Starting phenix.real_space_refine on Mon Mar 25 10:45:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5g_31724/03_2024/7v5g_31724.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5g_31724/03_2024/7v5g_31724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5g_31724/03_2024/7v5g_31724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5g_31724/03_2024/7v5g_31724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5g_31724/03_2024/7v5g_31724.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5g_31724/03_2024/7v5g_31724.pdb" } resolution = 4.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 299 5.16 5 C 30449 2.51 5 N 8235 2.21 5 O 9167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 48150 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1514 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "B" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1659 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Chain: "C" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1591 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "D" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1571 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "E" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1555 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 2, 'TRANS': 197} Chain: "F" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1643 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "G" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1655 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain: "H" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1514 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "I" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1659 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Chain: "J" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1591 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "K" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1571 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "L" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1555 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 2, 'TRANS': 197} Chain: "M" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1643 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "N" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1655 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain: "V" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1857 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "W" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1779 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 10, 'TRANS': 217} Chain: "X" Number of atoms: 1942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1942 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 5, 'TRANS': 241} Chain: "Y" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1825 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain: "Z" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1778 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 224} Chain: "a" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1828 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain: "b" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1874 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "O" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1857 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "P" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1779 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 10, 'TRANS': 217} Chain: "Q" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1950 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 5, 'TRANS': 242} Chain: "R" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1825 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain: "S" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1778 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 224} Chain: "T" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1828 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain: "U" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1874 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Time building chain proxies: 24.60, per 1000 atoms: 0.51 Number of scatterers: 48150 At special positions: 0 Unit cell: (191.11, 159.478, 137.072, 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 299 16.00 O 9167 8.00 N 8235 7.00 C 30449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.25 Conformation dependent library (CDL) restraints added in 9.0 seconds 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11410 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 68 sheets defined 38.5% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.21 Creating SS restraints... Processing helix chain 'A' and resid 48 through 71 removed outlier: 3.522A pdb=" N TYR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE A 65 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 68 " --> pdb=" O GLY A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 90 removed outlier: 4.070A pdb=" N ALA A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 135 through 142 removed outlier: 3.606A pdb=" N ALA A 141 " --> pdb=" O GLY A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 167 removed outlier: 3.741A pdb=" N GLN A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'B' and resid 48 through 71 removed outlier: 3.540A pdb=" N ASN B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 90 removed outlier: 3.580A pdb=" N ALA B 79 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 89 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 90 " --> pdb=" O MET B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 142 removed outlier: 3.694A pdb=" N VAL B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 140 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE B 142 " --> pdb=" O PHE B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 164 Processing helix chain 'C' and resid 55 through 77 removed outlier: 3.504A pdb=" N ALA C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 97 removed outlier: 3.637A pdb=" N SER C 88 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN C 92 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 93 " --> pdb=" O MET C 89 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 153 removed outlier: 3.703A pdb=" N GLY C 147 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET C 148 " --> pdb=" O GLN C 144 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS C 149 " --> pdb=" O MET C 145 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 152 " --> pdb=" O MET C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 174 removed outlier: 3.872A pdb=" N ASN C 172 " --> pdb=" O GLN C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'D' and resid 51 through 72 removed outlier: 3.590A pdb=" N GLN D 55 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN D 63 " --> pdb=" O TYR D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 91 removed outlier: 3.517A pdb=" N ASN D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS D 91 " --> pdb=" O ASN D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 147 removed outlier: 3.599A pdb=" N THR D 139 " --> pdb=" O GLY D 135 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER D 141 " --> pdb=" O PHE D 137 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 171 removed outlier: 3.738A pdb=" N GLU D 166 " --> pdb=" O LYS D 162 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU D 167 " --> pdb=" O CYS D 163 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 71 removed outlier: 3.777A pdb=" N ARG E 61 " --> pdb=" O ARG E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 90 removed outlier: 3.672A pdb=" N GLN E 89 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR E 90 " --> pdb=" O MET E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 143 removed outlier: 4.126A pdb=" N GLY E 137 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL E 138 " --> pdb=" O TYR E 134 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP E 140 " --> pdb=" O TYR E 136 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 167 removed outlier: 3.538A pdb=" N ASP E 154 " --> pdb=" O GLU E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 199 removed outlier: 3.992A pdb=" N GLU E 197 " --> pdb=" O ALA E 193 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS E 198 " --> pdb=" O ASP E 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 79 removed outlier: 4.006A pdb=" N LYS F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 99 removed outlier: 3.714A pdb=" N TYR F 97 " --> pdb=" O SER F 93 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG F 99 " --> pdb=" O ILE F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 153 removed outlier: 3.560A pdb=" N GLN F 146 " --> pdb=" O SER F 142 " (cutoff:3.500A) Proline residue: F 147 - end of helix removed outlier: 3.764A pdb=" N ASN F 151 " --> pdb=" O PRO F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 186 removed outlier: 3.543A pdb=" N ARG F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE F 179 " --> pdb=" O VAL F 175 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU F 184 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG F 185 " --> pdb=" O SER F 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 77 removed outlier: 3.938A pdb=" N TYR G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU G 77 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 102 removed outlier: 3.769A pdb=" N MET G 96 " --> pdb=" O LEU G 92 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG G 99 " --> pdb=" O ALA G 95 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS G 102 " --> pdb=" O SER G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 146 Processing helix chain 'G' and resid 146 through 157 removed outlier: 3.513A pdb=" N GLU G 152 " --> pdb=" O PRO G 148 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL G 153 " --> pdb=" O LEU G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 180 removed outlier: 3.814A pdb=" N ARG G 166 " --> pdb=" O GLN G 162 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL G 175 " --> pdb=" O ARG G 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 71 removed outlier: 3.513A pdb=" N ASP H 57 " --> pdb=" O GLN H 53 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR H 61 " --> pdb=" O ASP H 57 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE H 65 " --> pdb=" O TYR H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.829A pdb=" N ALA H 79 " --> pdb=" O LEU H 75 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET H 86 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 134 Processing helix chain 'H' and resid 135 through 142 removed outlier: 3.632A pdb=" N ALA H 141 " --> pdb=" O GLY H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 167 removed outlier: 3.683A pdb=" N GLN H 154 " --> pdb=" O GLU H 150 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU H 165 " --> pdb=" O ALA H 161 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 90 removed outlier: 3.934A pdb=" N ALA I 79 " --> pdb=" O ARG I 75 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG I 89 " --> pdb=" O GLN I 85 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR I 90 " --> pdb=" O MET I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 removed outlier: 3.669A pdb=" N VAL I 137 " --> pdb=" O ALA I 133 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE I 138 " --> pdb=" O ALA I 134 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP I 140 " --> pdb=" O ALA I 136 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE I 142 " --> pdb=" O PHE I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 164 Processing helix chain 'J' and resid 55 through 77 removed outlier: 3.526A pdb=" N ALA J 63 " --> pdb=" O VAL J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 96 removed outlier: 3.704A pdb=" N SER J 88 " --> pdb=" O TYR J 84 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN J 92 " --> pdb=" O SER J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 153 removed outlier: 3.672A pdb=" N GLY J 147 " --> pdb=" O GLU J 143 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET J 148 " --> pdb=" O GLN J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 174 removed outlier: 3.589A pdb=" N ASN J 172 " --> pdb=" O GLN J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 177 No H-bonds generated for 'chain 'J' and resid 175 through 177' Processing helix chain 'K' and resid 51 through 72 removed outlier: 3.714A pdb=" N ASN K 63 " --> pdb=" O TYR K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 91 removed outlier: 3.579A pdb=" N ASN K 82 " --> pdb=" O THR K 78 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE K 83 " --> pdb=" O ALA K 79 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR K 84 " --> pdb=" O ALA K 80 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU K 88 " --> pdb=" O THR K 84 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS K 91 " --> pdb=" O ASN K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 147 removed outlier: 3.558A pdb=" N THR K 139 " --> pdb=" O GLY K 135 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER K 141 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP K 144 " --> pdb=" O LEU K 140 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG K 145 " --> pdb=" O SER K 141 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR K 146 " --> pdb=" O ILE K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 168 removed outlier: 3.637A pdb=" N GLU K 166 " --> pdb=" O LYS K 162 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU K 167 " --> pdb=" O CYS K 163 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN K 168 " --> pdb=" O LEU K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 71 removed outlier: 3.595A pdb=" N CYS L 52 " --> pdb=" O GLY L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 90 removed outlier: 3.697A pdb=" N GLN L 89 " --> pdb=" O ASN L 85 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR L 90 " --> pdb=" O MET L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 140 removed outlier: 4.155A pdb=" N GLY L 137 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP L 140 " --> pdb=" O TYR L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 167 removed outlier: 3.810A pdb=" N ASP L 154 " --> pdb=" O GLU L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 200 removed outlier: 4.029A pdb=" N GLU L 197 " --> pdb=" O ALA L 193 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS L 198 " --> pdb=" O ASP L 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 79 removed outlier: 3.551A pdb=" N THR M 63 " --> pdb=" O GLY M 59 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS M 73 " --> pdb=" O