) cc_final: 0.5773 (Cg_exo) REVERT: E 210 GLN cc_start: 0.8064 (mp-120) cc_final: 0.7562 (mp10) REVERT: F 128 ASP cc_start: 0.8742 (m-30) cc_final: 0.8349 (m-30) REVERT: F 180 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9143 (pptt) REVERT: F 190 PHE cc_start: 0.7533 (m-10) cc_final: 0.6908 (m-80) REVERT: G 96 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8964 (mm) REVERT: G 211 MET cc_start: 0.7635 (tpp) cc_final: 0.7423 (tpt) REVERT: H 118 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7411 (mt-10) REVERT: H 174 TYR cc_start: 0.8912 (t80) cc_final: 0.8704 (t80) REVERT: H 223 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8875 (mm) REVERT: H 228 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8580 (mt) REVERT: I 143 ARG cc_start: 0.6755 (mpt90) cc_final: 0.5949 (mmm160) REVERT: I 178 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8246 (mm-30) REVERT: I 211 MET cc_start: 0.6355 (tpt) cc_final: 0.5781 (mmm) REVERT: J 86 ASN cc_start: 0.7725 (m-40) cc_final: 0.7485 (m-40) REVERT: J 190 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: K 84 MET cc_start: 0.6833 (ttt) cc_final: 0.6505 (ttt) REVERT: L 55 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8020 (tm-30) REVERT: L 58 LYS cc_start: 0.7326 (mmtt) cc_final: 0.7082 (mmtt) REVERT: L 63 GLU cc_start: 0.7953 (tm-30) cc_final: 0.6969 (tm-30) REVERT: L 75 MET cc_start: 0.8349 (ttp) cc_final: 0.7874 (ttm) REVERT: L 102 MET cc_start: 0.8604 (mpp) cc_final: 0.8286 (mtt) REVERT: M 96 TYR cc_start: 0.8757 (t80) cc_final: 0.8501 (t80) REVERT: M 102 MET cc_start: 0.8122 (mmt) cc_final: 0.7586 (mmm) REVERT: N 63 GLU cc_start: 0.6636 (pp20) cc_final: 0.6267 (pp20) REVERT: N 81 SER cc_start: 0.9430 (OUTLIER) cc_final: 0.8999 (p) REVERT: N 98 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7720 (tp30) REVERT: O 47 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8580 (p0) REVERT: O 74 ASP cc_start: 0.8715 (m-30) cc_final: 0.8309 (m-30) REVERT: P 57 GLU cc_start: 0.8486 (tt0) cc_final: 0.8150 (tt0) REVERT: P 74 ASP cc_start: 0.8382 (m-30) cc_final: 0.8069 (m-30) REVERT: P 82 MET cc_start: 0.8685 (tpp) cc_final: 0.8206 (tpp) REVERT: Q 22 ARG cc_start: 0.8540 (ttt90) cc_final: 0.8202 (ttt90) REVERT: Q 23 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8565 (mm-40) REVERT: Q 105 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7516 (mm-30) REVERT: R 42 ASP cc_start: 0.8457 (t0) cc_final: 0.8244 (t0) REVERT: R 131 MET cc_start: 0.8570 (mmm) cc_final: 0.8243 (mmt) REVERT: S 96 ASP cc_start: 0.8195 (p0) cc_final: 0.7762 (p0) REVERT: S 104 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.6942 (mtt180) REVERT: T 12 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8533 (mm110) REVERT: T 84 ASP cc_start: 0.7662 (p0) cc_final: 0.7447 (p0) REVERT: U 21 GLN cc_start: 0.8282 (mt0) cc_final: 0.7709 (mp10) REVERT: U 23 GLN cc_start: 0.8970 (tp40) cc_final: 0.8754 (tp-100) REVERT: U 118 MET cc_start: 0.8528 (ppp) cc_final: 0.8223 (tmm) REVERT: V 46 GLN cc_start: 0.8062 (mp10) cc_final: 0.7442 (mp10) REVERT: V 75 LYS cc_start: 0.8533 (mmmm) cc_final: 0.8277 (mmmm) REVERT: V 103 VAL cc_start: 0.8825 (m) cc_final: 0.8528 (p) REVERT: X 38 ASP cc_start: 0.7566 (p0) cc_final: 0.7140 (p0) REVERT: X 40 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8054 (mm-40) REVERT: X 111 SER cc_start: 0.9207 (OUTLIER) cc_final: 0.8578 (t) REVERT: Y 38 ASP cc_start: 0.8161 (p0) cc_final: 0.7960 (p0) REVERT: Y 45 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8799 (ptmt) REVERT: Y 97 ASP cc_start: 0.7569 (p0) cc_final: 0.7161 (p0) REVERT: Y 112 TYR cc_start: 0.7760 (t80) cc_final: 0.7351 (t80) REVERT: Y 117 GLU cc_start: 0.7867 (tp30) cc_final: 0.7259 (tp30) REVERT: Z 119 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9019 (tp) REVERT: a 5 ASN cc_start: 0.8402 (t0) cc_final: 0.7620 (m-40) REVERT: a 97 ASP cc_start: 0.8165 (p0) cc_final: 0.6795 (p0) REVERT: a 110 ARG cc_start: 0.8061 (mmt180) cc_final: 0.6533 (mmm160) REVERT: c 318 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.7980 (t0) REVERT: e 319 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7929 (mm110) REVERT: m 160 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7047 (ttm-80) REVERT: m 229 MET cc_start: 0.7480 (mtm) cc_final: 0.7069 (ptp) REVERT: n 9 MET cc_start: 0.8825 (tmm) cc_final: 0.8501 (tmm) REVERT: n 217 MET cc_start: 0.6641 (mmm) cc_final: 0.6413 (mmm) REVERT: n 225 ARG cc_start: 0.8186 (mmt-90) cc_final: 0.6762 (ttt-90) REVERT: o 223 ASN cc_start: 0.8850 (m-40) cc_final: 0.8528 (m-40) REVERT: o 225 ARG cc_start: 0.8050 (mmt180) cc_final: 0.5923 (mtt180) REVERT: p 1 MET cc_start: 0.7480 (mmm) cc_final: 0.7261 (tpp) REVERT: p 84 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7879 (mt0) REVERT: q 44 VAL cc_start: 0.8014 (OUTLIER) cc_final: 0.7597 (p) REVERT: q 106 GLN cc_start: 0.8225 (mp10) cc_final: 0.7905 (pm20) REVERT: q 123 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6355 (mp0) REVERT: q 167 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7279 (mt-10) REVERT: q 199 ILE cc_start: 0.7614 (mm) cc_final: 0.6952 (tt) REVERT: q 231 MET cc_start: 0.6197 (OUTLIER) cc_final: 0.5868 (ptm) REVERT: q 250 MET cc_start: 0.7958 (mpp) cc_final: 0.7529 (mpp) outliers start: 242 outliers final: 172 residues processed: 1372 average time/residue: 0.1972 time to fit residues: 454.2764 Evaluate side-chains 1341 residues out of total 3890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 1148 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 196 ILE Chi-restraints excluded: chain G residue 224 MET Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 190 PHE Chi-restraints excluded: chain J residue 216 THR Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 23 GLN Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 53 MET Chi-restraints excluded: chain Q residue 103 ASP Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain R residue 135 GLN Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 89 VAL Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 18 LEU Chi-restraints excluded: chain T residue 94 SER Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 121 THR Chi-restraints excluded: chain T residue 125 SER Chi-restraints excluded: chain U residue 85 LEU Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain W residue 33 SER Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 82 ASN Chi-restraints excluded: chain X residue 111 SER Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain X residue 122 VAL Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 23 VAL Chi-restraints excluded: chain Y residue 45 LYS Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 91 VAL Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 99 VAL Chi-restraints excluded: chain Y residue 118 VAL Chi-restraints excluded: chain Y residue 127 LEU Chi-restraints excluded: chain Z residue 18 SER Chi-restraints excluded: chain Z residue 46 GLN Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 106 MET Chi-restraints excluded: chain Z residue 119 LEU Chi-restraints excluded: chain Z residue 124 SER Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain a residue 6 ILE Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain b residue 316 LEU Chi-restraints excluded: chain c residue 318 ASN Chi-restraints excluded: chain d residue 328 ILE Chi-restraints excluded: chain f residue 318 ASN Chi-restraints excluded: chain j residue 312 VAL Chi-restraints excluded: chain j residue 319 GLN Chi-restraints excluded: chain l residue 317 SER Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain m residue 107 VAL Chi-restraints excluded: chain m residue 129 VAL Chi-restraints excluded: chain m residue 136 THR Chi-restraints excluded: chain m residue 160 ARG Chi-restraints excluded: chain n residue 24 SER Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 50 SER Chi-restraints excluded: chain n residue 142 THR Chi-restraints excluded: chain n residue 158 VAL Chi-restraints excluded: chain n residue 193 LEU Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 66 MET Chi-restraints excluded: chain o residue 82 LEU Chi-restraints excluded: chain o residue 110 THR Chi-restraints excluded: chain o residue 129 VAL Chi-restraints excluded: chain o residue 199 ILE Chi-restraints excluded: chain p residue 7 THR Chi-restraints excluded: chain p residue 15 THR Chi-restraints excluded: chain p residue 16 LEU Chi-restraints excluded: chain p residue 30 SER Chi-restraints excluded: chain p residue 44 VAL Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain p residue 84 GLN Chi-restraints excluded: chain p residue 120 VAL Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain p residue 161 LEU Chi-restraints excluded: chain p residue 181 LEU Chi-restraints excluded: chain p residue 205 VAL Chi-restraints excluded: chain q residue 44 VAL Chi-restraints excluded: chain q residue 51 LEU Chi-restraints excluded: chain q residue 60 SER Chi-restraints excluded: chain q residue 65 ASP Chi-restraints excluded: chain q residue 123 GLU Chi-restraints excluded: chain q residue 155 VAL Chi-restraints excluded: chain q residue 167 GLU Chi-restraints excluded: chain q residue 202 MET Chi-restraints excluded: chain q residue 231 MET Chi-restraints excluded: chain q residue 238 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 254 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 233 optimal weight: 0.6980 chunk 432 optimal weight: 4.9990 chunk 374 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 182 optimal weight: 8.9990 chunk 262 optimal weight: 0.9980 chunk 172 optimal weight: 0.8980 chunk 385 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 GLN I 76 ASN ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 GLN P 69 ASN ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 GLN ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 108 GLN ** U 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 ASN ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 104 ASN V 115 ASN ** X 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 134 GLN ** Y 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 113 GLN ** a 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 319 GLN ** c 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 3 HIS ** m 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 245 ASN ** n 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 240 ASN ** p 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.119132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.105163 restraints weight = 86574.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.107811 restraints weight = 42945.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.109563 restraints weight = 25621.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.110733 restraints weight = 17392.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.111518 restraints weight = 13087.406| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 36808 Z= 0.150 Angle : 0.759 15.291 50037 Z= 0.366 Chirality : 0.045 0.300 5998 Planarity : 0.005 0.079 6518 Dihedral : 4.281 38.576 5086 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.55 % Favored : 97.35 % Rotamer: Outliers : 4.78 % Allowed : 29.97 % Favored : 65.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.12), residues: 4749 helix: 1.88 (0.10), residues: 2816 sheet: -0.60 (0.26), residues: 369 loop : -0.32 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 19 TYR 0.029 0.002 TYR Y 42 PHE 0.017 0.001 PHE S 45 TRP 0.016 0.001 TRP C 68 HIS 0.004 0.001 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00355 (36808) covalent geometry : angle 0.75912 (50037) hydrogen bonds : bond 0.03925 ( 2382) hydrogen bonds : angle 4.09227 ( 6978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9498 Ramachandran restraints generated. 4749 Oldfield, 0 Emsley, 4749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9498 Ramachandran restraints generated. 