GLU M 69 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET M 74 " --> pdb=" O ALA M 70 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER M 78 " --> pdb=" O MET M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 99 removed outlier: 3.519A pdb=" N ALA M 89 " --> pdb=" O THR M 85 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR M 97 " --> pdb=" O SER M 93 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG M 99 " --> pdb=" O ILE M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 153 removed outlier: 3.533A pdb=" N GLN M 146 " --> pdb=" O SER M 142 " (cutoff:3.500A) Proline residue: M 147 - end of helix removed outlier: 3.801A pdb=" N ASN M 151 " --> pdb=" O PRO M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 167 through 186 removed outlier: 3.525A pdb=" N ARG M 173 " --> pdb=" O ASP M 169 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU M 184 " --> pdb=" O ILE M 180 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG M 185 " --> pdb=" O SER M 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 77 removed outlier: 3.917A pdb=" N TYR N 62 " --> pdb=" O ALA N 58 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN N 65 " --> pdb=" O GLN N 61 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU N 77 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 102 removed outlier: 3.538A pdb=" N HIS N 89 " --> pdb=" O PRO N 85 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET N 96 " --> pdb=" O LEU N 92 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 146 Processing helix chain 'N' and resid 146 through 157 removed outlier: 3.599A pdb=" N VAL N 153 " --> pdb=" O LEU N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 180 removed outlier: 3.797A pdb=" N ARG N 166 " --> pdb=" O GLN N 162 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL N 175 " --> pdb=" O ARG N 171 " (cutoff:3.500A) Processing helix chain 'V' and resid 23 through 31 removed outlier: 3.888A pdb=" N LYS V 31 " --> pdb=" O GLU V 27 " (cutoff:3.500A) Processing helix chain 'V' and resid 32 through 36 Processing helix chain 'V' and resid 84 through 105 removed outlier: 3.614A pdb=" N SER V 90 " --> pdb=" O ALA V 86 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN V 91 " --> pdb=" O ASP V 87 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL V 92 " --> pdb=" O SER V 88 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN V 93 " --> pdb=" O ARG V 89 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG V 94 " --> pdb=" O SER V 90 " (cutoff:3.500A) Processing helix chain 'V' and resid 111 through 129 removed outlier: 3.700A pdb=" N ILE V 119 " --> pdb=" O LEU V 115 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA V 120 " --> pdb=" O CYS V 116 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL V 125 " --> pdb=" O ASP V 121 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR V 126 " --> pdb=" O ILE V 122 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR V 127 " --> pdb=" O SER V 123 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN V 128 " --> pdb=" O GLN V 124 " (cutoff:3.500A) Processing helix chain 'V' and resid 172 through 182 removed outlier: 3.802A pdb=" N THR V 177 " --> pdb=" O GLN V 173 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER V 178 " --> pdb=" O THR V 174 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE V 179 " --> pdb=" O GLU V 175 " (cutoff:3.500A) Processing helix chain 'V' and resid 183 through 185 No H-bonds generated for 'chain 'V' and resid 183 through 185' Processing helix chain 'V' and resid 186 through 190 removed outlier: 3.567A pdb=" N ASP V 189 " --> pdb=" O LYS V 186 " (cutoff:3.500A) Processing helix chain 'V' and resid 194 through 208 removed outlier: 3.660A pdb=" N THR V 198 " --> pdb=" O GLN V 194 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU V 203 " --> pdb=" O ALA V 199 " (cutoff:3.500A) Processing helix chain 'V' and resid 232 through 241 removed outlier: 3.809A pdb=" N HIS V 239 " --> pdb=" O GLU V 235 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 23 removed outlier: 3.898A pdb=" N GLU W 22 " --> pdb=" O LEU W 18 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 29 removed outlier: 3.576A pdb=" N VAL W 28 " --> pdb=" O ALA W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 101 removed outlier: 3.685A pdb=" N LEU W 85 " --> pdb=" O ASP W 81 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL W 99 " --> pdb=" O GLN W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 105 through 123 removed outlier: 3.639A pdb=" N GLN W 111 " --> pdb=" O ALA W 107 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN W 118 " --> pdb=" O ALA W 114 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR W 120 " --> pdb=" O VAL W 116 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR W 121 " --> pdb=" O MET W 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 165 through 176 removed outlier: 3.769A pdb=" N THR W 171 " --> pdb=" O VAL W 167 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE W 172 " --> pdb=" O ASN W 168 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU W 173 " --> pdb=" O GLY W 169 " (cutoff:3.500A) Processing helix chain 'W' and resid 182 through 195 removed outlier: 3.794A pdb=" N HIS W 188 " --> pdb=" O GLU W 184 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR W 189 " --> pdb=" O ASP W 185 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU W 194 " --> pdb=" O ALA W 190 " (cutoff:3.500A) Processing helix chain 'W' and resid 221 through 229 removed outlier: 3.776A pdb=" N ASP W 227 " --> pdb=" O THR W 223 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR W 228 " --> pdb=" O GLU W 224 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 6 removed outlier: 3.554A pdb=" N TYR X 5 " --> pdb=" O SER X 2 " (cutoff:3.500A) Processing helix chain 'X' and resid 18 through 31 removed outlier: 3.504A pdb=" N MET X 25 " --> pdb=" O VAL X 21 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU X 26 " --> pdb=" O GLU X 22 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE X 28 " --> pdb=" O ALA X 24 " (cutoff:3.500A) Processing helix chain 'X' and resid 79 through 101 removed outlier: 3.504A pdb=" N LEU X 92 " --> pdb=" O ASN X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 106 through 124 removed outlier: 3.523A pdb=" N ILE X 117 " --> pdb=" O ALA X 113 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA X 120 " --> pdb=" O ASP X 116 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYR X 121 " --> pdb=" O ILE X 117 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR X 122 " --> pdb=" O LYS X 118 " (cutoff:3.500A) Processing helix chain 'X' and resid 167 through 179 removed outlier: 4.291A pdb=" N GLN X 177 " --> pdb=" O SER X 173 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP X 178 " --> pdb=" O MET X 174 " (cutoff:3.500A) Processing helix chain 'X' and resid 185 through 201 removed outlier: 3.618A pdb=" N LEU X 190 " --> pdb=" O LEU X 186 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE X 194 " --> pdb=" O LEU X 190 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS X 195 " --> pdb=" O ALA X 191 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL X 196 " --> pdb=" O LEU X 192 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS X 199 " --> pdb=" O LYS X 195 " (cutoff:3.500A) Processing helix chain 'X' and resid 229 through 248 Processing helix chain 'Y' and resid 11 through 15 removed outlier: 3.642A pdb=" N HIS Y 15 " --> pdb=" O PRO Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 27 removed outlier: 3.683A pdb=" N ALA Y 25 " --> pdb=" O TYR Y 21 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL Y 26 " --> pdb=" O ALA Y 22 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 99 removed outlier: 4.299A pdb=" N ALA Y 80 " --> pdb=" O LEU Y 76 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE Y 82 " --> pdb=" O ALA Y 78 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL Y 89 " --> pdb=" O ASN Y 85 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN Y 92 " --> pdb=" O ARG Y 88 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG Y 95 " --> pdb=" O CYS Y 91 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 119 removed outlier: 3.526A pdb=" N ILE Y 107 " --> pdb=" O THR Y 103 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR Y 110 " --> pdb=" O TYR Y 106 " (cutoff:3.500A) Processing helix chain 'Y' and resid 164 through 176 removed outlier: 3.608A pdb=" N LYS Y 174 " --> pdb=" O GLU Y 170 " (cutoff:3.500A) Processing helix chain 'Y' and resid 177 through 183 removed outlier: 3.670A pdb=" N ILE Y 181 " --> pdb=" O THR Y 177 " (cutoff:3.500A) Processing helix chain 'Y' and resid 183 through 199 removed outlier: 3.650A pdb=" N VAL Y 191 " --> pdb=" O THR Y 187 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL Y 198 " --> pdb=" O ALA Y 194 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL Y 199 " --> pdb=" O LEU Y 195 " (cutoff:3.500A) Processing helix chain 'Y' and resid 221 through 228 removed outlier: 3.855A pdb=" N TYR Y 228 " --> pdb=" O GLU Y 224 " (cutoff:3.500A) Processing helix chain 'Y' and resid 228 through 233 removed outlier: 3.507A pdb=" N ILE Y 232 " --> pdb=" O TYR Y 228 " (cutoff:3.500A) Processing helix chain 'Z' and resid 22 through 32 removed outlier: 3.580A pdb=" N GLU Z 29 " --> pdb=" O GLU Z 25 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA Z 30 " --> pdb=" O TYR Z 26 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE Z 31 " --> pdb=" O ALA Z 27 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS Z 32 " --> pdb=" O ILE Z 28 " (cutoff:3.500A) Processing helix chain 'Z' and resid 60 through 64 Processing helix chain 'Z' and resid 84 through 101 removed outlier: 3.706A pdb=" N LEU Z 88 " --> pdb=" O ASP Z 84 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP Z 90 " --> pdb=" O LYS Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 108 through 117 removed outlier: 3.657A pdb=" N THR Z 113 " --> pdb=" O VAL Z 109 " (cutoff:3.500A) Processing helix chain 'Z' and resid 173 through 185 removed outlier: 3.656A pdb=" N ALA Z 177 " --> pdb=" O ALA Z 173 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN Z 178 " --> pdb=" O SER Z 174 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER Z 179 " --> pdb=" O GLU Z 175 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER Z 180 " --> pdb=" O GLY Z 176 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN Z 182 " --> pdb=" O GLN Z 178 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU Z 183 " --> pdb=" O SER Z 179 " (cutoff:3.500A) Processing helix chain 'Z' and resid 190 through 206 removed outlier: 3.772A pdb=" N ILE Z 201 " --> pdb=" O SER Z 197 " (cutoff:3.500A) Processing helix chain 'Z' and resid 230 through 240 removed outlier: 3.814A pdb=" N VAL Z 237 " --> pdb=" O GLU Z 233 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 31 removed outlier: 3.594A pdb=" N GLU a 27 " --> pdb=" O GLU a 23 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA a 28 " --> pdb=" O TYR a 24 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL a 29 " --> pdb=" O ALA a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 78 through 98 Processing helix chain 'a' and resid 104 through 121 removed outlier: 4.037A pdb=" N SER a 110 " --> pdb=" O SER a 106 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE a 118 " --> pdb=" O SER a 114 " (cutoff:3.500A) Proline residue: a 119 - end of helix Processing helix chain 'a' and resid 164 through 173 removed outlier: 3.650A pdb=" N ALA a 168 " --> pdb=" O ARG a 164 " (cutoff:3.500A) Processing helix chain 'a' and resid 174 through 180 removed outlier: 4.241A pdb=" N SER a 177 " --> pdb=" O ARG a 174 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET a 180 " --> pdb=" O SER a 177 " (cutoff:3.500A) Processing helix chain 'a' and resid 183 through 199 removed outlier: 4.016A pdb=" N VAL a 188 " --> pdb=" O LEU a 184 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG a 193 " --> pdb=" O LYS a 189 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU a 197 " --> pdb=" O ARG a 193 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR a 198 " --> pdb=" O ALA a 194 " (cutoff:3.500A) Processing helix chain 'b' and resid 20 through 32 removed outlier: 4.307A pdb=" N ALA b 29 " --> pdb=" O TYR b 25 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL b 30 " --> pdb=" O ALA b 26 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU b 31 " --> pdb=" O MET b 27 " (cutoff:3.500A) Processing helix chain 'b' and resid 80 through 102 removed outlier: 3.532A pdb=" N ASP b 89 " --> pdb=" O ARG b 85 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU b 94 " --> pdb=" O ILE b 90 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG b 99 " --> pdb=" O ALA b 95 " (cutoff:3.500A) Processing helix chain 'b' and resid 107 through 122 removed outlier: 3.514A pdb=" N ALA b 116 " --> pdb=" O ALA b 112 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR b 122 " --> pdb=" O TYR b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 171 through 178 removed outlier: 4.425A pdb=" N GLU b 175 " --> pdb=" O ALA b 171 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE b 176 " --> pdb=" O ALA b 172 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS b 178 " --> pdb=" O THR b 174 " (cutoff:3.500A) Processing helix chain 'b' and resid 180 through 184 Processing helix chain 'b' and resid 185 through 200 removed outlier: 3.879A pdb=" N VAL b 190 " --> pdb=" O CYS b 186 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LYS b 191 " --> pdb=" O ARG b 187 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU b 192 " --> pdb=" O ASP b 188 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE b 199 " --> pdb=" O LYS b 195 " (cutoff:3.500A) Processing helix chain 'b' and resid 228 through 237 removed outlier: 3.834A pdb=" N GLU b 234 " --> pdb=" O ASP b 230 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA b 235 " --> pdb=" O ILE b 231 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU b 236 " --> pdb=" O ARG b 232 " (cutoff:3.500A) Processing helix chain 'b' and resid 240 through 244 removed outlier: 3.589A pdb=" N LYS b 244 " --> pdb=" O GLU b 241 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 24 No H-bonds generated for 'chain 'O' and resid 22 through 24' Processing helix chain 'O' and resid 25 through 30 removed outlier: 3.616A pdb=" N LYS O 30 " --> pdb=" O GLU O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 35 removed outlier: 3.550A pdb=" N GLY O 35 " --> pdb=" O ILE O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 100 removed outlier: 3.560A pdb=" N SER O 89 " --> pdb=" O ALA O 85 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN O 90 " --> pdb=" O ASP O 86 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL O 91 " --> pdb=" O SER O 87 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN O 92 " --> pdb=" O ARG O 88 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG O 93 " --> pdb=" O SER O 89 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 128 removed outlier: 3.762A pdb=" N ILE O 118 " --> pdb=" O LEU O 114 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA O 119 " --> pdb=" O CYS O 115 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL O 124 " --> pdb=" O ASP O 120 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR O 125 " --> pdb=" O ILE O 121 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR O 126 " --> pdb=" O SER O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 173 No H-bonds generated for 'chain 'O' and resid 171 through 173' Processing helix chain 'O' and resid 174 through 181 removed outlier: 4.063A pdb=" N PHE O 178 " --> pdb=" O GLU O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 184 No H-bonds generated for 'chain 'O' and resid 182 through 184' Processing helix chain 'O' and resid 185 through 189 removed outlier: 3.563A pdb=" N ASP O 188 " --> pdb=" O LYS O 185 " (cutoff:3.500A) Processing helix chain 'O' and resid 193 through 207 removed outlier: 3.676A pdb=" N THR O 197 " --> pdb=" O GLN O 193 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU O 202 " --> pdb=" O ALA O 198 " (cutoff:3.500A) Processing helix chain 'O' and resid 231 through 241 removed outlier: 3.751A pdb=" N HIS O 238 " --> pdb=" O GLU O 234 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA O 241 " --> pdb=" O ALA O 237 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 30 removed outlier: 4.673A pdb=" N ALA P 26 " --> pdb=" O GLU P 22 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA P 27 " --> pdb=" O TYR P 23 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY P 30 " --> pdb=" O ALA P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 101 removed outlier: 3.540A pdb=" N TYR P 82 " --> pdb=" O MET P 78 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG P 83 " --> pdb=" O GLY P 79 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU P 85 " --> pdb=" O ASP P 81 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL P 99 " --> pdb=" O GLN P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 123 removed outlier: 3.721A pdb=" N GLN P 111 " --> pdb=" O ALA P 107 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR P 120 " --> pdb=" O VAL P 116 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 176 removed outlier: 3.788A pdb=" N THR P 171 " --> pdb=" O VAL P 167 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE P 172 " --> pdb=" O ASN P 168 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU P 173 " --> pdb=" O GLY P 169 " (cutoff:3.500A) Processing helix chain 'P' and resid 182 through 195 removed outlier: 3.601A pdb=" N ILE P 187 " --> pdb=" O LEU P 183 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS P 188 " --> pdb=" O GLU P 184 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR P 189 " --> pdb=" O ASP P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 229 removed outlier: 3.737A pdb=" N ASP P 227 " --> pdb=" O THR P 223 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR P 228 " --> pdb=" O GLU P 224 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 30 removed outlier: 3.754A pdb=" N GLU Q 26 " --> pdb=" O GLU Q 22 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA Q 27 " --> pdb=" O TYR Q 23 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE Q 28 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 101 removed outlier: 3.581A pdb=" N LEU Q 86 " --> pdb=" O ASP Q 82 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU Q 92 " --> pdb=" O ASN Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 122 removed outlier: 3.883A pdb=" N ILE Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA Q 120 " --> pdb=" O ASP Q 116 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR Q 121 " --> pdb=" O ILE Q 117 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR Q 122 " --> pdb=" O LYS Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 179 removed outlier: 4.253A pdb=" N GLN Q 177 " --> pdb=" O SER Q 173 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP Q 178 " --> pdb=" O MET Q 174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 201 removed outlier: 3.809A pdb=" N LEU Q 190 " --> pdb=" O LEU Q 186 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE Q 194 " --> pdb=" O LEU Q 190 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS Q 195 " --> pdb=" O ALA Q 191 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL Q 196 " --> pdb=" O LEU Q 192 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS Q 199 " --> pdb=" O LYS Q 195 " (cutoff:3.500A) Processing helix chain 'Q' and resid 229 through 248 Processing helix chain 'R' and resid 11 through 15 removed outlier: 3.759A pdb=" N HIS R 15 " --> pdb=" O PRO R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 27 removed outlier: 3.866A pdb=" N ALA R 25 " --> pdb=" O TYR R 21 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL R 26 " --> pdb=" O ALA R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 99 removed outlier: 3.551A pdb=" N ARG R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN R 92 " --> pdb=" O ARG R 88 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR R 97 " --> pdb=" O SER R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 119 removed outlier: 3.632A pdb=" N ILE R 107 " --> pdb=" O THR R 103 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR R 119 " --> pdb=" O LYS R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 176 removed outlier: 3.670A pdb=" N LYS R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 183 removed outlier: 3.614A pdb=" N ILE R 181 " --> pdb=" O THR R 177 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU R 182 " --> pdb=" O ASP R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 199 removed outlier: 3.851A pdb=" N VAL R 191 " --> pdb=" O THR R 187 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL R 198 " --> pdb=" O ALA R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 228 removed outlier: 3.917A pdb=" N TYR R 228 " --> pdb=" O GLU R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 233 removed outlier: 3.694A pdb=" N ILE R 232 " --> pdb=" O TYR R 228 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 29 removed outlier: 3.527A pdb=" N GLU S 29 " --> pdb=" O GLU S 25 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 64 Processing helix chain 'S' and resid 81 through 101 removed outlier: 3.955A pdb=" N ALA S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP S 90 " --> pdb=" O LYS S 86 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL S 94 " --> pdb=" O ASP S 90 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 117 Processing helix chain 'S' and resid 118 through 120 No H-bonds generated for 'chain 'S' and resid 118 through 120' Processing helix chain 'S' and resid 173 through 185 removed outlier: 3.598A pdb=" N ALA S 177 " --> pdb=" O ALA S 173 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N SER S 179 " --> pdb=" O GLU S 175 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU S 183 " --> pdb=" O SER S 179 " (cutoff:3.500A) Processing helix chain 'S' and resid 190 through 206 removed outlier: 3.707A pdb=" N ILE S 201 " --> pdb=" O SER S 197 " (cutoff:3.500A) Processing helix chain 'S' and resid 230 through 241 removed outlier: 3.595A pdb=" N VAL S 237 " --> pdb=" O GLU S 233 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 31 removed outlier: 3.554A pdb=" N GLU T 27 " --> pdb=" O GLU T 23 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA T 28 " --> pdb=" O TYR T 24 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN T 31 " --> pdb=" O GLU T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 98 removed outlier: 3.582A pdb=" N ALA T 81 " --> pdb=" O LEU T 77 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG T 96 " --> pdb=" O CYS T 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 121 removed outlier: 3.891A pdb=" N SER T 110 " --> pdb=" O SER T 106 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE T 118 " --> pdb=" O SER T 114 " (cutoff:3.500A) Proline residue: T 119 - end of helix Processing helix chain 'T' and resid 164 through 173 removed outlier: 3.582A pdb=" N ALA T 168 " --> pdb=" O ARG T 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 176 through 180 removed outlier: 3.518A pdb=" N MET T 180 " --> pdb=" O SER T 177 " (cutoff:3.500A) Processing helix chain 'T' and resid 183 through 199 removed outlier: 3.884A pdb=" N VAL T 188 " --> pdb=" O LEU T 184 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG T 193 " --> pdb=" O LYS T 189 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU T 197 " --> pdb=" O ARG T 193 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR T 198 " --> pdb=" O ALA T 194 " (cutoff:3.500A) Processing helix chain 'T' and resid 230 through 234 removed outlier: 3.534A pdb=" N LEU T 233 " --> pdb=" O SER T 230 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU T 234 " --> pdb=" O PRO T 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 230 through 234' Processing helix chain 'U' and resid 20 through 32 removed outlier: 3.576A pdb=" N LYS U 28 " --> pdb=" O GLU U 24 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA U 29 " --> pdb=" O TYR U 25 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL U 30 " --> pdb=" O ALA U 26 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU U 31 " --> pdb=" O MET U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 102 removed outlier: 3.529A pdb=" N SER U 86 " --> pdb=" O ALA U 82 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU U 94 " --> pdb=" O ILE U 90 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA U 95 " --> pdb=" O ALA U 91 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER U 100 " --> pdb=" O SER U 96 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 125 removed outlier: 3.588A pdb=" N ALA U 116 " --> pdb=" O ALA U 112 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR U 122 " --> pdb=" O TYR U 118 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR U 123 " --> pdb=" O VAL U 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 178 removed outlier: 3.740A pdb=" N ILE U 176 " --> pdb=" O ALA U 172 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS U 178 " --> pdb=" O THR U 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 180 through 184 Processing helix chain 'U' and resid 185 through 201 removed outlier: 3.758A pdb=" N VAL U 190 " --> pdb=" O CYS U 186 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS U 191 " --> pdb=" O ARG U 187 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU U 192 " --> pdb=" O ASP U 188 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA U 194 " --> pdb=" O VAL U 190 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE U 199 " --> pdb=" O LYS U 195 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS U 201 " --> pdb=" O ILE U 197 " (cutoff:3.500A) Processing helix chain 'U' and resid 228 through 233 Processing helix chain 'U' and resid 240 through 244 removed outlier: 3.627A pdb=" N LYS U 244 " --> pdb=" O GLU U 241 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 129 removed outlier: 3.610A pdb=" N GLY A 11 " --> pdb=" O PHE A 8 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 12 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 176 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 22 removed outlier: 7.117A pdb=" N THR A 20 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 47 removed outlier: 3.778A pdb=" N ILE A 99 " --> pdb=" O CYS A 44 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 46 " --> pdb=" O GLY A 97 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 97 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 124 through 128 removed outlier: 6.643A pdb=" N THR B 2 " --> pdb=" O ASP B 17 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE B 173 " --> pdb=" O PRO B 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 20 through 22 removed outlier: 5.583A pdb=" N GLU B 22 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 38 removed outlier: 5.108A pdb=" N PHE B 36 " --> pdb=" O CYS B 43 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N CYS B 43 " --> pdb=" O PHE B 36 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA B 97 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 38 removed outlier: 5.108A pdb=" N PHE B 36 " --> pdb=" O CYS B 43 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N CYS B 43 " --> pdb=" O PHE B 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 211 through 218 removed outlier: 4.006A pdb=" N THR B 213 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL C 184 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C 19 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA C 9 " --> pdb=" O ASP C 24 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.644A pdb=" N ALA C 109 " --> pdb=" O TYR C 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 129 through 132 removed outlier: 3.608A pdb=" N ALA D 130 " --> pdb=" O GLY D 6 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 4 " --> pdb=" O HIS D 132 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 42 through 47 removed outlier: 3.602A pdb=" N ALA D 105 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.555A pdb=" N SER E 188 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N HIS E 178 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ARG E 186 " --> pdb=" O HIS E 178 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG E 180 " --> pdb=" O TRP E 184 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TRP E 184 " --> pdb=" O ARG E 180 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 20 through 22 removed outlier: 7.380A pdb=" N ALA E 20 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 34 through 38 removed outlier: 4.675A pdb=" N GLU E 36 " --> pdb=" O GLY E 43 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY E 43 " --> pdb=" O GLU E 36 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N MET E 100 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY E 103 " --> pdb=" O GLY E 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 135 through 137 removed outlier: 3.514A pdb=" N THR F 199 " --> pdb=" O GLY F 202 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 29 through 31 removed outlier: 7.112A pdb=" N LEU F 29 " --> pdb=" O HIS F 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 43 through 45 removed outlier: 3.513A pdb=" N TYR F 44 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE F 110 " --> pdb=" O TYR F 122 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY F 112 " --> pdb=" O ALA F 