4749 Oldfield, 0 Emsley, 4749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1464 residues out of total 3890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 1278 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASN cc_start: 0.8361 (m110) cc_final: 0.8133 (m110) REVERT: B 7 MET cc_start: 0.9073 (mmm) cc_final: 0.8721 (tmm) REVERT: C 70 LEU cc_start: 0.8920 (mm) cc_final: 0.8490 (tp) REVERT: D 1 MET cc_start: 0.6216 (tpp) cc_final: 0.5563 (ttm) REVERT: D 71 ASN cc_start: 0.8317 (m110) cc_final: 0.7925 (m110) REVERT: D 78 ARG cc_start: 0.8245 (ttp-110) cc_final: 0.8021 (ttp-110) REVERT: E 9 TRP cc_start: 0.7974 (OUTLIER) cc_final: 0.7341 (m100) REVERT: E 52 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7073 (mp) REVERT: E 100 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7654 (pp20) REVERT: E 106 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.8015 (tmm) REVERT: E 185 MET cc_start: 0.8086 (mmm) cc_final: 0.7273 (ttt) REVERT: E 209 PRO cc_start: 0.6246 (Cg_endo) cc_final: 0.5667 (Cg_exo) REVERT: E 210 GLN cc_start: 0.8086 (mp-120) cc_final: 0.7740 (mp10) REVERT: E 229 MET cc_start: 0.8095 (ppp) cc_final: 0.7035 (ppp) REVERT: F 128 ASP cc_start: 0.8759 (m-30) cc_final: 0.8399 (m-30) REVERT: F 149 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7821 (tp) REVERT: F 180 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.9023 (pptt) REVERT: F 190 PHE cc_start: 0.7390 (m-10) cc_final: 0.6817 (m-80) REVERT: F 211 MET cc_start: 0.6059 (mmp) cc_final: 0.5680 (mmp) REVERT: G 38 TRP cc_start: 0.8083 (m-10) cc_final: 0.7883 (m-10) REVERT: G 96 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8717 (mm) REVERT: G 236 MET cc_start: 0.8966 (mmm) cc_final: 0.8630 (mmm) REVERT: H 180 LYS cc_start: 0.8168 (mttm) cc_final: 0.7963 (mttm) REVERT: H 223 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8814 (mm) REVERT: H 228 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8513 (mt) REVERT: I 143 ARG cc_start: 0.6554 (mpt90) cc_final: 0.6037 (mmm160) REVERT: J 190 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.7869 (m-80) REVERT: K 68 LEU cc_start: 0.8886 (tp) cc_final: 0.8615 (tt) REVERT: K 84 MET cc_start: 0.6700 (ttt) cc_final: 0.6438 (ttt) REVERT: L 57 GLU cc_start: 0.7060 (tt0) cc_final: 0.6676 (tt0) REVERT: L 58 LYS cc_start: 0.7145 (mmtt) cc_final: 0.6710 (mmtt) REVERT: L 63 GLU cc_start: 0.7905 (tm-30) cc_final: 0.6995 (tm-30) REVERT: L 75 MET cc_start: 0.8234 (ttp) cc_final: 0.7628 (ttm) REVERT: L 96 TYR cc_start: 0.8888 (t80) cc_final: 0.8575 (t80) REVERT: L 102 MET cc_start: 0.8434 (mpp) cc_final: 0.8209 (mtt) REVERT: M 96 TYR cc_start: 0.8688 (t80) cc_final: 0.8409 (t80) REVERT: M 102 MET cc_start: 0.7917 (mmt) cc_final: 0.7678 (mmm) REVERT: N 63 GLU cc_start: 0.6477 (pp20) cc_final: 0.6146 (pp20) REVERT: N 81 SER cc_start: 0.9481 (OUTLIER) cc_final: 0.9045 (p) REVERT: O 43 ASP cc_start: 0.7347 (m-30) cc_final: 0.7059 (m-30) REVERT: O 47 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.8485 (p0) REVERT: O 74 ASP cc_start: 0.8675 (m-30) cc_final: 0.8264 (m-30) REVERT: O 90 ASN cc_start: 0.8767 (m-40) cc_final: 0.8315 (t0) REVERT: P 74 ASP cc_start: 0.8371 (m-30) cc_final: 0.8050 (m-30) REVERT: P 82 MET cc_start: 0.8701 (tpp) cc_final: 0.8195 (tpp) REVERT: Q 50 LYS cc_start: 0.8778 (ptmt) cc_final: 0.8065 (pttm) REVERT: Q 101 ASP cc_start: 0.7807 (t0) cc_final: 0.7311 (t0) REVERT: R 42 ASP cc_start: 0.8241 (t0) cc_final: 0.8000 (t0) REVERT: R 49 LEU cc_start: 0.9484 (tp) cc_final: 0.9276 (tp) REVERT: R 53 MET cc_start: 0.8080 (mmm) cc_final: 0.7778 (mmm) REVERT: R 131 MET cc_start: 0.8480 (mmm) cc_final: 0.8212 (mmt) REVERT: S 32 ASN cc_start: 0.8490 (t0) cc_final: 0.7860 (t0) REVERT: S 96 ASP cc_start: 0.8152 (p0) cc_final: 0.7679 (p0) REVERT: T 12 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8338 (mm-40) REVERT: T 22 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8817 (ttt-90) REVERT: T 50 LYS cc_start: 0.8670 (mmtp) cc_final: 0.8359 (mmtm) REVERT: T 84 ASP cc_start: 0.7686 (p0) cc_final: 0.7417 (p0) REVERT: T 91 ASP cc_start: 0.8349 (t0) cc_final: 0.8001 (t0) REVERT: U 11 PHE cc_start: 0.8455 (t80) cc_final: 0.8174 (t80) REVERT: U 118 MET cc_start: 0.8589 (ppp) cc_final: 0.8385 (tmm) REVERT: V 21 LEU cc_start: 0.9458 (tt) cc_final: 0.9225 (tp) REVERT: V 46 GLN cc_start: 0.7996 (mp10) cc_final: 0.7367 (mp10) REVERT: V 75 LYS cc_start: 0.8376 (mmmm) cc_final: 0.8158 (mmmm) REVERT: V 103 VAL cc_start: 0.8703 (m) cc_final: 0.8464 (p) REVERT: V 112 TYR cc_start: 0.8781 (t80) cc_final: 0.8537 (t80) REVERT: W 7 PHE cc_start: 0.9153 (m-80) cc_final: 0.8925 (m-80) REVERT: W 124 SER cc_start: 0.8595 (t) cc_final: 0.8032 (t) REVERT: X 38 ASP cc_start: 0.7464 (p0) cc_final: 0.7158 (p0) REVERT: X 111 SER cc_start: 0.9100 (OUTLIER) cc_final: 0.8248 (t) REVERT: X 117 GLU cc_start: 0.7988 (tp30) cc_final: 0.7419 (tm-30) REVERT: Y 38 ASP cc_start: 0.8158 (p0) cc_final: 0.7892 (p0) REVERT: Y 97 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7097 (p0) REVERT: Y 112 TYR cc_start: 0.7674 (t80) cc_final: 0.7440 (t80) REVERT: Y 117 GLU cc_start: 0.7697 (tp30) cc_final: 0.7086 (tp30) REVERT: Z 119 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8925 (tp) REVERT: a 5 ASN cc_start: 0.8254 (t0) cc_final: 0.7608 (m-40) REVERT: a 7 PHE cc_start: 0.9102 (m-80) cc_final: 0.8898 (m-10) REVERT: a 57 GLN cc_start: 0.7423 (mp10) cc_final: 0.7078 (mp-120) REVERT: a 86 ASP cc_start: 0.6398 (p0) cc_final: 0.6121 (p0) REVERT: a 110 ARG cc_start: 0.7961 (mmt180) cc_final: 0.6531 (mmm160) REVERT: a 113 GLN cc_start: 0.8047 (mt0) cc_final: 0.7778 (mt0) REVERT: c 318 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.8210 (t0) REVERT: e 319 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7939 (mm110) REVERT: f 324 ASN cc_start: 0.8161 (p0) cc_final: 0.7791 (p0) REVERT: m 160 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.6996 (ttm-80) REVERT: m 232 LYS cc_start: 0.9158 (tptm) cc_final: 0.7809 (mttt) REVERT: n 9 MET cc_start: 0.8678 (tmm) cc_final: 0.8298 (tmm) REVERT: n 225 ARG cc_start: 0.8075 (mmt-90) cc_final: 0.6728 (ttt-90) REVERT: o 223 ASN cc_start: 0.8761 (m-40) cc_final: 0.8460 (m-40) REVERT: o 225 ARG cc_start: 0.7771 (mmt180) cc_final: 0.5784 (mtt180) REVERT: p 85 ASP cc_start: 0.5923 (m-30) cc_final: 0.5554 (m-30) REVERT: p 162 LYS cc_start: 0.8661 (tptt) cc_final: 0.8421 (tptt) REVERT: q 44 VAL cc_start: 0.7831 (OUTLIER) cc_final: 0.7372 (p) REVERT: q 106 GLN cc_start: 0.8023 (mp10) cc_final: 0.7697 (pm20) REVERT: q 123 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6210 (mp0) REVERT: q 199 ILE cc_start: 0.7647 (mm) cc_final: 0.7054 (tt) REVERT: q 231 MET cc_start: 0.6082 (OUTLIER) cc_final: 0.5752 (ptm) REVERT: q 239 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7612 (tm-30) REVERT: q 250 MET cc_start: 0.7792 (mpp) cc_final: 0.7433 (mpp) outliers start: 186 outliers final: 131 residues processed: 1383 average time/residue: 0.2100 time to fit residues: 486.9101 Evaluate side-chains 1350 residues out of total 3890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 1198 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain E residue 9 TRP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 196 ILE Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 190 PHE Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain M residue 72 MET Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 53 MET Chi-restraints excluded: chain Q residue 103 ASP Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain R residue 135 GLN Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 89 VAL Chi-restraints excluded: chain T residue 18 LEU Chi-restraints excluded: chain T residue 22 ARG Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 SER Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain U residue 125 SER Chi-restraints excluded: chain V residue 34 VAL Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain W residue 33 SER Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 111 SER Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 23 VAL Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 88 ASN Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 97 ASP Chi-restraints excluded: chain Y residue 99 VAL Chi-restraints excluded: chain Z residue 18 SER Chi-restraints excluded: chain Z residue 46 GLN Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 119 LEU Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain a residue 6 ILE Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 70 SER Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain c residue 318 ASN Chi-restraints excluded: chain j residue 312 VAL Chi-restraints excluded: chain j residue 319 GLN Chi-restraints excluded: chain m residue 129 VAL Chi-restraints excluded: chain m residue 136 THR Chi-restraints excluded: chain m residue 160 ARG Chi-restraints excluded: chain m residue 245 ASN Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 142 THR Chi-restraints excluded: chain n residue 164 VAL Chi-restraints excluded: chain n residue 193 LEU Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 82 LEU Chi-restraints excluded: chain o residue 110 THR Chi-restraints excluded: chain o residue 129 VAL Chi-restraints excluded: chain o residue 154 THR Chi-restraints excluded: chain o residue 199 ILE Chi-restraints excluded: chain p residue 16 LEU Chi-restraints excluded: chain p residue 44 VAL Chi-restraints excluded: chain p residue 49 LEU Chi-restraints excluded: chain p residue 104 ASN Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain p residue 161 LEU Chi-restraints excluded: chain p residue 181 LEU Chi-restraints excluded: chain p residue 205 VAL Chi-restraints excluded: chain q residue 44 VAL Chi-restraints excluded: chain q residue 51 LEU Chi-restraints excluded: chain q residue 65 ASP Chi-restraints excluded: chain q residue 123 GLU Chi-restraints excluded: chain q residue 155 VAL Chi-restraints excluded: chain q residue 192 VAL Chi-restraints excluded: chain q residue 231 MET Chi-restraints excluded: chain q residue 238 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 37 optimal weight: 7.9990 chunk 412 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 370 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 126 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 430 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 GLN ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 23 GLN Q 112 ASN ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 ASN ** X 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 319 GLN ** c 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 240 ASN p 84 GLN ** p 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 240 ASN q 230 GLN ** q 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.117578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.103711 restraints weight = 87930.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.106332 restraints weight = 43620.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.108076 restraints weight = 26079.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.109227 restraints weight = 17728.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.110013 restraints weight = 13324.531| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.6120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 36808 Z= 0.175 Angle : 0.794 15.052 50037 Z= 0.383 Chirality : 0.046 0.281 5998 Planarity : 0.005 0.078 6518 Dihedral : 4.271 33.752 5086 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.59 % Favored : 97.30 % Rotamer: Outliers : 4.47 % Allowed : 30.49 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.12), residues: 4749 helix: 1.84 (0.10), residues: 2815 sheet: -0.71 (0.26), residues: 390 loop : -0.25 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 41 TYR 0.025 0.002 TYR V 112 PHE 0.049 0.002 PHE S 45 TRP 0.029 0.001 TRP C 68 HIS 0.003 0.001 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00418 (36808) covalent geometry : angle 0.79357 (50037) hydrogen bonds : bond 0.03935 ( 2382) hydrogen bonds : angle 4.15088 ( 6978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9498 Ramachandran restraints generated. 