120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 136 through 138 removed outlier: 3.801A pdb=" N ALA G 23 " --> pdb=" O LEU G 12 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY G 19 " --> pdb=" O PHE G 16 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL G 20 " --> pdb=" O VAL G 192 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AC2, first strand: chain 'H' and resid 125 through 129 removed outlier: 3.629A pdb=" N GLY H 11 " --> pdb=" O PHE H 8 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 20 through 22 removed outlier: 7.101A pdb=" N THR H 20 " --> pdb=" O ALA H 27 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 44 through 47 removed outlier: 3.843A pdb=" N ILE H 99 " --> pdb=" O CYS H 44 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER H 46 " --> pdb=" O GLY H 97 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY H 97 " --> pdb=" O SER H 46 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 124 through 128 removed outlier: 6.517A pdb=" N THR I 2 " --> pdb=" O ASP I 17 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE I 173 " --> pdb=" O PRO I 188 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 20 through 22 removed outlier: 5.764A pdb=" N GLU I 22 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 35 through 36 removed outlier: 3.640A pdb=" N ALA I 97 " --> pdb=" O ALA I 46 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 35 through 36 Processing sheet with id=AC9, first strand: chain 'I' and resid 211 through 218 removed outlier: 3.963A pdb=" N THR I 213 " --> pdb=" O THR J 198 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL J 184 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL J 19 " --> pdb=" O ILE J 189 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA J 9 " --> pdb=" O ASP J 24 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 48 through 51 removed outlier: 3.727A pdb=" N ALA J 109 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 129 through 132 removed outlier: 3.858A pdb=" N LEU K 4 " --> pdb=" O HIS K 132 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 42 through 47 removed outlier: 3.530A pdb=" N ALA K 105 " --> pdb=" O LEU K 43 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 125 through 129 removed outlier: 6.898A pdb=" N HIS L 178 " --> pdb=" O ARG L 186 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ARG L 186 " --> pdb=" O HIS L 178 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 20 through 22 removed outlier: 7.270A pdb=" N ALA L 20 " --> pdb=" O ALA L 27 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 34 through 38 removed outlier: 4.760A pdb=" N GLU L 36 " --> pdb=" O GLY L 43 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY L 43 " --> pdb=" O GLU L 36 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR L 44 " --> pdb=" O MET L 100 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N MET L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY L 103 " --> pdb=" O GLY L 110 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 135 through 139 removed outlier: 6.072A pdb=" N THR M 11 " --> pdb=" O ASP M 26 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL M 23 " --> pdb=" O CYS M 196 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR M 199 " --> pdb=" O GLY M 202 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 29 through 31 removed outlier: 6.438A pdb=" N GLU M 31 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE M 35 " --> pdb=" O GLU M 31 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 43 through 44 removed outlier: 3.528A pdb=" N TYR M 44 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE M 110 " --> pdb=" O TYR M 122 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 14 through 16 removed outlier: 3.517A pdb=" N GLY N 19 " --> pdb=" O PHE N 16 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE N 187 " --> pdb=" O PRO N 202 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE N 189 " --> pdb=" O GLU N 200 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 42 through 44 Processing sheet with id=AE3, first strand: chain 'V' and resid 166 through 170 removed outlier: 5.865A pdb=" N THR V 39 " --> pdb=" O GLN V 54 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN V 54 " --> pdb=" O THR V 39 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL V 50 " --> pdb=" O VAL V 43 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR V 53 " --> pdb=" O GLU V 217 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU V 217 " --> pdb=" O THR V 53 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 70 through 72 removed outlier: 3.512A pdb=" N GLY V 78 " --> pdb=" O ILE V 142 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE V 142 " --> pdb=" O GLY V 78 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'W' and resid 34 through 38 removed outlier: 3.590A pdb=" N ALA W 46 " --> pdb=" O VAL W 35 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 64 through 66 removed outlier: 3.515A pdb=" N ASN W 139 " --> pdb=" O ARG W 142 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 43 through 47 removed outlier: 3.760A pdb=" N ILE X 37 " --> pdb=" O LEU X 44 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY X 36 " --> pdb=" O THR X 162 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR X 162 " --> pdb=" O GLY X 36 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'X' and resid 72 through 78 removed outlier: 3.618A pdb=" N ALA X 77 " --> pdb=" O SER X 133 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR X 148 " --> pdb=" O TYR X 136 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY X 157 " --> pdb=" O GLN X 149 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'X' and resid 214 through 219 Processing sheet with id=AF1, first strand: chain 'Y' and resid 158 through 161 removed outlier: 3.522A pdb=" N VAL Y 42 " --> pdb=" O VAL Y 35 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL Y 210 " --> pdb=" O LYS Y 218 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS Y 218 " --> pdb=" O VAL Y 210 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 70 through 75 removed outlier: 3.528A pdb=" N VAL Y 134 " --> pdb=" O CYS Y 70 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER Y 130 " --> pdb=" O ALA Y 74 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA Y 131 " --> pdb=" O THR Y 147 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY Y 135 " --> pdb=" O ARG Y 143 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Z' and resid 167 through 170 removed outlier: 3.701A pdb=" N ALA Z 49 " --> pdb=" O ILE Z 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 77 through 80 removed outlier: 4.158A pdb=" N LEU Z 141 " --> pdb=" O MET Z 156 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 159 through 161 removed outlier: 4.005A pdb=" N MET a 159 " --> pdb=" O GLY a 37 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY a 37 " --> pdb=" O MET a 159 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE a 212 " --> pdb=" O TYR a 224 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE a 214 " --> pdb=" O THR a 222 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 63 through 65 removed outlier: 3.502A pdb=" N ILE a 72 " --> pdb=" O LEU a 64 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'b' and resid 162 through 163 removed outlier: 3.810A pdb=" N GLY b 38 " --> pdb=" O CYS b 163 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL b 45 " --> pdb=" O VAL b 216 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU b 212 " --> pdb=" O VAL b 49 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP b 215 " --> pdb=" O GLU b 225 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU b 225 " --> pdb=" O TRP b 215 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'b' and resid 66 through 68 removed outlier: 3.505A pdb=" N GLY b 74 " --> pdb=" O GLY b 138 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY b 138 " --> pdb=" O GLY b 74 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE b 135 " --> pdb=" O ILE b 151 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET b 150 " --> pdb=" O TYR b 158 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR b 158 " --> pdb=" O MET b 150 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 165 through 169 removed outlier: 5.990A pdb=" N THR O 38 " --> pdb=" O GLN O 53 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN O 53 " --> pdb=" O THR O 38 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU O 216 " --> pdb=" O THR O 52 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 69 through 71 removed outlier: 3.526A pdb=" N PHE O 70 " --> pdb=" O CYS O 78 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY O 77 " --> pdb=" O ILE O 141 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE O 141 " --> pdb=" O GLY O 77 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR O 81 " --> pdb=" O CYS O 137 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS O 137 " --> pdb=" O THR O 81 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'P' and resid 34 through 38 removed outlier: 3.578A pdb=" N ALA P 46 " --> pdb=" O VAL P 35 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 65 through 66 removed outlier: 3.530A pdb=" N ASN P 139 " --> pdb=" O ARG P 142 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Q' and resid 46 through 47 removed outlier: 3.545A pdb=" N GLY Q 36 " --> pdb=" O THR Q 162 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR Q 162 " --> pdb=" O GLY Q 36 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Q' and resid 43 through 44 Processing sheet with id=AG6, first strand: chain 'Q' and resid 72 through 75 removed outlier: 3.513A pdb=" N TYR Q 148 " --> pdb=" O TYR Q 136 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN Q 149 " --> pdb=" O GLY Q 157 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY Q 157 " --> pdb=" O GLN Q 149 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'R' and resid 158 through 161 removed outlier: 4.317A pdb=" N VAL R 210 " --> pdb=" O LYS R 218 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS R 218 " --> pdb=" O VAL R 210 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'R' and resid 69 through 75 removed outlier: 3.937A pdb=" N SER R 130 " --> pdb=" O ALA R 74 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA R 131 " --> pdb=" O THR R 147 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY R 135 " --> pdb=" O ARG R 143 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'S' and resid 167 through 170 removed outlier: 3.661A pdb=" N ALA S 49 " --> pdb=" O ILE S 38 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS S 227 " --> pdb=" O THR S 219 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'S' and resid 78 through 80 removed outlier: 4.194A pdb=" N LEU S 141 " --> pdb=" O MET S 156 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP S 147 " --> pdb=" O GLY S 150 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'T' and resid 158 through 161 removed outlier: 3.852A pdb=" N ILE T 212 " --> pdb=" O TYR T 224 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR T 224 " --> pdb=" O ILE T 212 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE T 214 " --> pdb=" O THR T 222 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'T' and resid 63 through 65 removed outlier: 3.831A pdb=" N ILE T 72 " --> pdb=" O LEU T 64 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE T 144 " --> pdb=" O CYS T 156 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'U' and resid 162 through 163 removed outlier: 3.712A pdb=" N GLY U 38 " --> pdb=" O CYS U 163 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU U 212 " --> pdb=" O VAL U 49 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP U 215 " --> pdb=" O GLU U 225 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU U 225 " --> pdb=" O TRP U 215 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'U' and resid 66 through 68 removed outlier: 3.702A pdb=" N GLY U 74 " --> pdb=" O GLY U 138 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY U 138 " --> pdb=" O GLY U 74 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE U 135 " --> pdb=" O ILE U 151 " (cutoff:3.500A) 2156 hydrogen bonds defined for protein. 6072 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.07 Time building geometry restraints manager: 19.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 14021 1.33 - 1.45: 7381 1.45 - 1.57: 27124 1.57 - 1.69: 0 1.69 - 1.81: 488 Bond restraints: 49014 Sorted by residual: bond pdb=" CA PHE U 14 " pdb=" C PHE U 14 " ideal model delta sigma weight residual 1.521 1.557 -0.036 1.19e-02 7.06e+03 9.15e+00 bond pdb=" N VAL W 19 " pdb=" CA VAL W 19 " ideal model delta sigma weight residual 1.460 1.433 0.027 1.21e-02 6.83e+03 4.92e+00 bond pdb=" CA ARG Z 20 " pdb=" C ARG Z 20 " ideal model delta sigma weight residual 1.524 1.551 -0.028 1.29e-02 6.01e+03 4.57e+00 bond pdb=" N THR U 13 " pdb=" CA THR U 13 " ideal model delta sigma weight residual 1.455 1.482 -0.027 1.27e-02 6.20e+03 4.43e+00 bond pdb=" CA THR U 13 " pdb=" C THR U 13 " ideal model delta sigma weight residual 1.525 1.551 -0.026 1.32e-02 5.74e+03 3.97e+00 ... (remaining 49009 not shown) Histogram of bond angle deviations from ideal: 99.42 - 106.34: 1093 106.34 - 113.25: 26536 113.25 - 120.16: 17390 120.16 - 127.08: 20837 127.08 - 133.99: 366 Bond angle restraints: 66222 Sorted by residual: angle pdb=" N SER U 126 " pdb=" CA SER U 126 " pdb=" C SER U 126 " ideal model delta sigma weight residual 111.28 122.96 -11.68 1.09e+00 8.42e-01 1.15e+02 angle pdb=" N ARG Z 20 " pdb=" CA ARG Z 20 " pdb=" C ARG Z 20 " ideal model delta sigma weight residual 111.36 119.81 -8.45 1.09e+00 8.42e-01 6.01e+01 angle pdb=" N LEU U 9 " pdb=" CA LEU U 9 " pdb=" C LEU U 9 " ideal model delta sigma weight residual 111.28 118.73 -7.45 1.09e+00 8.42e-01 4.68e+01 angle pdb=" N SER U 10 " pdb=" CA SER U 10 " pdb=" C SER U 10 " ideal model delta sigma weight residual 108.74 117.16 -8.42 1.38e+00 5.25e-01 3.73e+01 angle pdb=" N PHE X 60 " pdb=" CA PHE X 60 " pdb=" C PHE X 60 " ideal model delta sigma weight residual 109.11 117.60 -8.49 1.42e+00 4.96e-01 3.57e+01 ... (remaining 66217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 28903 16.31 - 32.62: 454 32.62 - 48.94: 164 48.94 - 65.25: 21 65.25 - 81.56: 14 Dihedral angle restraints: 29556 sinusoidal: 11685 harmonic: 17871 Sorted by residual: dihedral pdb=" CA SER b 10 " pdb=" C SER b 10 " pdb=" N ALA b 11 " pdb=" CA ALA b 11 " ideal model delta harmonic sigma weight residual 180.00 151.93 28.07 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA GLY Z 19 " pdb=" C GLY Z 19 " pdb=" N ARG Z 20 " pdb=" CA ARG Z 20 " ideal model delta harmonic sigma weight residual 180.00 153.95 26.05 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA SER b 12 " pdb=" C SER b 12 " pdb=" N THR b 13 " pdb=" CA THR b 13 " ideal model delta harmonic sigma weight residual -180.00 -154.94 -25.06 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 29553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 6799 0.078 - 0.156: 624 0.156 - 0.233: 8 0.233 - 0.311: 7 0.311 - 0.389: 3 Chirality restraints: 7441 Sorted by residual: chirality pdb=" CA GLN W 20 " pdb=" N GLN W 20 " pdb=" C GLN W 20 " pdb=" CB GLN W 20 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" CA SER U 126 " pdb=" N SER U 126 " pdb=" C SER U 126 " pdb=" CB SER U 126 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA ILE W 21 " pdb=" N ILE W 21 " pdb=" C ILE W 21 " pdb=" CB ILE W 21 " both_signs ideal model delta sigma weight residual False 2.43 2.10 0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 7438 not shown) Planarity restraints: 8531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER Z 16 " 0.072 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO Z 17 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO Z 17 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO Z 17 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER W 13 " -0.064 5.00e-02 4.00e+02 9.76e-02 1.52e+01 pdb=" N PRO W 14 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO W 14 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO W 14 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY O 20 " 0.018 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C GLY O 20 " -0.066 2.00e-02 2.50e+03 pdb=" O GLY O 20 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG O 21 " 0.022 2.00e-02 2.50e+03 ... (remaining 8528 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 5152 2.75 - 3.29: 47171 3.29 - 3.82: 77691 3.82 - 4.36: 94747 4.36 - 4.90: 161199 Nonbonded interactions: 385960 Sorted by model distance: nonbonded pdb=" NE2 GLN D 27 " pdb=" O LYS K 169 " model vdw 2.210 2.520 nonbonded pdb=" O SER P 151 " pdb=" OG SER Q 81 " model vdw 2.218 2.440 nonbonded pdb=" O THR L 44 " pdb=" OG1 THR L 99 " model vdw 2.218 2.440 nonbonded pdb=" O THR E 44 " pdb=" OG1 THR E 99 " model vdw 2.221 2.440 nonbonded pdb=" O LYS P 38 " pdb=" OH TYR P 177 " model vdw 2.227 2.440 ... (remaining 385955 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'V' } ncs_group { reference = chain 'P' selection = chain 'W' } ncs_group { reference = (chain 'Q' and resid 2 through 248) selection = chain 'X' } ncs_group { reference = chain 'R' selection = chain 'Y' } ncs_group { reference = chain 'S' selection = chain 'Z' } ncs_group { reference = chain 'T' selection = chain 'a' } ncs_group { reference = chain 'U' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 5.210 Check model and map are aligned: 0.820 Set scattering table: 0.490 Process input model: 120.430 Find NCS groups from input model: 4.420 Set up NCS constraints: 0.450 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 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 : 0.002 0.036 49014 Z= 0.123 Angle : 0.502 11.679 66222 Z= 0.306 Chirality : 0.043 0.389 7441 Planarity : 0.004 0.110 8531 Dihedral : 7.724 81.561 18146 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.69 % Favored : 94.18 % Rotamer: Outliers : 0.08 % Allowed : 0.14 % Favored : 99.79 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.09), residues: 6137 helix: -3.36 (0.07), residues: 2045 sheet: -0.84 (0.12), residues: 1408 loop : -0.92 (0.11), residues: 2684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP V 102 HIS 0.004 0.001 HIS U 72 PHE 0.018 0.001 PHE K 171 TYR 0.029 0.001 TYR O 103 ARG 0.005 0.000 ARG N 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1809 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1805 time to evaluate : 5.768 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 148 THR cc_start: 0.9106 (p) cc_final: 0.8798 (t) REVERT: C 27 PHE cc_start: 0.8041 (t80) cc_final: 0.7808 (t80) REVERT: C 71 ASN cc_start: 0.8888 (m-40) cc_final: 0.7801 (m110) REVERT: C 170 MET cc_start: 0.8558 (mmp) cc_final: 0.8243 (mmm) REVERT: C 185 ILE cc_start: 0.8471 (mt) cc_final: 0.7941 (mt) REVERT: D 186 ASN cc_start: 0.9120 (m-40) cc_final: 0.8710 (m-40) REVERT: E 71 LYS cc_start: 0.8788 (mttt) cc_final: 0.7859 (mtmm) REVERT: F 75 TYR cc_start: 0.7765 (t80) cc_final: 0.6723 (t80) REVERT: F 213 ASP cc_start: 0.2921 (m-30) cc_final: 0.2238 (t70) REVERT: G 39 ILE cc_start: 0.7550 (mt) cc_final: 0.7006 (mt) REVERT: G 73 ASP cc_start: 0.7948 (m-30) cc_final: 0.7271 (m-30) REVERT: H 148 THR cc_start: 0.8887 (p) cc_final: 0.8018 (t) REVERT: H 165 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7857 (pt0) REVERT: I 58 LEU cc_start: 0.9379 (mt) cc_final: 0.9117 (tp) REVERT: J 84 TYR cc_start: 0.8142 (t80) cc_final: 0.7922 (t80) REVERT: J 148 MET cc_start: 0.9156 (mmm) cc_final: 0.8494 (mmm) REVERT: J 170 MET cc_start: 0.8778 (mmp) cc_final: 0.8539 (mmm) REVERT: K 52 ASP cc_start: 0.7763 (m-30) cc_final: 0.6812 (m-30) REVERT: K 53 THR cc_start: 0.8262 (m) cc_final: 0.7979 (p) REVERT: K 68 LYS cc_start: 0.9472 (tttt) cc_final: 0.8806 (ttmt) REVERT: L 51 ASP cc_start: 0.8404 (m-30) cc_final: 0.8141 (m-30) REVERT: N 61 GLN cc_start: 0.8210 (mt0) cc_final: 0.7721 (mt0) REVERT: N 64 LYS cc_start: 0.9008 (mttt) cc_final: 0.8713 (tmmt) REVERT: N 83 TYR cc_start: 0.6717 (m-80) cc_final: 0.5858 (m-80) REVERT: N 117 ASP cc_start: 0.8410 (m-30) cc_final: 0.7943 (m-30) REVERT: N 188 GLN cc_start: 0.7909 (mm110) cc_final: 0.7637 (mm110) REVERT: V 17 PHE cc_start: 0.6119 (m-10) cc_final: 0.5903 (m-10) REVERT: V 106 TYR cc_start: 0.6931 (m-10) cc_final: 0.5856 (m-10) REVERT: V 126 TYR cc_start: 0.7994 (m-10) cc_final: 0.7218 (m-10) REVERT: W 20 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7510 (tp-100) REVERT: W 99 VAL cc_start: 0.9036 (t) cc_final: 0.8756 (p) REVERT: X 45 LEU cc_start: 0.7952 (pp) cc_final: 0.7216 (mt) REVERT: X 82 ASP cc_start: 0.8139 (m-30) cc_final: 0.7666 (t70) REVERT: X 101 TYR cc_start: 0.7999 (m-80) cc_final: 0.7793 (m-80) REVERT: X 124 PHE cc_start: 0.7879 (p90) cc_final: 0.7568 (p90) REVERT: X 155 ASN cc_start: 0.8253 (m-40) cc_final: 0.7993 (m110) REVERT: X 194 ILE cc_start: 0.9283 (mt) cc_final: 0.9016 (tp) REVERT: X 240 HIS cc_start: 0.8194 (t70) cc_final: 0.7985 (t-170) REVERT: Y 77 THR cc_start: 0.6006 (m) cc_final: 0.5265 (m) REVERT: Y 88 ARG cc_start: 0.7870 (mtt180) cc_final: 0.6754 (mtt180) REVERT: Y 114 LEU cc_start: 0.8995 (mt) cc_final: 0.8787 (mt) REVERT: Y 192 ILE cc_start: 0.9465 (mt) cc_final: 0.9061 (pt) REVERT: Y 219 ILE cc_start: 0.7946 (mt) cc_final: 0.7571 (tp) REVERT: Z 86 LYS cc_start: 0.9111 (mttm) cc_final: 0.8906 (tppt) REVERT: Z 99 HIS cc_start: 0.7534 (t-90) cc_final: 0.7280 (t-90) REVERT: Z 112 VAL cc_start: 0.9092 (t) cc_final: 0.8790 (t) REVERT: Z 119 LEU cc_start: 0.8973 (mt) cc_final: 0.8547 (tt) REVERT: Z 166 ASP cc_start: 0.7181 (m-30) cc_final: 0.6774 (m-30) REVERT: Z 203 LYS cc_start: 0.9073 (tttt) cc_final: 0.8615 (tppt) REVERT: a 41 LYS cc_start: 0.8855 (tttt) cc_final: 0.8632 (mtmm) REVERT: a 69 HIS cc_start: 0.8055 (p-80) cc_final: 0.7825 (p90) REVERT: a 80 ASP cc_start: 0.8571 (m-30) cc_final: 0.8103 (m-30) REVERT: a 94 ASP cc_start: 0.9103 (m-30) cc_final: 0.8653 (m-30) REVERT: a 115 LYS cc_start: 0.9382 (mmtp) cc_final: 0.9129 (mmtm) REVERT: a 123 TYR cc_start: 0.6987 (t80) cc_final: 0.6663 (t80) REVERT: a 128 TYR cc_start: 0.6965 (m-80) cc_final: 0.6664 (m-80) REVERT: a 154 PHE cc_start: 0.8612 (m-10) cc_final: 0.7547 (m-80) REVERT: a 225 ASP cc_start: 0.8534 (p0) cc_final: 0.8073 (p0) REVERT: a 227 ASP cc_start: 0.8781 (m-30) cc_final: 0.8326 (m-30) REVERT: b 75 MET cc_start: 0.8253 (ttm) cc_final: 0.7770 (ttm) REVERT: b 97 ASN cc_start: 0.9122 (m-40) cc_final: 0.8909 (m-40) REVERT: b 150 MET cc_start: 0.6602 (ttm) cc_final: 0.5754 (ttm) REVERT: O 16 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.6087 (m-80) REVERT: O 73 THR cc_start: 0.8712 (p) cc_final: 0.8240 (t) REVERT: O 104 LYS cc_start: 0.8218 (mttt) cc_final: 0.7721 (tmmt) REVERT: O 196 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8278 (tp30) REVERT: P 102 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7223 (mt-10) REVERT: P 112 ARG cc_start: 0.7658 (mtt-85) cc_final: 0.7455 (mtt90) REVERT: P 139 ASN cc_start: 0.6620 (m110) cc_final: 0.6107 (t0) REVERT: Q 61 PHE cc_start: 0.6755 (m-10) cc_final: 0.6333 (t80) REVERT: Q 91 ARG cc_start: 0.9201 (mtt180) cc_final: 0.8275 (mtt90) REVERT: Q 136 TYR cc_start: 0.7468 (m-80) cc_final: 0.7232 (m-80) REVERT: Q 201 MET cc_start: 0.8165 (tpt) cc_final: 0.7665 (tpt) REVERT: R 66 ASP cc_start: 0.7428 (p0) cc_final: 0.7140 (p0) REVERT: R 70 CYS cc_start: 0.7927 (m) cc_final: 0.7544 (p) REVERT: R 77 THR cc_start: 0.6970 (m) cc_final: 0.6519 (m) REVERT: R 110 TYR cc_start: 0.7592 (m-10) cc_final: 0.7368 (m-10) REVERT: R 211 MET cc_start: 0.7384 (ttp) cc_final: 0.7115 (tpp) REVERT: R 221 ASN cc_start: 0.9262 (m-40) cc_final: 0.8850 (m-40) REVERT: S 84 ASP cc_start: 0.8039 (m-30) cc_final: 0.7729 (m-30) REVERT: S 88 LEU cc_start: 0.9452 (mt) cc_final: 0.8935 (mt) REVERT: S 98 ASN cc_start: 0.8861 (m-40) cc_final: 0.8407 (m-40) REVERT: S 105 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7529 (mm-30) REVERT: S 201 ILE cc_start: 0.9360 (mt) cc_final: 0.9133 (tp) REVERT: T 49 LEU cc_start: 0.8693 (tp) cc_final: 0.8261 (tt) REVERT: T 67 ASP cc_start: 0.8626 (t0) cc_final: 0.8383 (t70) REVERT: T 215 VAL cc_start: 0.8450 (p) cc_final: 0.7505 (p) REVERT: U 97 ASN cc_start: 0.9060 (m-40) cc_final: 0.8860 (t0) REVERT: U 111 LEU cc_start: 0.8770 (tp) cc_final: 0.8468 (mt) REVERT: U 147 GLN cc_start: 0.7073 (mm-40) cc_final: 0.5825 (mm-40) outliers start: 4 outliers final: 0 residues processed: 1809 average time/residue: 0.7394 time to fit residues: 2060.4485 Evaluate side-chains 882 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 880 time to evaluate : 5.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 513 optimal weight: 20.0000 chunk 460 optimal weight: 6.9990 chunk 255 optimal weight: 30.0000 chunk 157 optimal weight: 30.0000 chunk 310 optimal weight: 0.8980 chunk 246 optimal weight: 30.0000 chunk 476 optimal weight: 6.9990 chunk 184 optimal weight: 9.9990 chunk 289 optimal weight: 50.0000 chunk 354 optimal weight: 10.0000 chunk 552 optimal weight: 20.0000 overall best weight: 6.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 HIS A 77 HIS ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 165 ASN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS F 36 HIS F 131 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 GLN ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 GLN ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 GLN K 101 ASN M 79 ASN M 108 ASN ** M 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN W 87 HIS ** W 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 206 ASN ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 119 GLN X 146 GLN ** X 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 94 HIS ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 114 GLN ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 143 ASN O 12 HIS ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 150 GLN P 51 GLN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 ASN ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 98 ASN ** T 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 49014 Z= 0.335 Angle : 0.700 11.651 66222 Z= 0.370 Chirality : 0.046 0.292 7441 Planarity : 0.006 0.161 8531 Dihedral : 4.707 31.277 6803 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.84 % Favored : 97.10 % Rotamer: Outliers : 0.10 % Allowed : 1.96 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.10), residues: 6137 helix: -1.30 (0.10), residues: 2107 sheet: -0.46 (0.12), residues: 1458 loop : -0.58 (0.12), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP V 190 HIS 0.013 0.002 HIS U 224 PHE 0.031 0.002 PHE W 172 TYR 0.046 0.002 TYR O 103 ARG 0.014 0.001 ARG R 125 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1042 time to evaluate : 5.596 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 62 GLN cc_start: 0.9234 (pt0) cc_final: 0.9029 (pm20) REVERT: A 95 MET cc_start: 0.7868 (tmm) cc_final: 0.7462 (tmm) REVERT: A 116 MET cc_start: 0.7353 (pmm) cc_final: 0.7103 (pmm) REVERT: B 30 ASN cc_start: 0.7912 (t0) cc_final: 0.7702 (t0) REVERT: B 75 ARG cc_start: 0.7583 (ttm110) cc_final: 0.7378 (ttm110) REVERT: B 149 GLU cc_start: 0.8751 (tp30) cc_final: 0.8542 (tm-30) REVERT: B 204 CYS cc_start: 0.8205 (m) cc_final: 0.7777 (m) REVERT: C 27 PHE cc_start: 0.8220 (t80) cc_final: 0.8018 (t80) REVERT: C 79 ARG cc_start: 0.7721 (mmt-90) cc_final: 0.6441 (mmt-90) REVERT: C 84 TYR cc_start: 0.8072 (t80) cc_final: 0.7622 (t80) REVERT: C 130 MET cc_start: 0.6975 (ttm) cc_final: 0.6470 (ttp) REVERT: C 161 HIS cc_start: 0.8196 (m-70) cc_final: 0.7505 (m170) REVERT: D 38 MET cc_start: 0.7624 (mtp) cc_final: 0.6321 (tpp) REVERT: D 68 LYS cc_start: 0.9300 (mtmt) cc_final: 0.8949 (mttt) REVERT: D 69 MET cc_start: 0.7649 (ttm) cc_final: 0.7244 (tpp) REVERT: D 139 THR cc_start: 0.9115 (p) cc_final: 0.8802 (p) REVERT: E 62 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8545 (mp10) REVERT: E 97 MET cc_start: 0.6855 (tmm) cc_final: 0.5983 (tmm) REVERT: F 158 MET cc_start: 0.7012 (mmp) cc_final: 0.6545 (mmm) REVERT: G 38 ASN cc_start: 0.7525 (p0) cc_final: 0.7303 (p0) REVERT: G 73 ASP cc_start: 0.7717 (m-30) cc_final: 0.7461 (m-30) REVERT: G 110 MET cc_start: 0.6254 (mpp) cc_final: 0.6020 (mpp) REVERT: G 156 LYS cc_start: 0.8665 (ptpp) cc_final: 0.8309 (mtpp) REVERT: H 62 GLN cc_start: 0.8783 (mp10) cc_final: 0.8441 (mp10) REVERT: H 119 MET cc_start: 0.8618 (ptm) cc_final: 0.8334 (ptt) REVERT: H 120 MET cc_start: 0.7419 (tmm) cc_final: 0.7160 (tmm) REVERT: I 58 LEU cc_start: 0.9619 (mt) cc_final: 0.9312 (tp) REVERT: I 62 ASN cc_start: 0.9225 (m-40) cc_final: 0.8990 (m-40) REVERT: J 69 ARG cc_start: 0.9077 (mtt180) cc_final: 0.8851 (mtt180) REVERT: J 148 MET cc_start: 0.8753 (mmm) cc_final: 0.8361 (mmm) REVERT: J 157 MET cc_start: 0.7960 (mmm) cc_final: 0.7005 (mmm) REVERT: J 170 MET cc_start: 0.8984 (mmp) cc_final: 0.8732 (mmm) REVERT: K 38 MET cc_start: 0.7279 (mmm) cc_final: 0.7067 (mmm) REVERT: M 172 MET cc_start: 0.8772 (mmp) cc_final: 0.8461 (mmm) REVERT: N 26 MET cc_start: 0.7007 (mpp) cc_final: 0.5016 (mpp) REVERT: N 39 ILE cc_start: 0.8393 (mt) cc_final: 0.8180 (mt) REVERT: N 50 MET cc_start: 0.8019 (ttp) cc_final: 0.7552 (ppp) REVERT: N 59 ASP cc_start: 0.6509 (p0) cc_final: 0.5988 (p0) REVERT: N 117 ASP cc_start: 0.8510 (m-30) cc_final: 0.8210 (m-30) REVERT: V 17 PHE cc_start: 0.6747 (m-10) cc_final: 0.6419 (m-10) REVERT: V 106 TYR cc_start: 0.7326 (m-10) cc_final: 0.6883 (m-10) REVERT: W 117 MET cc_start: 0.8087 (tpp) cc_final: 0.7159 (tpp) REVERT: X 11 ILE cc_start: 0.7154 (pt) cc_final: 0.6939 (pt) REVERT: X 19 TYR cc_start: 0.7762 (m-80) cc_final: 0.7208 (m-80) REVERT: X 45 LEU cc_start: 0.7944 (pp) cc_final: 0.7116 (mt) REVERT: X 82 ASP cc_start: 0.8836 (m-30) cc_final: 0.8373 (m-30) REVERT: X 87 THR cc_start: 0.8819 (m) cc_final: 0.8396 (p) REVERT: X 124 PHE cc_start: 0.8079 (p90) cc_final: 0.7584 (p90) REVERT: X 155 ASN cc_start: 0.8705 (m-40) cc_final: 0.8210 (m110) REVERT: X 174 MET cc_start: 0.9017 (mmp) cc_final: 0.8740 (mmm) REVERT: X 194 ILE cc_start: 0.9343 (mt) cc_final: 0.9027 (tp) REVERT: X 240 HIS cc_start: 0.8327 (t70) cc_final: 0.8087 (t70) REVERT: Y 77 THR cc_start: 0.7446 (m) cc_final: 0.7153 (p) REVERT: Y 86 ARG cc_start: 0.8024 (mtm180) cc_final: 0.7318 (mtm180) REVERT: Y 211 MET cc_start: 0.8485 (tpp) cc_final: 0.8203 (tpp) REVERT: Z 69 GLU cc_start: 0.8933 (tt0) cc_final: 0.8534 (tm-30) REVERT: Z 86 LYS cc_start: 0.9333 (mttm) cc_final: 0.8895 (tppt) REVERT: Z 90 ASP cc_start: 0.8665 (m-30) cc_final: 0.8427 (m-30) REVERT: Z 98 ASN cc_start: 0.9214 (m-40) cc_final: 0.8722 (m-40) REVERT: Z 119 LEU cc_start: 0.8682 (mt) cc_final: 0.8416 (tt) REVERT: Z 122 GLN cc_start: 0.7575 (mt0) cc_final: 0.7333 (mt0) REVERT: Z 203 LYS cc_start: 0.9031 (tttt) cc_final: 0.8688 (tppt) REVERT: a 41 LYS cc_start: 0.9013 (tttt) cc_final: 0.8699 (ptpt) REVERT: a 80 ASP cc_start: 0.8647 (m-30) cc_final: 0.8445 (m-30) REVERT: a 94 ASP cc_start: 0.9124 (m-30) cc_final: 0.8577 (m-30) REVERT: a 123 TYR cc_start: 0.7453 (t80) cc_final: 0.7165 (t80) REVERT: a 154 PHE cc_start: 0.8098 (m-10) cc_final: 0.7291 (m-80) REVERT: a 215 VAL cc_start: 0.8701 (p) cc_final: 0.8473 (p) REVERT: b 93 GLU cc_start: 0.9277 (pt0) cc_final: 0.8736 (pt0) REVERT: b 97 ASN cc_start: 0.9188 (m-40) cc_final: 0.8787 (m-40) REVERT: b 101 ASN cc_start: 0.8014 (m-40) cc_final: 0.7568 (m-40) REVERT: b 150 MET cc_start: 0.7205 (ttm) cc_final: 0.6908 (ttm) REVERT: b 181 MET cc_start: 0.9248 (pmm) cc_final: 0.9006 (pmm) REVERT: O 96 TYR cc_start: 0.8130 (m-80) cc_final: 0.7819 (m-80) REVERT: O 196 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8194 (mm-30) REVERT: P 92 LEU cc_start: 0.8175 (mt) cc_final: 0.7710 (mt) REVERT: Q 61 PHE cc_start: 0.6542 (m-10) cc_final: 0.6229 (t80) REVERT: Q 95 GLN cc_start: 0.8923 (mp-120) cc_final: 0.8506 (mm-40) REVERT: Q 201 MET cc_start: 0.8151 (tpt) cc_final: 0.7667 (tpt) REVERT: R 21 TYR cc_start: 0.7328 (m-10) cc_final: 0.7073 (m-10) REVERT: R 77 THR cc_start: 0.7143 (m) cc_final: 0.6636 (m) REVERT: R 91 CYS cc_start: 0.8764 (m) cc_final: 0.8454 (m) REVERT: S 98 ASN cc_start: 0.9141 (m110) cc_final: 0.8815 (m110) REVERT: S 201 ILE cc_start: 0.9623 (mt) cc_final: 0.9374 (tp) REVERT: T 49 LEU cc_start: 0.8680 (tp) cc_final: 0.8401 (tt) REVERT: T 99 PHE cc_start: 0.6959 (m-10) cc_final: 0.6251 (m-10) REVERT: U 97 ASN cc_start: 0.8900 (m-40) cc_final: 0.8660 (m-40) outliers start: 5 outliers final: 0 residues processed: 1045 average time/residue: 0.6571 time to fit residues: 1087.4872 Evaluate side-chains 686 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 686 time to evaluate : 5.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 306 optimal weight: 20.0000 chunk 171 optimal weight: 6.9990 chunk 459 optimal weight: 0.0020 chunk 375 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 553 optimal weight: 10.0000 chunk 597 optimal weight: 4.9990 chunk 492 optimal weight: 40.0000 chunk 548 optimal weight: 5.9990 chunk 188 optimal weight: 20.0000 chunk 443 optimal weight: 9.9990 overall best weight: 4.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN B 85 GLN B 193 ASN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 ASN F 131 GLN ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 GLN ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 GLN I 193 ASN ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN ** M 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN ** V 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 151 GLN ** W 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 206 ASN Y 120 GLN ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 87 HIS ** P 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 188 HIS ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 105 ASN U 143 ASN ** U 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 49014 Z= 0.249 Angle : 0.606 10.749 66222 Z= 0.319 Chirality : 0.044 0.231 7441 Planarity : 0.005 0.112 8531 Dihedral : 4.695 32.215 6803 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.97 % Favored : 97.00 % Rotamer: Outliers : 0.06 % Allowed : 2.55 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.10), residues: 6137 helix: -0.51 (0.10), residues: 2151 sheet: -0.21 (0.13), residues: 1480 loop : -0.54 (0.12), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 55 HIS 0.010 0.001 HIS I 66 PHE 0.022 0.002 PHE V 188 TYR 0.037 0.002 TYR O 103 ARG 0.011 0.001 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 906 time to evaluate : 5.399 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 4 MET cc_start: 0.7038 (tpt) cc_final: 0.6712 (tpt) REVERT: A 62 GLN cc_start: 0.9296 (pt0) cc_final: 0.8934 (pm20) REVERT: A 116 MET cc_start: 0.7278 (pmm) cc_final: 0.6780 (pmm) REVERT: A 134 TYR cc_start: 0.8818 (m-80) cc_final: 0.8602 (m-80) REVERT: B 30 ASN cc_start: 0.7794 (t0) cc_final: 0.7552 (t0) REVERT: C 75 LEU cc_start: 0.9104 (mt) cc_final: 0.8881 (mp) REVERT: C 79 ARG cc_start: 0.7929 (mmt-90) cc_final: 0.7666 (mmt-90) REVERT: C 84 TYR cc_start: 0.7990 (t80) cc_final: 0.7572 (t80) REVERT: C 96 GLU cc_start: 0.7985 (pp20) cc_final: 0.7611 (pp20) REVERT: C 130 MET cc_start: 0.6930 (ttm) cc_final: 0.6153 (ttm) REVERT: C 161 HIS cc_start: 0.8148 (m-70) cc_final: 0.7552 (m-70) REVERT: C 185 ILE cc_start: 0.8793 (mm) cc_final: 0.8419 (mm) REVERT: C 203 MET cc_start: 0.7996 (mmm) cc_final: 0.7764 (mmm) REVERT: D 38 MET cc_start: 0.7324 (mtp) cc_final: 0.6105 (mmt) REVERT: D 62 LYS cc_start: 0.9120 (tttp) cc_final: 0.8896 (tttp) REVERT: D 69 MET cc_start: 0.7757 (ttm) cc_final: 0.7246 (tpp) REVERT: E 62 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8869 (mm-40) REVERT: E 67 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8134 (mm-30) REVERT: E 97 MET cc_start: 0.6500 (tmm) cc_final: 0.5694 (tmm) REVERT: F 76 LYS cc_start: 0.9171 (mmtt) cc_final: 0.8631 (mmtm) REVERT: F 158 MET cc_start: 0.6993 (mmp) cc_final: 0.6754 (mmm) REVERT: G 3 ASN cc_start: 0.8483 (p0) cc_final: 0.8280 (p0) REVERT: G 110 MET cc_start: 0.6232 (mpp) cc_final: 0.5992 (mpp) REVERT: G 156 LYS cc_start: 0.8611 (ptpp) cc_final: 0.8222 (mtpp) REVERT: H 62 GLN cc_start: 0.8803 (mp10) cc_final: 0.8464 (mp10) REVERT: I 58 LEU cc_start: 0.9583 (mt) cc_final: 0.9269 (tp) REVERT: I 62 ASN cc_start: 0.9235 (m-40) cc_final: 0.8869 (m110) REVERT: J 33 MET cc_start: 0.7902 (tmm) cc_final: 0.7690 (tmm) REVERT: J 69 ARG cc_start: 0.8965 (mtt180) cc_final: 0.8701 (mtt180) REVERT: J 93 LEU cc_start: 0.9473 (tt) cc_final: 0.9234 (tt) REVERT: J 96 GLU cc_start: 0.8448 (pp20) cc_final: 0.7939 (pp20) REVERT: J 148 MET cc_start: 0.8719 (mmm) cc_final: 0.8372 (mmm) REVERT: J 170 MET cc_start: 0.8932 (mmp) cc_final: 0.8690 (mmm) REVERT: K 27 GLN cc_start: 0.7746 (pt0) cc_final: 0.7138 (pt0) REVERT: K 38 MET cc_start: 0.7599 (mmm) cc_final: 0.7209 (mmm) REVERT: K 62 LYS cc_start: 0.9156 (tptt) cc_final: 0.8813 (tptt) REVERT: K 68 LYS cc_start: 0.9155 (ttmm) cc_final: 0.8860 (ttmm) REVERT: L 97 MET cc_start: 0.7178 (tpp) cc_final: 0.6953 (tpp) REVERT: M 83 MET cc_start: 0.8941 (tpp) cc_final: 0.8429 (mmm) REVERT: N 56 ASP cc_start: 0.7847 (t0) cc_final: 0.7618 (t0) REVERT: N 59 ASP cc_start: 0.6716 (p0) cc_final: 0.5626 (p0) REVERT: V 17 PHE cc_start: 0.7223 (m-10) cc_final: 0.7008 (m-10) REVERT: V 101 ASN cc_start: 0.8266 (t0) cc_final: 0.8055 (t0) REVERT: V 113 ASP cc_start: 0.8079 (p0) cc_final: 0.7826 (p0) REVERT: W 83 ARG cc_start: 0.8812 (ttm110) cc_final: 0.8272 (mtt-85) REVERT: W 117 MET cc_start: 0.7925 (tpp) cc_final: 0.7234 (tpp) REVERT: W 226 LYS cc_start: 0.9510 (mmpt) cc_final: 0.9244 (mmmt) REVERT: X 19 TYR cc_start: 0.7849 (m-80) cc_final: 0.7510 (m-80) REVERT: X 79 ILE cc_start: 0.8300 (tt) cc_final: 0.8059 (tt) REVERT: X 82 ASP cc_start: 0.8934 (m-30) cc_final: 0.8398 (m-30) REVERT: X 87 THR cc_start: 0.8683 (m) cc_final: 0.8286 (p) REVERT: X 124 PHE cc_start: 0.8266 (p90) cc_final: 0.7899 (p90) REVERT: X 194 ILE cc_start: 0.9282 (mt) cc_final: 0.9008 (tp) REVERT: X 240 HIS cc_start: 0.8323 (t70) cc_final: 0.8039 (t-90) REVERT: Y 4 ASP cc_start: 0.6743 (t0) cc_final: 0.4702 (m-30) REVERT: Y 77 THR cc_start: 0.7234 (m) cc_final: 0.6673 (m) REVERT: Z 69 GLU cc_start: 0.8862 (tt0) cc_final: 0.8550 (tm-30) REVERT: Z 86 LYS cc_start: 0.9411 (mttm) cc_final: 0.8897 (tppt) REVERT: Z 98 ASN cc_start: 0.9266 (m-40) cc_final: 0.8982 (m-40) REVERT: Z 203 LYS cc_start: 0.9178 (tttt) cc_final: 0.8886 (tptt) REVERT: a 41 LYS cc_start: 0.9079 (tttt) cc_final: 0.8718 (ptpt) REVERT: a 80 ASP cc_start: 0.8593 (m-30) cc_final: 0.8380 (m-30) REVERT: a 94 ASP cc_start: 0.9165 (m-30) cc_final: 0.8911 (m-30) REVERT: a 97 PHE cc_start: 0.8754 (m-10) cc_final: 0.8461 (m-80) REVERT: a 123 TYR cc_start: 0.7534 (t80) cc_final: 0.7333 (t80) REVERT: a 128 TYR cc_start: 0.7540 (m-10) cc_final: 0.7275 (m-80) REVERT: a 154 PHE cc_start: 0.8203 (m-10) cc_final: 0.7578 (m-80) REVERT: b 75 MET cc_start: 0.7440 (ttm) cc_final: 0.6526 (ttp) REVERT: b 89 ASP cc_start: 0.9134 (m-30) cc_final: 0.8587 (p0) REVERT: b 93 GLU cc_start: 0.9194 (pt0) cc_final: 0.8521 (pp20) REVERT: b 97 ASN cc_start: 0.9205 (m-40) cc_final: 0.8922 (m-40) REVERT: b 150 MET cc_start: 0.7136 (ttm) cc_final: 0.6506 (tmm) REVERT: O 96 TYR cc_start: 0.8229 (m-80) cc_final: 0.7752 (m-80) REVERT: O 102 LYS cc_start: 0.8579 (tppt) cc_final: 0.7743 (tppt) REVERT: P 118 GLN cc_start: 0.8197 (tp40) cc_final: 0.7936 (tp40) REVERT: Q 84 ASN cc_start: 0.9277 (t0) cc_final: 0.8904 (m110) REVERT: Q 95 GLN cc_start: 0.9067 (mp-120) cc_final: 0.8444 (mm-40) REVERT: Q 201 MET cc_start: 0.8447 (tpt) cc_final: 0.8203 (tpt) REVERT: S 69 GLU cc_start: 0.8208 (tt0) cc_final: 0.7918 (tm-30) REVERT: S 98 ASN cc_start: 0.9143 (m110) cc_final: 0.8798 (m110) REVERT: S 201 ILE cc_start: 0.9595 (mt) cc_final: 0.9340 (tp) REVERT: S 206 MET cc_start: 0.8150 (mmt) cc_final: 0.7743 (mmm) REVERT: U 135 PHE cc_start: 0.7401 (p90) cc_final: 0.7158 (p90) outliers start: 3 outliers final: 1 residues processed: 908 average time/residue: 0.6683 time to fit residues: 982.5759 Evaluate side-chains 663 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 662 time to evaluate : 6.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 546 optimal weight: 6.9990 chunk 415 optimal weight: 4.9990 chunk 287 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 263 optimal weight: 6.9990 chunk 371 optimal weight: 5.9990 chunk 555 optimal weight: 30.0000 chunk 587 optimal weight: 20.0000 chunk 290 optimal weight: 30.0000 chunk 526 optimal weight: 9.9990 chunk 158 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 ASN ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 ASN ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 84 ASN ** X 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 200 GLN ** Z 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 GLN ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 240 HIS ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 205 ASN S 118 ASN S 182 GLN ** T 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 105 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.5938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 49014 Z= 0.298 Angle : 0.640 11.645 66222 Z= 0.337 Chirality : 0.044 0.232 7441 Planarity : 0.005 0.101 8531 Dihedral : 4.831 33.275 6803 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.13 % Favored : 96.84 % Rotamer: Outliers : 0.02 % Allowed : 2.20 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.10), residues: 6137 helix: -0.26 (0.11), residues: 2171 sheet: -0.29 (0.13), residues: 1502 loop : -0.59 (0.12), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP X 159 HIS 0.009 0.002 HIS A 77 PHE 0.024 0.002 PHE T 87 TYR 0.022 0.002 TYR O 103 ARG 0.011 0.001 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 824 time to evaluate : 5.651 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 134 TYR cc_start: 0.8781 (m-80) cc_final: 0.8476 (m-80) REVERT: B 145 ASP cc_start: 0.7673 (t0) cc_final: 0.7395 (t0) REVERT: C 84 TYR cc_start: 0.7817 (t80) cc_final: 0.7424 (t80) REVERT: C 86 LEU cc_start: 0.8836 (tp) cc_final: 0.8542 (tp) REVERT: C 130 MET cc_start: 0.7400 (ttm) cc_final: 0.6732 (ttp) REVERT: C 161 HIS cc_start: 0.8633 (m-70) cc_final: 0.8144 (m170) REVERT: C 185 ILE cc_start: 0.8740 (mm) cc_final: 0.8259 (mm) REVERT: D 38 MET cc_start: 0.7496 (mtp) cc_final: 0.6404 (tpp) REVERT: D 68 LYS cc_start: 0.9368 (mttt) cc_final: 0.8868 (mttm) REVERT: D 69 MET cc_start: 0.7576 (ttm) cc_final: 0.7108 (tpp) REVERT: E 56 GLU cc_start: 0.9230 (pt0) cc_final: 0.8875 (pt0) REVERT: E 90 TYR cc_start: 0.8421 (m-80) cc_final: 0.8181 (m-80) REVERT: E 93 MET cc_start: 0.8163 (mtt) cc_final: 0.7617 (mtm) REVERT: F 75 TYR cc_start: 0.8523 (t80) cc_final: 0.8173 (t80) REVERT: F 76 LYS cc_start: 0.9107 (mmtt) cc_final: 0.8840 (mmtm) REVERT: F 158 MET cc_start: 0.7148 (mmp) cc_final: 0.6924 (mmm) REVERT: G 3 ASN cc_start: 0.8467 (p0) cc_final: 0.8141 (p0) REVERT: G 156 LYS cc_start: 0.8605 (ptpp) cc_final: 0.8278 (mtpp) REVERT: H 4 MET cc_start: 0.6602 (tpt) cc_final: 0.6058 (tpt) REVERT: H 62 GLN cc_start: 0.8870 (mp10) cc_final: 0.8501 (mp10) REVERT: H 119 MET cc_start: 0.8824 (ptt) cc_final: 0.8615 (ptp) REVERT: H 120 MET cc_start: 0.8366 (tmm) cc_final: 0.7991 (tmm) REVERT: H 136 TYR cc_start: 0.7653 (m-10) cc_final: 0.7160 (m-10) REVERT: I 54 MET cc_start: 0.8299 (mmm) cc_final: 0.7896 (mmm) REVERT: I 58 LEU cc_start: 0.9602 (mt) cc_final: 0.9279 (tp) REVERT: I 62 ASN cc_start: 0.9184 (m-40) cc_final: 0.8848 (m-40) REVERT: J 71 ASN cc_start: 0.8661 (m110) cc_final: 0.7752 (m110) REVERT: J 93 LEU cc_start: 0.9524 (tt) cc_final: 0.9179 (tt) REVERT: J 96 GLU cc_start: 0.8410 (pp20) cc_final: 0.7855 (pp20) REVERT: J 148 MET cc_start: 0.8738 (mmm) cc_final: 0.8476 (mmm) REVERT: K 38 MET cc_start: 0.7865 (mmm) cc_final: 0.7448 (mmm) REVERT: K 68 LYS cc_start: 0.9048 (ttmm) cc_final: 0.8732 (ttmm) REVERT: K 69 MET cc_start: 0.8988 (tpp) cc_final: 0.8540 (tpp) REVERT: M 83 MET cc_start: 0.9054 (tpp) cc_final: 0.8627 (tpp) REVERT: M 158 MET cc_start: 0.8157 (mtt) cc_final: 0.7894 (mtt) REVERT: N 26 MET cc_start: 0.7075 (mpp) cc_final: 0.5458 (mpp) REVERT: N 50 MET cc_start: 0.8240 (ptm) cc_final: 0.7411 (ppp) REVERT: N 56 ASP cc_start: 0.7981 (t0) cc_final: 