4749 Oldfield, 0 Emsley, 4749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9498 Ramachandran restraints generated. 4749 Oldfield, 0 Emsley, 4749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1398 residues out of total 3890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 1224 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASN cc_start: 0.8454 (m110) cc_final: 0.8164 (m110) REVERT: B 7 MET cc_start: 0.9089 (mmm) cc_final: 0.8740 (tmm) REVERT: C 70 LEU cc_start: 0.8972 (mm) cc_final: 0.8510 (tp) REVERT: D 1 MET cc_start: 0.6310 (tpp) cc_final: 0.5767 (ttm) REVERT: D 71 ASN cc_start: 0.8351 (m110) cc_final: 0.7969 (m110) REVERT: D 78 ARG cc_start: 0.8355 (ttp-110) cc_final: 0.8153 (ttp-110) REVERT: E 9 TRP cc_start: 0.7990 (OUTLIER) cc_final: 0.7353 (m100) REVERT: E 52 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7089 (mp) REVERT: E 100 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7750 (pp20) REVERT: E 106 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7927 (tmm) REVERT: E 134 MET cc_start: 0.7887 (mmp) cc_final: 0.7643 (mmp) REVERT: E 209 PRO cc_start: 0.6297 (Cg_endo) cc_final: 0.5720 (Cg_exo) REVERT: E 210 GLN cc_start: 0.8256 (mp-120) cc_final: 0.7873 (mp10) REVERT: F 128 ASP cc_start: 0.8774 (m-30) cc_final: 0.8404 (m-30) REVERT: F 149 LEU cc_start: 0.8506 (tp) cc_final: 0.7907 (tp) REVERT: F 180 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9087 (pptt) REVERT: F 190 PHE cc_start: 0.7407 (m-10) cc_final: 0.6979 (m-80) REVERT: G 96 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8939 (mm) REVERT: H 178 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8539 (mm-30) REVERT: H 223 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8835 (mm) REVERT: H 228 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8406 (mt) REVERT: J 167 MET cc_start: 0.7018 (pmm) cc_final: 0.6753 (pmm) REVERT: J 190 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.7895 (m-80) REVERT: K 68 LEU cc_start: 0.8954 (tp) cc_final: 0.8663 (tt) REVERT: K 84 MET cc_start: 0.6763 (ttt) cc_final: 0.6478 (ttt) REVERT: L 55 GLN cc_start: 0.8402 (tm-30) cc_final: 0.8138 (tm-30) REVERT: L 57 GLU cc_start: 0.7194 (tt0) cc_final: 0.6842 (tt0) REVERT: L 58 LYS cc_start: 0.7352 (mmtt) cc_final: 0.6960 (mmtt) REVERT: L 63 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7008 (tm-30) REVERT: L 96 TYR cc_start: 0.8936 (t80) cc_final: 0.8608 (t80) REVERT: L 102 MET cc_start: 0.8504 (mpp) cc_final: 0.8291 (mtt) REVERT: M 96 TYR cc_start: 0.8772 (t80) cc_final: 0.8450 (t80) REVERT: N 63 GLU cc_start: 0.6464 (pp20) cc_final: 0.6167 (pp20) REVERT: N 81 SER cc_start: 0.9435 (OUTLIER) cc_final: 0.8999 (p) REVERT: O 47 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8494 (p0) REVERT: O 74 ASP cc_start: 0.8697 (m-30) cc_final: 0.8304 (m-30) REVERT: O 90 ASN cc_start: 0.8739 (m-40) cc_final: 0.8333 (m110) REVERT: P 53 ARG cc_start: 0.8666 (tmm-80) cc_final: 0.8453 (tmm-80) REVERT: P 74 ASP cc_start: 0.8366 (m-30) cc_final: 0.8018 (m-30) REVERT: P 82 MET cc_start: 0.8696 (tpp) cc_final: 0.8212 (tpp) REVERT: Q 50 LYS cc_start: 0.8789 (ptmt) cc_final: 0.8069 (pttm) REVERT: Q 87 TYR cc_start: 0.8241 (m-80) cc_final: 0.7597 (m-10) REVERT: Q 118 MET cc_start: 0.8562 (ptm) cc_final: 0.8191 (tmm) REVERT: R 128 LYS cc_start: 0.8069 (tppt) cc_final: 0.7841 (ttmt) REVERT: R 131 MET cc_start: 0.8539 (mmm) cc_final: 0.8026 (mmt) REVERT: S 50 LYS cc_start: 0.8963 (mtmm) cc_final: 0.8389 (mtmt) REVERT: S 96 ASP cc_start: 0.8141 (p0) cc_final: 0.7701 (p0) REVERT: T 12 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8385 (mm-40) REVERT: T 22 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8145 (ttt90) REVERT: T 50 LYS cc_start: 0.8650 (mmtp) cc_final: 0.8388 (mmtm) REVERT: T 84 ASP cc_start: 0.7440 (p0) cc_final: 0.7188 (p0) REVERT: T 91 ASP cc_start: 0.8330 (t0) cc_final: 0.8025 (t0) REVERT: U 10 ARG cc_start: 0.7025 (ttt180) cc_final: 0.6734 (ttp80) REVERT: V 21 LEU cc_start: 0.9463 (tt) cc_final: 0.9242 (tp) REVERT: V 46 GLN cc_start: 0.8059 (mp10) cc_final: 0.7414 (mp10) REVERT: W 7 PHE cc_start: 0.9169 (m-80) cc_final: 0.8935 (m-80) REVERT: W 117 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7910 (mm-30) REVERT: W 124 SER cc_start: 0.8581 (t) cc_final: 0.8061 (t) REVERT: X 38 ASP cc_start: 0.7260 (p0) cc_final: 0.6959 (p0) REVERT: X 117 GLU cc_start: 0.8052 (tp30) cc_final: 0.7403 (tm-30) REVERT: Y 38 ASP cc_start: 0.8085 (p0) cc_final: 0.7850 (p0) REVERT: Y 97 ASP cc_start: 0.7505 (p0) cc_final: 0.7160 (p0) REVERT: Y 112 TYR cc_start: 0.7806 (t80) cc_final: 0.7433 (t80) REVERT: Z 119 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8907 (tp) REVERT: a 5 ASN cc_start: 0.8365 (t0) cc_final: 0.7629 (m-40) REVERT: a 7 PHE cc_start: 0.9153 (m-80) cc_final: 0.8908 (m-10) REVERT: a 30 ASN cc_start: 0.8884 (m-40) cc_final: 0.8519 (t0) REVERT: a 57 GLN cc_start: 0.7361 (mp10) cc_final: 0.6987 (mp-120) REVERT: a 79 GLU cc_start: 0.7755 (tp30) cc_final: 0.7248 (tm-30) REVERT: a 86 ASP cc_start: 0.6300 (p0) cc_final: 0.6077 (p0) REVERT: a 110 ARG cc_start: 0.8079 (mmt180) cc_final: 0.6561 (mmm160) REVERT: a 113 GLN cc_start: 0.8072 (mt0) cc_final: 0.7699 (mt0) REVERT: c 318 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.8151 (t0) REVERT: e 319 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7990 (mm110) REVERT: f 324 ASN cc_start: 0.8086 (p0) cc_final: 0.7687 (p0) REVERT: m 160 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.6956 (ttm-80) REVERT: m 232 LYS cc_start: 0.9168 (tptm) cc_final: 0.7741 (mttt) REVERT: n 9 MET cc_start: 0.8682 (tmm) cc_final: 0.8291 (tmm) REVERT: n 26 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9082 (mm) REVERT: n 51 LEU cc_start: 0.8549 (mm) cc_final: 0.8303 (mm) REVERT: n 225 ARG cc_start: 0.8077 (mmt-90) cc_final: 0.6589 (ttt-90) REVERT: o 82 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8393 (tt) REVERT: o 212 LYS cc_start: 0.8032 (mmmt) cc_final: 0.7508 (mmtt) REVERT: o 223 ASN cc_start: 0.8794 (m-40) cc_final: 0.8509 (m-40) REVERT: o 225 ARG cc_start: 0.7947 (mmt180) cc_final: 0.5938 (mtt180) REVERT: q 44 VAL cc_start: 0.7863 (OUTLIER) cc_final: 0.7421 (p) REVERT: q 106 GLN cc_start: 0.8017 (mp10) cc_final: 0.7817 (pm20) REVERT: q 123 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6217 (mp0) REVERT: q 231 MET cc_start: 0.6118 (OUTLIER) cc_final: 0.5783 (ptm) REVERT: q 239 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7607 (tm-30) REVERT: q 250 MET cc_start: 0.7688 (mpp) cc_final: 0.7428 (mpp) outliers start: 174 outliers final: 138 residues processed: 1318 average time/residue: 0.2121 time to fit residues: 469.0658 Evaluate side-chains 1330 residues out of total 3890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 1172 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain E residue 9 TRP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 196 ILE Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 190 PHE Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 98 GLU Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 53 MET Chi-restraints excluded: chain Q residue 103 ASP Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain R residue 135 GLN Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 89 VAL Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 18 LEU Chi-restraints excluded: chain T residue 22 ARG Chi-restraints excluded: chain T residue 125 SER Chi-restraints excluded: chain U residue 125 SER Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 33 SER Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 111 SER Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 23 VAL Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 88 ASN Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 99 VAL Chi-restraints excluded: chain Y residue 127 LEU Chi-restraints excluded: chain Z residue 18 SER Chi-restraints excluded: chain Z residue 46 GLN Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 119 LEU Chi-restraints excluded: chain Z residue 122 VAL Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain a residue 6 ILE Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain b residue 319 GLN Chi-restraints excluded: chain c residue 318 ASN Chi-restraints excluded: chain f residue 318 ASN Chi-restraints excluded: chain j residue 312 VAL Chi-restraints excluded: chain m residue 129 VAL Chi-restraints excluded: chain m residue 136 THR Chi-restraints excluded: chain m residue 160 ARG Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 142 THR Chi-restraints excluded: chain n residue 164 VAL Chi-restraints excluded: chain n residue 193 LEU Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 82 LEU Chi-restraints excluded: chain o residue 110 THR Chi-restraints excluded: chain o residue 129 VAL Chi-restraints excluded: chain o residue 154 THR Chi-restraints excluded: chain o residue 199 ILE Chi-restraints excluded: chain p residue 16 LEU Chi-restraints excluded: chain p residue 44 VAL Chi-restraints excluded: chain p residue 49 LEU Chi-restraints excluded: chain p residue 104 ASN Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain p residue 161 LEU Chi-restraints excluded: chain p residue 181 LEU Chi-restraints excluded: chain p residue 205 VAL Chi-restraints excluded: chain q residue 44 VAL Chi-restraints excluded: chain q residue 51 LEU Chi-restraints excluded: chain q residue 65 ASP Chi-restraints excluded: chain q residue 123 GLU Chi-restraints excluded: chain q residue 155 VAL Chi-restraints excluded: chain q residue 192 VAL Chi-restraints excluded: chain q residue 202 MET Chi-restraints excluded: chain q residue 231 MET Chi-restraints excluded: chain q residue 238 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 204 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 chunk 414 optimal weight: 5.9990 chunk 432 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 108 GLN ** S 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 13 GLN U 29 ASN X 40 GLN ** X 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 115 ASN b 319 GLN c 319 GLN ** m 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 245 ASN ** n 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 230 GLN ** q 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.118278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.104413 restraints weight = 87615.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.107056 restraints weight = 43539.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.108807 restraints weight = 26000.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.109966 restraints weight = 17648.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.110739 restraints weight = 13232.491| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.6237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 36808 Z= 0.163 Angle : 0.810 14.855 50037 Z= 0.390 Chirality : 0.046 0.304 5998 Planarity : 0.005 0.077 6518 Dihedral : 4.256 36.073 5084 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.76 % Favored : 97.14 % Rotamer: Outliers : 4.40 % Allowed : 30.85 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.12), residues: 4749 helix: 1.79 (0.10), residues: 2812 sheet: -0.59 (0.27), residues: 365 loop : -0.27 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 19 TYR 0.046 0.002 TYR H 174 PHE 0.040 0.002 PHE S 45 TRP 0.029 0.002 TRP C 68 HIS 0.003 0.001 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00392 (36808) covalent geometry : angle 0.81021 (50037) hydrogen bonds : bond 0.03890 ( 2382) hydrogen bonds : angle 4.14662 ( 6978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9498 Ramachandran restraints generated. 4749 Oldfield, 0 Emsley, 4749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9498 Ramachandran restraints generated. 4749 Oldfield, 0 Emsley, 4749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1387 residues out of total 3890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 1216 time to evaluate : 1.412 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: B 7 MET cc_start: 0.9074 (mmm) cc_final: 0.8729 (tmm) REVERT: B 47 MET cc_start: 0.8522 (ppp) cc_final: 0.8085 (tmm) REVERT: C 70 LEU cc_start: 0.8957 (mm) cc_final: 0.8492 (tp) REVERT: D 1 MET cc_start: 0.6175 (tpp) cc_final: 0.5853 (ttm) REVERT: D 71 ASN cc_start: 0.8370 (m110) cc_final: 0.7977 (m110) REVERT: D 78 ARG cc_start: 0.8383 (ttp-110) cc_final: 0.8178 (ttp-110) REVERT: E 9 TRP cc_start: 0.7951 (OUTLIER) cc_final: 0.7309 (m100) REVERT: E 52 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6899 (mp) REVERT: E 100 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7730 (pp20) REVERT: E 106 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7912 (tmm) REVERT: E 134 MET cc_start: 0.7880 (mmp) cc_final: 0.7625 (mmp) REVERT: E 185 MET cc_start: 0.8124 (mmm) cc_final: 0.7351 (ttt) REVERT: E 209 PRO cc_start: 0.6296 (Cg_endo) cc_final: 0.5725 (Cg_exo) REVERT: E 210 GLN cc_start: 0.8116 (mp-120) cc_final: 0.7757 (mp10) REVERT: F 128 ASP cc_start: 0.8767 (m-30) cc_final: 0.8395 (m-30) REVERT: F 149 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7856 (tp) REVERT: F 180 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.9061 (pptt) REVERT: F 190 PHE cc_start: 0.7382 (m-10) cc_final: 0.6947 (m-80) REVERT: G 61 MET cc_start: 0.8601 (mmm) cc_final: 0.7793 (mpp) REVERT: G 96 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8916 (mm) REVERT: H 178 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8542 (mm-30) REVERT: H 223 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8796 (mm) REVERT: H 228 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8396 (mt) REVERT: I 143 ARG cc_start: 0.7846 (tpp80) cc_final: 0.7234 (mmt90) REVERT: I 207 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8697 (pp) REVERT: J 167 MET cc_start: 0.6979 (pmm) cc_final: 0.6733 (pmm) REVERT: J 190 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.7857 (m-80) REVERT: K 68 LEU cc_start: 0.8927 (tp) cc_final: 0.8666 (tt) REVERT: K 84 MET cc_start: 0.6735 (ttt) cc_final: 0.6446 (ttt) REVERT: L 43 ASP cc_start: 0.8629 (t0) cc_final: 0.8336 (m-30) REVERT: L 55 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8173 (tm-30) REVERT: L 57 GLU cc_start: 0.7117 (tt0) cc_final: 0.6766 (tt0) REVERT: L 58 LYS cc_start: 0.7219 (mmtt) cc_final: 0.6851 (mmtt) REVERT: L 63 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7020 (tm-30) REVERT: L 75 MET cc_start: 0.8333 (ttp) cc_final: 0.7719 (ttm) REVERT: L 96 TYR cc_start: 0.8940 (t80) cc_final: 0.8583 (t80) REVERT: L 102 MET cc_start: 0.8440 (mpp) cc_final: 0.8233 (mtt) REVERT: L 103 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7927 (mm-40) REVERT: M 96 TYR cc_start: 0.8752 (t80) cc_final: 0.8434 (t80) REVERT: N 63 GLU cc_start: 0.6433 (pp20) cc_final: 0.6152 (pp20) REVERT: N 81 SER cc_start: 0.9433 (OUTLIER) cc_final: 0.9005 (p) REVERT: O 47 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8481 (p0) REVERT: O 74 ASP cc_start: 0.8673 (m-30) cc_final: 0.8244 (m-30) REVERT: O 90 ASN cc_start: 0.8733 (m-40) cc_final: 0.8323 (m110) REVERT: P 74 ASP cc_start: 0.8282 (m-30) cc_final: 0.7955 (m-30) REVERT: P 82 MET cc_start: 0.8707 (tpp) cc_final: 0.8236 (tpp) REVERT: Q 87 TYR cc_start: 0.8209 (m-80) cc_final: 0.7542 (m-10) REVERT: Q 118 MET cc_start: 0.8621 (ptm) cc_final: 0.8162 (tmm) REVERT: R 130 MET cc_start: 0.8442 (mmm) cc_final: 0.8022 (tpp) REVERT: R 131 MET cc_start: 0.8518 (mmm) cc_final: 0.7997 (mmt) REVERT: S 96 ASP cc_start: 0.8134 (p0) cc_final: 0.7686 (p0) REVERT: T 12 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8349 (mm-40) REVERT: T 50 LYS cc_start: 0.8631 (mmtp) cc_final: 0.8395 (mmtm) REVERT: T 91 ASP cc_start: 0.8333 (t0) cc_final: 0.8008 (t0) REVERT: U 6 ASP cc_start: 0.8417 (m-30) cc_final: 0.8210 (m-30) REVERT: U 10 ARG cc_start: 0.6981 (ttt180) cc_final: 0.6621 (ttp80) REVERT: U 131 MET cc_start: 0.8758 (mmm) cc_final: 0.8266 (tpt) REVERT: V 21 LEU cc_start: 0.9423 (tt) cc_final: 0.9206 (tp) REVERT: V 46 GLN cc_start: 0.8035 (mp10) cc_final: 0.7408 (mp10) REVERT: W 7 PHE cc_start: 0.9138 (m-80) cc_final: 0.8907 (m-80) REVERT: W 124 SER cc_start: 0.8641 (t) cc_final: 0.8120 (t) REVERT: X 38 ASP cc_start: 0.7374 (p0) cc_final: 0.7108 (p0) REVERT: X 111 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8060 (t) REVERT: X 117 GLU cc_start: 0.8028 (tp30) cc_final: 0.7377 (tm-30) REVERT: Y 38 ASP cc_start: 0.8082 (p0) cc_final: 0.7823 (p0) REVERT: Y 97 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.6951 (p0) REVERT: Y 112 TYR cc_start: 0.7674 (t80) cc_final: 0.7345 (t80) REVERT: Y 117 GLU cc_start: 0.7774 (tp30) cc_final: 0.7173 (tp30) REVERT: Z 119 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8934 (tp) REVERT: a 5 ASN cc_start: 0.8417 (t0) cc_final: 0.7713 (m-40) REVERT: a 7 PHE cc_start: 0.9109 (m-80) cc_final: 0.8899 (m-10) REVERT: a 30 ASN cc_start: 0.8908 (m-40) cc_final: 0.8536 (t0) REVERT: a 68 ILE cc_start: 0.8698 (mm) cc_final: 0.8433 (mt) REVERT: a 79 GLU cc_start: 0.7733 (tp30) cc_final: 0.7286 (tm-30) REVERT: a 86 ASP cc_start: 0.6296 (p0) cc_final: 0.6095 (p0) REVERT: a 110 ARG cc_start: 0.8102 (mmt180) cc_final: 0.6546 (mmm160) REVERT: a 113 GLN cc_start: 0.8108 (mt0) cc_final: 0.7680 (mt0) REVERT: c 318 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.8117 (t0) REVERT: f 324 ASN cc_start: 0.8097 (p0) cc_final: 0.7709 (p0) REVERT: m 160 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.6944 (ttm-80) REVERT: m 232 LYS cc_start: 0.9138 (tptm) cc_final: 0.7716 (mttt) REVERT: n 26 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9107 (mm) REVERT: n 51 LEU cc_start: 