0.7517 (t0) REVERT: N 59 ASP cc_start: 0.6387 (p0) cc_final: 0.5249 (p0) REVERT: V 113 ASP cc_start: 0.8072 (p0) cc_final: 0.7764 (p0) REVERT: W 7 PHE cc_start: 0.7990 (p90) cc_final: 0.7699 (p90) REVERT: W 117 MET cc_start: 0.7930 (tpp) cc_final: 0.7333 (tpp) REVERT: W 205 ASP cc_start: 0.8738 (m-30) cc_final: 0.8481 (p0) REVERT: X 194 ILE cc_start: 0.9357 (mt) cc_final: 0.9049 (tp) REVERT: X 240 HIS cc_start: 0.8305 (t70) cc_final: 0.7960 (t-90) REVERT: Y 4 ASP cc_start: 0.7298 (t0) cc_final: 0.4714 (m-30) REVERT: Y 77 THR cc_start: 0.7516 (m) cc_final: 0.7063 (m) REVERT: Z 69 GLU cc_start: 0.9032 (tt0) cc_final: 0.8776 (tt0) REVERT: Z 71 ASP cc_start: 0.6223 (t70) cc_final: 0.5977 (t70) REVERT: Z 86 LYS cc_start: 0.9354 (mttm) cc_final: 0.8939 (tppt) REVERT: Z 98 ASN cc_start: 0.9080 (m-40) cc_final: 0.8877 (m-40) REVERT: Z 107 MET cc_start: 0.7066 (tpt) cc_final: 0.6413 (tpp) REVERT: Z 133 MET cc_start: 0.7408 (ttt) cc_final: 0.5936 (tmm) REVERT: Z 203 LYS cc_start: 0.9247 (tttt) cc_final: 0.8931 (tptt) REVERT: a 41 LYS cc_start: 0.9149 (tttt) cc_final: 0.8645 (ptpp) REVERT: a 62 LYS cc_start: 0.8763 (mmmt) cc_final: 0.8364 (mtpt) REVERT: a 80 ASP cc_start: 0.8672 (m-30) cc_final: 0.8435 (m-30) REVERT: a 128 TYR cc_start: 0.7395 (m-10) cc_final: 0.7157 (m-80) REVERT: a 152 ASN cc_start: 0.8929 (t0) cc_final: 0.8715 (t0) REVERT: a 154 PHE cc_start: 0.8260 (m-10) cc_final: 0.7820 (m-80) REVERT: b 87 LEU cc_start: 0.8837 (pp) cc_final: 0.8603 (pp) REVERT: b 93 GLU cc_start: 0.9272 (pt0) cc_final: 0.8482 (pp20) REVERT: b 97 ASN cc_start: 0.9229 (m-40) cc_final: 0.8600 (m-40) REVERT: b 150 MET cc_start: 0.7224 (ttm) cc_final: 0.6375 (tmm) REVERT: O 95 ARG cc_start: 0.8360 (mtt180) cc_final: 0.7640 (mtt-85) REVERT: O 96 TYR cc_start: 0.8109 (m-80) cc_final: 0.7454 (m-80) REVERT: O 131 MET cc_start: 0.8783 (mmm) cc_final: 0.8316 (mmm) REVERT: O 196 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8267 (mm-30) REVERT: P 118 GLN cc_start: 0.8256 (tp40) cc_final: 0.8031 (tp40) REVERT: Q 84 ASN cc_start: 0.9324 (t0) cc_final: 0.8988 (m110) REVERT: Q 95 GLN cc_start: 0.8890 (mp-120) cc_final: 0.8532 (mm-40) REVERT: Q 201 MET cc_start: 0.8429 (tpt) cc_final: 0.8149 (tpt) REVERT: R 77 THR cc_start: 0.7397 (m) cc_final: 0.6933 (m) REVERT: S 101 PHE cc_start: 0.7617 (m-10) cc_final: 0.7137 (m-80) REVERT: S 103 TYR cc_start: 0.8313 (m-80) cc_final: 0.7691 (m-80) REVERT: S 201 ILE cc_start: 0.9565 (mt) cc_final: 0.9255 (tp) REVERT: S 206 MET cc_start: 0.8440 (mmt) cc_final: 0.7768 (mmm) REVERT: T 26 MET cc_start: 0.7733 (mmp) cc_final: 0.7089 (mmm) REVERT: U 135 PHE cc_start: 0.7465 (p90) cc_final: 0.7188 (p90) REVERT: U 150 MET cc_start: 0.6828 (ttm) cc_final: 0.5938 (tmm) outliers start: 1 outliers final: 1 residues processed: 825 average time/residue: 0.6245 time to fit residues: 829.8330 Evaluate side-chains 625 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 624 time to evaluate : 5.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 489 optimal weight: 5.9990 chunk 333 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 437 optimal weight: 6.9990 chunk 242 optimal weight: 8.9990 chunk 501 optimal weight: 10.0000 chunk 406 optimal weight: 0.0050 chunk 0 optimal weight: 20.0000 chunk 300 optimal weight: 0.1980 chunk 527 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 overall best weight: 3.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN D 87 ASN F 79 ASN G 81 HIS ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 ASN K 8 GLN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 ASN K 101 ASN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN ** W 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 69 ASN Y 94 HIS ** Z 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 152 GLN ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 110 HIS ** b 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 GLN ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 98 ASN S 118 ASN S 182 GLN T 21 GLN ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 105 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.6101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 49014 Z= 0.197 Angle : 0.570 11.307 66222 Z= 0.297 Chirality : 0.043 0.188 7441 Planarity : 0.004 0.082 8531 Dihedral : 4.627 31.438 6803 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.75 % Favored : 97.21 % Rotamer: Outliers : 0.04 % Allowed : 1.79 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.10), residues: 6137 helix: 0.04 (0.11), residues: 2188 sheet: -0.22 (0.13), residues: 1484 loop : -0.57 (0.12), residues: 2465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 91 HIS 0.011 0.001 HIS M 36 PHE 0.031 0.002 PHE Z 162 TYR 0.020 0.001 TYR J 95 ARG 0.023 0.001 ARG S 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 819 time to evaluate : 5.510 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 134 TYR cc_start: 0.8852 (m-80) cc_final: 0.8521 (m-80) REVERT: C 68 PHE cc_start: 0.7940 (t80) cc_final: 0.7238 (t80) REVERT: C 70 LEU cc_start: 0.9642 (tt) cc_final: 0.9073 (tt) REVERT: C 84 TYR cc_start: 0.7649 (t80) cc_final: 0.7407 (t80) REVERT: C 96 GLU cc_start: 0.8125 (pp20) cc_final: 0.7688 (pp20) REVERT: C 130 MET cc_start: 0.7250 (ttm) cc_final: 0.6277 (ttp) REVERT: C 161 HIS cc_start: 0.8512 (m-70) cc_final: 0.7909 (m170) REVERT: C 185 ILE cc_start: 0.8639 (mm) cc_final: 0.8175 (mm) REVERT: D 44 LEU cc_start: 0.8941 (tt) cc_final: 0.8588 (pp) REVERT: D 62 LYS cc_start: 0.9071 (tttp) cc_final: 0.8753 (tttp) REVERT: D 68 LYS cc_start: 0.9406 (mttt) cc_final: 0.8948 (mttm) REVERT: D 69 MET cc_start: 0.7618 (ttm) cc_final: 0.7139 (tpp) REVERT: E 67 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8434 (mm-30) REVERT: E 90 TYR cc_start: 0.8386 (m-80) cc_final: 0.7998 (m-80) REVERT: E 93 MET cc_start: 0.8112 (mtt) cc_final: 0.7492 (mtm) REVERT: F 74 MET cc_start: 0.9117 (mtp) cc_final: 0.8905 (mtp) REVERT: G 3 ASN cc_start: 0.8397 (p0) cc_final: 0.7973 (p0) REVERT: G 156 LYS cc_start: 0.8598 (ptpp) cc_final: 0.8298 (mtpp) REVERT: H 4 MET cc_start: 0.6787 (tpt) cc_final: 0.6280 (tpt) REVERT: H 62 GLN cc_start: 0.8766 (mp10) cc_final: 0.8392 (mp10) REVERT: H 119 MET cc_start: 0.8724 (ptt) cc_final: 0.8463 (ptp) REVERT: I 58 LEU cc_start: 0.9581 (mt) cc_final: 0.9234 (tp) REVERT: I 62 ASN cc_start: 0.9224 (m-40) cc_final: 0.8816 (m110) REVERT: J 96 GLU cc_start: 0.8462 (pp20) cc_final: 0.8007 (pp20) REVERT: J 148 MET cc_start: 0.8912 (mmm) cc_final: 0.8704 (mmm) REVERT: K 68 LYS cc_start: 0.8984 (ttmm) cc_final: 0.8704 (ttmm) REVERT: K 69 MET cc_start: 0.9010 (tpp) cc_final: 0.8463 (tpp) REVERT: L 139 MET cc_start: 0.7911 (ttp) cc_final: 0.7247 (ptm) REVERT: M 83 MET cc_start: 0.9053 (tpp) cc_final: 0.8709 (tpt) REVERT: M 91 MET cc_start: 0.8544 (mmp) cc_final: 0.7823 (mmp) REVERT: N 50 MET cc_start: 0.8269 (ptm) cc_final: 0.7423 (ppp) REVERT: N 56 ASP cc_start: 0.7942 (t0) cc_final: 0.7629 (t0) REVERT: N 59 ASP cc_start: 0.6432 (p0) cc_final: 0.5181 (p0) REVERT: V 71 PHE cc_start: 0.8475 (m-10) cc_final: 0.8249 (m-80) REVERT: X 5 TYR cc_start: 0.7689 (m-80) cc_final: 0.7346 (m-10) REVERT: X 194 ILE cc_start: 0.9322 (mt) cc_final: 0.8965 (tp) REVERT: X 240 HIS cc_start: 0.8310 (t70) cc_final: 0.7907 (t-90) REVERT: Y 77 THR cc_start: 0.7529 (m) cc_final: 0.7013 (m) REVERT: Z 71 ASP cc_start: 0.6270 (t70) cc_final: 0.6020 (t70) REVERT: Z 86 LYS cc_start: 0.9346 (mttm) cc_final: 0.8896 (tppt) REVERT: Z 90 ASP cc_start: 0.8851 (m-30) cc_final: 0.8416 (m-30) REVERT: Z 98 ASN cc_start: 0.9054 (m-40) cc_final: 0.8821 (m-40) REVERT: Z 107 MET cc_start: 0.7097 (tpt) cc_final: 0.6120 (tpt) REVERT: Z 203 LYS cc_start: 0.9245 (tttt) cc_final: 0.8914 (tptt) REVERT: a 62 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8284 (mtpt) REVERT: a 80 ASP cc_start: 0.8554 (m-30) cc_final: 0.8351 (m-30) REVERT: a 154 PHE cc_start: 0.8305 (m-10) cc_final: 0.7940 (m-80) REVERT: b 89 ASP cc_start: 0.9291 (m-30) cc_final: 0.8923 (p0) REVERT: b 93 GLU cc_start: 0.9147 (pt0) cc_final: 0.8464 (pp20) REVERT: b 97 ASN cc_start: 0.9068 (m-40) cc_final: 0.8258 (m-40) REVERT: b 150 MET cc_start: 0.7078 (ttm) cc_final: 0.6308 (tmm) REVERT: O 96 TYR cc_start: 0.8110 (m-80) cc_final: 0.7595 (m-80) REVERT: O 102 LYS cc_start: 0.8603 (tppt) cc_final: 0.8382 (tptp) REVERT: O 131 MET cc_start: 0.8810 (mmm) cc_final: 0.8346 (mmm) REVERT: Q 84 ASN cc_start: 0.9324 (t0) cc_final: 0.9016 (m110) REVERT: Q 95 GLN cc_start: 0.8905 (mp-120) cc_final: 0.8551 (mm-40) REVERT: Q 201 MET cc_start: 0.8381 (tpt) cc_final: 0.8131 (tpt) REVERT: Q 228 LEU cc_start: 0.9161 (mt) cc_final: 0.8789 (mp) REVERT: R 77 THR cc_start: 0.7428 (m) cc_final: 0.7085 (m) REVERT: R 114 LEU cc_start: 0.9063 (mt) cc_final: 0.8849 (mp) REVERT: R 118 TYR cc_start: 0.7781 (m-80) cc_final: 0.7436 (m-80) REVERT: S 107 MET cc_start: 0.8813 (ttt) cc_final: 0.7897 (ttt) REVERT: S 201 ILE cc_start: 0.9565 (mt) cc_final: 0.9260 (tp) REVERT: S 206 MET cc_start: 0.8433 (mmt) cc_final: 0.7680 (mmm) REVERT: U 135 PHE cc_start: 0.7361 (p90) cc_final: 0.6655 (p90) REVERT: U 136 MET cc_start: 0.5054 (mpp) cc_final: 0.4380 (mpp) outliers start: 2 outliers final: 1 residues processed: 820 average time/residue: 0.6483 time to fit residues: 864.7533 Evaluate side-chains 629 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 628 time to evaluate : 6.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 197 optimal weight: 0.0030 chunk 529 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 chunk 345 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 588 optimal weight: 9.9990 chunk 488 optimal weight: 20.0000 chunk 272 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 308 optimal weight: 2.9990 overall best weight: 4.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 ASN K 101 ASN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 194 GLN ** W 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 168 ASN Y 120 GLN ** Z 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 GLN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 HIS S 118 ASN ** T 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 105 ASN ** U 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.6333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 49014 Z= 0.229 Angle : 0.591 11.449 66222 Z= 0.307 Chirality : 0.043 0.308 7441 Planarity : 0.004 0.103 8531 Dihedral : 4.630 30.918 6803 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.32 % Favored : 96.64 % Rotamer: Outliers : 0.02 % Allowed : 1.54 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.10), residues: 6137 helix: 0.12 (0.11), residues: 2191 sheet: -0.23 (0.13), residues: 1520 loop : -0.57 (0.13), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP N 91 HIS 0.016 0.001 HIS U 224 PHE 0.028 0.002 PHE O 187 TYR 0.021 0.001 TYR X 101 ARG 0.024 0.001 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 788 time to evaluate : 5.740 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: 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 134 TYR cc_start: 0.8855 (m-80) cc_final: 0.8464 (m-80) REVERT: C 68 PHE cc_start: 0.7935 (t80) cc_final: 0.7374 (t80) REVERT: C 96 GLU cc_start: 0.8031 (pp20) cc_final: 0.7673 (pp20) REVERT: C 130 MET cc_start: 0.6795 (ttm) cc_final: 0.5982 (ttm) REVERT: C 161 HIS cc_start: 0.8284 (m-70) cc_final: 0.7920 (m170) REVERT: C 170 MET cc_start: 0.8821 (mmm) cc_final: 0.8351 (mtp) REVERT: C 185 ILE cc_start: 0.8699 (mm) cc_final: 0.8321 (mm) REVERT: D 62 LYS cc_start: 0.8987 (tttp) cc_final: 0.8736 (tttp) REVERT: D 68 LYS cc_start: 0.9372 (mttt) cc_final: 0.8839 (mttm) REVERT: D 87 ASN cc_start: 0.8982 (m-40) cc_final: 0.8592 (m-40) REVERT: E 65 ILE cc_start: 0.9555 (pt) cc_final: 0.8640 (pt) REVERT: E 67 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8354 (mm-30) REVERT: F 69 GLU cc_start: 0.9211 (mp0) cc_final: 0.8491 (mp0) REVERT: F 158 MET cc_start: 0.6797 (mmp) cc_final: 0.6558 (mmm) REVERT: G 3 ASN cc_start: 0.8333 (p0) cc_final: 0.7924 (p0) REVERT: G 156 LYS cc_start: 0.8607 (ptpp) cc_final: 0.8308 (mtpp) REVERT: H 62 GLN cc_start: 0.8938 (mp10) cc_final: 0.8441 (mp10) REVERT: I 58 LEU cc_start: 0.9589 (mt) cc_final: 0.9238 (tp) REVERT: I 62 ASN cc_start: 0.9194 (m-40) cc_final: 0.8800 (m110) REVERT: J 93 LEU cc_start: 0.9386 (tt) cc_final: 0.9171 (tt) REVERT: J 96 GLU cc_start: 0.8478 (pp20) cc_final: 0.7976 (pp20) REVERT: J 148 MET cc_start: 0.8913 (mmm) cc_final: 0.8701 (mmm) REVERT: K 68 LYS cc_start: 0.8945 (ttmm) cc_final: 0.8657 (ttmm) REVERT: K 69 MET cc_start: 0.9019 (tpp) cc_final: 0.8446 (tpp) REVERT: L 45 MET cc_start: 0.1924 (mmm) cc_final: 0.1590 (mmm) REVERT: L 93 MET cc_start: 0.8060 (mtt) cc_final: 0.7836 (mtt) REVERT: M 83 MET cc_start: 0.9037 (tpp) cc_final: 0.8286 (tpp) REVERT: M 91 MET cc_start: 0.8360 (mmp) cc_final: 0.7987 (mmm) REVERT: M 158 MET cc_start: 0.7905 (mtt) cc_final: 0.7703 (mtt) REVERT: N 50 MET cc_start: 0.8299 (ptm) cc_final: 0.7234 (ppp) REVERT: N 56 ASP cc_start: 0.7878 (t0) cc_final: 0.7537 (t0) REVERT: V 71 PHE cc_start: 0.8544 (m-10) cc_final: 0.8224 (m-80) REVERT: W 109 LEU cc_start: 0.8642 (mm) cc_final: 0.8394 (tp) REVERT: X 5 TYR cc_start: 0.7867 (m-80) cc_final: 0.7533 (m-10) REVERT: Y 77 THR cc_start: 0.7659 (m) cc_final: 0.7197 (m) REVERT: Z 71 ASP cc_start: 0.6416 (t70) cc_final: 0.6158 (t70) REVERT: Z 86 LYS cc_start: 0.9331 (mttm) cc_final: 0.8880 (tppt) REVERT: Z 90 ASP cc_start: 0.8823 (m-30) cc_final: 0.8616 (m-30) REVERT: Z 98 ASN cc_start: 0.9027 (m-40) cc_final: 0.8792 (m-40) REVERT: Z 133 MET cc_start: 0.6828 (ttt) cc_final: 0.5755 (tmm) REVERT: Z 203 LYS cc_start: 0.9248 (tttt) cc_final: 0.8938 (tptt) REVERT: a 62 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8288 (mtpt) REVERT: a 94 ASP cc_start: 0.8917 (m-30) cc_final: 0.8703 (m-30) REVERT: b 75 MET cc_start: 0.7328 (tpp) cc_final: 0.7118 (tpp) REVERT: b 89 ASP cc_start: 0.9302 (m-30) cc_final: 0.8935 (p0) REVERT: b 93 GLU cc_start: 0.9176 (pt0) cc_final: 0.8406 (pp20) REVERT: b 97 ASN cc_start: 0.9059 (m-40) cc_final: 0.8179 (m-40) REVERT: b 150 MET cc_start: 0.7177 (ttm) cc_final: 0.6393 (tmm) REVERT: O 96 TYR cc_start: 0.8122 (m-80) cc_final: 0.7614 (m-80) REVERT: O 131 MET cc_start: 0.8713 (mmm) cc_final: 0.8338 (mmm) REVERT: O 196 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8206 (mm-30) REVERT: Q 66 TYR cc_start: 0.8424 (m-80) cc_final: 0.8174 (m-80) REVERT: Q 84 ASN cc_start: 0.9376 (t0) cc_final: 0.9016 (m110) REVERT: Q 95 GLN cc_start: 0.8866 (mp-120) cc_final: 0.8628 (mm-40) REVERT: Q 174 MET cc_start: 0.8572 (mmp) cc_final: 0.8336 (mmm) REVERT: Q 201 MET cc_start: 0.8386 (tpt) cc_final: 0.8113 (tpt) REVERT: Q 228 LEU cc_start: 0.9166 (mt) cc_final: 0.8797 (mp) REVERT: R 77 THR cc_start: 0.7578 (m) cc_final: 0.7214 (m) REVERT: S 201 ILE cc_start: 0.9570 (mt) cc_final: 0.9280 (tp) REVERT: S 206 MET cc_start: 0.8521 (mmt) cc_final: 0.7790 (mmm) REVERT: T 26 MET cc_start: 0.7348 (mmp) cc_final: 0.6563 (mmm) REVERT: U 135 PHE cc_start: 0.7588 (p90) cc_final: 0.7137 (p90) REVERT: U 136 MET cc_start: 0.5436 (mpp) cc_final: 0.5232 (mpp) outliers start: 1 outliers final: 1 residues processed: 789 average time/residue: 0.6017 time to fit residues: 776.4464 Evaluate side-chains 615 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 614 time to evaluate : 6.