0.8507 (mm) cc_final: 0.8176 (mm) REVERT: n 225 ARG cc_start: 0.7980 (mmt-90) cc_final: 0.6575 (ttt-90) REVERT: o 82 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8385 (tt) REVERT: o 223 ASN cc_start: 0.8762 (m-40) cc_final: 0.8503 (m-40) REVERT: o 243 ARG cc_start: 0.8045 (mmm160) cc_final: 0.7824 (mmm160) REVERT: p 116 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7555 (tm-30) REVERT: q 44 VAL cc_start: 0.7812 (OUTLIER) cc_final: 0.7375 (p) REVERT: q 123 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6146 (mp0) REVERT: q 199 ILE cc_start: 0.7492 (mm) cc_final: 0.7074 (tp) REVERT: q 231 MET cc_start: 0.5990 (OUTLIER) cc_final: 0.5661 (ptm) REVERT: q 239 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7643 (tm-30) REVERT: q 250 MET cc_start: 0.7660 (mpp) cc_final: 0.7394 (mpp) outliers start: 171 outliers final: 134 residues processed: 1308 average time/residue: 0.2140 time to fit residues: 469.2625 Evaluate side-chains 1327 residues out of total 3890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 1170 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain E residue 9 TRP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 196 ILE Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 190 PHE Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 53 MET Chi-restraints excluded: chain Q residue 103 ASP Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain R residue 135 GLN Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 89 VAL Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain T residue 18 LEU Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 SER Chi-restraints excluded: chain U residue 125 SER Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 33 SER Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 111 SER Chi-restraints excluded: chain X residue 122 VAL Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 23 VAL Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 88 ASN Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 97 ASP Chi-restraints excluded: chain Y residue 99 VAL Chi-restraints excluded: chain Z residue 18 SER Chi-restraints excluded: chain Z residue 46 GLN Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 119 LEU Chi-restraints excluded: chain Z residue 124 SER Chi-restraints excluded: chain a residue 6 ILE Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 63 LYS Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain c residue 318 ASN Chi-restraints excluded: chain j residue 312 VAL Chi-restraints excluded: chain m residue 129 VAL Chi-restraints excluded: chain m residue 136 THR Chi-restraints excluded: chain m residue 160 ARG Chi-restraints excluded: chain m residue 245 ASN Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 142 THR Chi-restraints excluded: chain n residue 164 VAL Chi-restraints excluded: chain n residue 193 LEU Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 82 LEU Chi-restraints excluded: chain o residue 110 THR Chi-restraints excluded: chain o residue 129 VAL Chi-restraints excluded: chain o residue 154 THR Chi-restraints excluded: chain o residue 199 ILE Chi-restraints excluded: chain p residue 16 LEU Chi-restraints excluded: chain p residue 44 VAL Chi-restraints excluded: chain p residue 49 LEU Chi-restraints excluded: chain p residue 104 ASN Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain p residue 161 LEU Chi-restraints excluded: chain p residue 181 LEU Chi-restraints excluded: chain p residue 205 VAL Chi-restraints excluded: chain q residue 44 VAL Chi-restraints excluded: chain q residue 51 LEU Chi-restraints excluded: chain q residue 65 ASP Chi-restraints excluded: chain q residue 66 MET Chi-restraints excluded: chain q residue 123 GLU Chi-restraints excluded: chain q residue 155 VAL Chi-restraints excluded: chain q residue 192 VAL Chi-restraints excluded: chain q residue 202 MET Chi-restraints excluded: chain q residue 231 MET Chi-restraints excluded: chain q residue 238 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 443 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 442 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 421 optimal weight: 1.9990 chunk 342 optimal weight: 0.0010 chunk 343 optimal weight: 0.8980 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 108 GLN ** S 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 126 GLN U 29 ASN X 40 GLN ** X 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 245 ASN ** n 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.118236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.104508 restraints weight = 86620.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.107122 restraints weight = 43057.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.108840 restraints weight = 25773.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.109988 restraints weight = 17557.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.110763 restraints weight = 13181.414| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.6272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.181 36808 Z= 0.223 Angle : 0.876 59.190 50037 Z= 0.448 Chirality : 0.046 0.655 5998 Planarity : 0.005 0.077 6518 Dihedral : 4.270 36.071 5084 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.72 % Favored : 97.18 % Rotamer: Outliers : 4.27 % Allowed : 31.03 % Favored : 64.70 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.12), residues: 4749 helix: 1.79 (0.10), residues: 2811 sheet: -0.58 (0.27), residues: 365 loop : -0.27 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG U 106 TYR 0.038 0.002 TYR V 112 PHE 0.036 0.002 PHE S 45 TRP 0.028 0.001 TRP C 68 HIS 0.003 0.001 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00488 (36808) covalent geometry : angle 0.87622 (50037) hydrogen bonds : bond 0.03941 ( 2382) hydrogen bonds : angle 4.15697 ( 6978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10029.20 seconds wall clock time: 172 minutes 51.29 seconds (10371.29 seconds total)