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 567 optimal weight: 30.0000 chunk 66 optimal weight: 2.9990 chunk 335 optimal weight: 5.9990 chunk 429 optimal weight: 8.9990 chunk 332 optimal weight: 20.0000 chunk 495 optimal weight: 30.0000 chunk 328 optimal weight: 0.0670 chunk 586 optimal weight: 20.0000 chunk 366 optimal weight: 10.0000 chunk 357 optimal weight: 0.8980 chunk 270 optimal weight: 20.0000 overall best weight: 3.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 ASN ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN K 101 ASN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 224 HIS ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 GLN ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 99 HIS ** T 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 105 ASN U 224 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 49014 Z= 0.205 Angle : 0.585 10.012 66222 Z= 0.303 Chirality : 0.043 0.230 7441 Planarity : 0.004 0.100 8531 Dihedral : 4.604 30.437 6803 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.11), residues: 6137 helix: 0.22 (0.11), residues: 2191 sheet: -0.17 (0.13), residues: 1500 loop : -0.55 (0.13), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP U 215 HIS 0.010 0.001 HIS U 224 PHE 0.036 0.002 PHE S 101 TYR 0.023 0.001 TYR J 95 ARG 0.011 0.001 ARG R 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 783 time to evaluate : 4.704 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.7653 (ptp) cc_final: 0.7257 (ptp) REVERT: A 134 TYR cc_start: 0.8852 (m-80) cc_final: 0.8524 (m-80) REVERT: B 145 ASP cc_start: 0.7523 (t0) cc_final: 0.7304 (t0) REVERT: C 68 PHE cc_start: 0.8017 (t80) cc_final: 0.7444 (t80) REVERT: C 96 GLU cc_start: 0.8023 (pp20) cc_final: 0.7667 (pp20) REVERT: C 130 MET cc_start: 0.7178 (ttm) cc_final: 0.6068 (ttm) REVERT: C 161 HIS cc_start: 0.8162 (m-70) cc_final: 0.7751 (m170) REVERT: C 185 ILE cc_start: 0.8699 (mm) cc_final: 0.8348 (mm) REVERT: D 37 LYS cc_start: 0.8860 (tppp) cc_final: 0.8556 (tptp) REVERT: D 62 LYS cc_start: 0.8898 (tttp) cc_final: 0.8664 (tttp) REVERT: D 68 LYS cc_start: 0.9351 (mttt) cc_final: 0.9138 (mttt) REVERT: D 69 MET cc_start: 0.8128 (tpp) cc_final: 0.7891 (tpp) REVERT: D 87 ASN cc_start: 0.8975 (m-40) cc_final: 0.8491 (m110) REVERT: E 62 GLN cc_start: 0.9202 (mm-40) cc_final: 0.8909 (mm-40) REVERT: E 65 ILE cc_start: 0.9303 (pt) cc_final: 0.8694 (pt) REVERT: F 69 GLU cc_start: 0.9177 (mp0) cc_final: 0.8487 (mp0) REVERT: F 108 ASN cc_start: 0.8735 (p0) cc_final: 0.8519 (p0) REVERT: G 3 ASN cc_start: 0.8446 (p0) cc_final: 0.7844 (p0) REVERT: H 62 GLN cc_start: 0.8831 (mp10) cc_final: 0.8334 (mp10) REVERT: H 120 MET cc_start: 0.8463 (tmm) cc_final: 0.8089 (tmm) REVERT: H 136 TYR cc_start: 0.7298 (m-10) cc_final: 0.6822 (m-10) REVERT: I 58 LEU cc_start: 0.9562 (mt) cc_final: 0.9212 (tp) REVERT: I 62 ASN cc_start: 0.9254 (m-40) cc_final: 0.8851 (m110) REVERT: J 70 LEU cc_start: 0.9395 (tt) cc_final: 0.9064 (tt) REVERT: J 93 LEU cc_start: 0.9375 (tt) cc_final: 0.9164 (tt) REVERT: J 96 GLU cc_start: 0.8414 (pp20) cc_final: 0.7936 (pp20) REVERT: K 38 MET cc_start: 0.8695 (mmm) cc_final: 0.8384 (tpp) REVERT: K 69 MET cc_start: 0.8972 (tpp) cc_final: 0.8104 (tpp) REVERT: L 45 MET cc_start: 0.2095 (mmm) cc_final: 0.1698 (mmm) REVERT: L 93 MET cc_start: 0.8077 (mtt) cc_final: 0.7867 (mtt) REVERT: L 139 MET cc_start: 0.7971 (ttp) cc_final: 0.7719 (tmm) REVERT: M 71 ARG cc_start: 0.8991 (mmm-85) cc_final: 0.8540 (mmm-85) REVERT: M 83 MET cc_start: 0.9077 (tpp) cc_final: 0.8378 (tpp) REVERT: M 91 MET cc_start: 0.8291 (mmp) cc_final: 0.7910 (mmm) REVERT: N 50 MET cc_start: 0.8430 (ptm) cc_final: 0.7391 (ppp) REVERT: N 56 ASP cc_start: 0.7921 (t0) cc_final: 0.7396 (t0) REVERT: N 59 ASP cc_start: 0.5832 (p0) cc_final: 0.4990 (p0) REVERT: V 71 PHE cc_start: 0.8540 (m-10) cc_final: 0.8183 (m-80) REVERT: X 5 TYR cc_start: 0.7838 (m-80) cc_final: 0.7624 (m-10) REVERT: Y 77 THR cc_start: 0.7679 (m) cc_final: 0.7219 (m) REVERT: Z 86 LYS cc_start: 0.9328 (mttm) cc_final: 0.9031 (tppt) REVERT: Z 98 ASN cc_start: 0.9056 (m-40) cc_final: 0.8763 (m-40) REVERT: Z 133 MET cc_start: 0.7066 (ttt) cc_final: 0.5691 (tmm) REVERT: Z 203 LYS cc_start: 0.9261 (tttt) cc_final: 0.8810 (tppt) REVERT: a 62 LYS cc_start: 0.8667 (mmmt) cc_final: 0.8369 (mtpt) REVERT: a 94 ASP cc_start: 0.8925 (m-30) cc_final: 0.8688 (m-30) REVERT: a 154 PHE cc_start: 0.7803 (m-80) cc_final: 0.7560 (m-80) REVERT: b 75 MET cc_start: 0.7272 (tpp) cc_final: 0.6996 (tpp) REVERT: b 89 ASP cc_start: 0.9243 (m-30) cc_final: 0.8901 (p0) REVERT: b 93 GLU cc_start: 0.9090 (pt0) cc_final: 0.8265 (pp20) REVERT: b 97 ASN cc_start: 0.9071 (m-40) cc_final: 0.8146 (m-40) REVERT: b 150 MET cc_start: 0.7134 (ttm) cc_final: 0.6481 (tmm) REVERT: O 96 TYR cc_start: 0.8021 (m-80) cc_final: 0.7632 (m-80) REVERT: O 102 LYS cc_start: 0.8693 (tppt) cc_final: 0.8483 (tptp) REVERT: O 131 MET cc_start: 0.8719 (mmm) cc_final: 0.8392 (mmm) REVERT: O 196 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8401 (tm-30) REVERT: Q 84 ASN cc_start: 0.9372 (t0) cc_final: 0.9049 (m110) REVERT: Q 95 GLN cc_start: 0.8809 (mp-120) cc_final: 0.8577 (mm-40) REVERT: Q 174 MET cc_start: 0.8667 (mmp) cc_final: 0.8399 (mmm) REVERT: Q 201 MET cc_start: 0.8392 (tpt) cc_final: 0.8130 (tpt) REVERT: Q 228 LEU cc_start: 0.9158 (mt) cc_final: 0.8791 (mp) REVERT: R 71 MET cc_start: 0.7080 (tmm) cc_final: 0.6858 (tmm) REVERT: R 77 THR cc_start: 0.7510 (m) cc_final: 0.7146 (m) REVERT: S 101 PHE cc_start: 0.7234 (m-80) cc_final: 0.6738 (m-80) REVERT: S 201 ILE cc_start: 0.9567 (mt) cc_final: 0.9286 (tp) REVERT: T 26 MET cc_start: 0.7294 (mmp) cc_final: 0.6509 (mmm) REVERT: T 208 LYS cc_start: 0.9234 (pptt) cc_final: 0.8856 (tptp) REVERT: U 135 PHE cc_start: 0.7571 (p90) cc_final: 0.7361 (p90) outliers start: 0 outliers final: 0 residues processed: 783 average time/residue: 0.6110 time to fit residues: 780.2416 Evaluate side-chains 612 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 612 time to evaluate : 5.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 362 optimal weight: 20.0000 chunk 234 optimal weight: 10.0000 chunk 349 optimal weight: 20.0000 chunk 176 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 372 optimal weight: 9.9990 chunk 399 optimal weight: 3.9990 chunk 289 optimal weight: 30.0000 chunk 54 optimal weight: 3.9990 chunk 460 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 ASN ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 ASN K 101 ASN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 13 HIS ** V 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 40 ASN ** X 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN O 193 GLN ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 105 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.6680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 49014 Z= 0.217 Angle : 0.598 10.845 66222 Z= 0.308 Chirality : 0.043 0.231 7441 Planarity : 0.004 0.084 8531 Dihedral : 4.619 30.501 6803 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.52 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.11), residues: 6137 helix: 0.29 (0.11), residues: 2186 sheet: -0.13 (0.13), residues: 1512 loop : -0.59 (0.13), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP G 91 HIS 0.009 0.001 HIS A 77 PHE 0.035 0.002 PHE S 101 TYR 0.039 0.001 TYR Q 136 ARG 0.012 0.001 ARG R 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 769 time to evaluate : 6.291 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.7646 (ptp) cc_final: 0.7376 (ptp) REVERT: A 134 TYR cc_start: 0.8847 (m-80) cc_final: 0.8515 (m-80) REVERT: C 68 PHE cc_start: 0.7862 (t80) cc_final: 0.7509 (t80) REVERT: C 86 LEU cc_start: 0.8735 (tp) cc_final: 0.8215 (tp) REVERT: C 96 GLU cc_start: 0.7979 (pp20) cc_final: 0.7665 (pp20) REVERT: C 130 MET cc_start: 0.7238 (ttm) cc_final: 0.6582 (ttm) REVERT: C 161 HIS cc_start: 0.8015 (m-70) cc_final: 0.7592 (m170) REVERT: D 60 ILE cc_start: 0.9336 (pt) cc_final: 0.9066 (pt) REVERT: D 62 LYS cc_start: 0.8854 (tttp) cc_final: 0.8635 (tttp) REVERT: D 69 MET cc_start: 0.8056 (tpp) cc_final: 0.7806 (tpp) REVERT: D 87 ASN cc_start: 0.8932 (m-40) cc_final: 0.8533 (m-40) REVERT: E 62 GLN cc_start: 0.9225 (mm-40) cc_final: 0.8873 (mm-40) REVERT: E 63 CYS cc_start: 0.8815 (t) cc_final: 0.8612 (t) REVERT: E 65 ILE cc_start: 0.9300 (pt) cc_final: 0.8633 (pt) REVERT: E 67 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8496 (mm-30) REVERT: E 139 MET cc_start: 0.8197 (tmm) cc_final: 0.7833 (tmm) REVERT: F 69 GLU cc_start: 0.9219 (mp0) cc_final: 0.8606 (mp0) REVERT: F 158 MET cc_start: 0.6493 (mmp) cc_final: 0.6173 (mmm) REVERT: G 3 ASN cc_start: 0.8270 (p0) cc_final: 0.7705 (p0) REVERT: H 4 MET cc_start: 0.6666 (tpt) cc_final: 0.6137 (tpp) REVERT: H 62 GLN cc_start: 0.8951 (mp10) cc_final: 0.8383 (mp10) REVERT: H 120 MET cc_start: 0.8289 (tmm) cc_final: 0.7954 (tmm) REVERT: H 136 TYR cc_start: 0.7317 (m-10) cc_final: 0.6906 (m-10) REVERT: I 58 LEU cc_start: 0.9590 (mt) cc_final: 0.9235 (tp) REVERT: I 62 ASN cc_start: 0.9199 (m110) cc_final: 0.8803 (m110) REVERT: J 73 TYR cc_start: 0.8585 (t80) cc_final: 0.8381 (t80) REVERT: J 96 GLU cc_start: 0.8317 (pp20) cc_final: 0.7900 (pp20) REVERT: L 45 MET cc_start: 0.2290 (mmm) cc_final: 0.1829 (mmm) REVERT: L 93 MET cc_start: 0.8263 (mtt) cc_final: 0.7992 (mtt) REVERT: L 139 MET cc_start: 0.8009 (ttp) cc_final: 0.7572 (tmm) REVERT: M 71 ARG cc_start: 0.9053 (mmm-85) cc_final: 0.8599 (mmm-85) REVERT: M 74 MET cc_start: 0.8992 (mtp) cc_final: 0.8790 (mtp) REVERT: M 83 MET cc_start: 0.9035 (tpp) cc_final: 0.8345 (tpp) REVERT: M 91 MET cc_start: 0.8291 (mmp) cc_final: 0.7864 (mmp) REVERT: M 158 MET cc_start: 0.7981 (mtt) cc_final: 0.7627 (mtt) REVERT: N 50 MET cc_start: 0.8468 (ptm) cc_final: 0.7388 (ppp) REVERT: V 71 PHE cc_start: 0.8531 (m-10) cc_final: 0.8173 (m-80) REVERT: V 94 ARG cc_start: 0.8589 (ptt180) cc_final: 0.8228 (ptt180) REVERT: V 239 HIS cc_start: 0.8335 (m90) cc_final: 0.8046 (m90) REVERT: X 5 TYR cc_start: 0.7892 (m-80) cc_final: 0.7642 (m-10) REVERT: Y 77 THR cc_start: 0.7714 (m) cc_final: 0.7253 (m) REVERT: Z 86 LYS cc_start: 0.9310 (mttm) cc_final: 0.8841 (tppt) REVERT: Z 90 ASP cc_start: 0.8801 (m-30) cc_final: 0.8535 (m-30) REVERT: Z 98 ASN cc_start: 0.9024 (m-40) cc_final: 0.8697 (m-40) REVERT: Z 133 MET cc_start: 0.7087 (ttt) cc_final: 0.5855 (tmm) REVERT: Z 203 LYS cc_start: 0.9278 (tttt) cc_final: 0.8935 (tptt) REVERT: a 41 LYS cc_start: 0.9189 (tttt) cc_final: 0.8730 (ptpt) REVERT: a 62 LYS cc_start: 0.8672 (mmmt) cc_final: 0.8410 (mtpt) REVERT: a 94 ASP cc_start: 0.8836 (m-30) cc_final: 0.8596 (m-30) REVERT: b 89 ASP cc_start: 0.9238 (m-30) cc_final: 0.8927 (p0) REVERT: b 93 GLU cc_start: 0.9021 (pt0) cc_final: 0.8134 (pp20) REVERT: b 97 ASN cc_start: 0.9105 (m-40) cc_final: 0.8218 (m-40) REVERT: b 150 MET cc_start: 0.7136 (ttm) cc_final: 0.6699 (tmm) REVERT: O 96 TYR cc_start: 0.8180 (m-80) cc_final: 0.7752 (m-80) REVERT: O 131 MET cc_start: 0.8712 (mmm) cc_final: 0.8363 (mmm) REVERT: Q 72 MET cc_start: 0.8448 (ptm) cc_final: 0.8203 (ptm) REVERT: Q 84 ASN cc_start: 0.9357 (t0) cc_final: 0.9045 (m110) REVERT: Q 95 GLN cc_start: 0.8804 (mp-120) cc_final: 0.8562 (mm-40) REVERT: Q 201 MET cc_start: 0.8373 (tpt) cc_final: 0.8108 (tpt) REVERT: Q 228 LEU cc_start: 0.9151 (mt) cc_final: 0.8785 (mp) REVERT: R 71 MET cc_start: 0.7169 (tmm) cc_final: 0.6917 (tmm) REVERT: R 77 THR cc_start: 0.7620 (m) cc_final: 0.7237 (m) REVERT: S 101 PHE cc_start: 0.7161 (m-80) cc_final: 0.6623 (m-80) REVERT: S 103 TYR cc_start: 0.8301 (m-80) cc_final: 0.8038 (m-80) REVERT: S 201 ILE cc_start: 0.9573 (mt) cc_final: 0.9281 (tp) REVERT: S 206 MET cc_start: 0.8451 (mmt) cc_final: 0.7740 (mmm) REVERT: T 26 MET cc_start: 0.7296 (mmp) cc_final: 0.6517 (mmm) REVERT: T 185 ASN cc_start: 0.9049 (m-40) cc_final: 0.8841 (t0) REVERT: U 135 PHE cc_start: 0.7717 (p90) cc_final: 0.7350 (p90) outliers start: 0 outliers final: 0 residues processed: 769 average time/residue: 0.6077 time to fit residues: 763.5882 Evaluate side-chains 599 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 599 time to evaluate : 5.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 533 optimal weight: 30.0000 chunk 561 optimal weight: 7.9990 chunk 512 optimal weight: 9.9990 chunk 546 optimal weight: 7.9990 chunk 328 optimal weight: 5.9990 chunk 237 optimal weight: 1.9990 chunk 428 optimal weight: 10.0000 chunk 167 optimal weight: 20.0000 chunk 493 optimal weight: 9.9990 chunk 516 optimal weight: 20.0000 chunk 544 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 ASN ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 94 HIS ** Y 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 GLN ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 200 GLN ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 105 ASN U 224 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.6915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 49014 Z= 0.289 Angle : 0.651 13.108 66222 Z= 0.337 Chirality : 0.044 0.272 7441 Planarity : 0.005 0.105 8531 Dihedral : 4.794 31.625 6803 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.98 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.10), residues: 6137 helix: 0.18 (0.11), residues: 2196 sheet: -0.27 (0.13), residues: 1520 loop : -0.68 (0.13), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP O 189 HIS 0.009 0.001 HIS A 77 PHE 0.032 0.002 PHE S 101 TYR 0.035 0.002 TYR O 103 ARG 0.013 0.001 ARG R 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 738 time to evaluate : 5.619 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.7647 (ptp) cc_final: 0.7349 (ptp) REVERT: A 134 TYR cc_start: 0.8815 (m-80) cc_final: 0.8431 (m-80) REVERT: C 130 MET cc_start: 0.7077 (ttm) cc_final: 0.5994 (ttm) REVERT: C 161 HIS cc_start: 0.8086 (m-70) cc_final: 0.7659 (m170) REVERT: D 87 ASN cc_start: 0.8926 (m-40) cc_final: 0.8476 (m-40) REVERT: D 168 GLN cc_start: 0.8268 (mp10) cc_final: 0.8062 (mp10) REVERT: D 186 ASN cc_start: 0.9085 (m-40) cc_final: 0.8884 (m-40) REVERT: E 62 GLN cc_start: 0.9259 (mm-40) cc_final: 0.8876 (mm-40) REVERT: E 97 MET cc_start: 0.6134 (tmm) cc_final: 0.5775 (tmm) REVERT: E 139 MET cc_start: 0.8139 (tmm) cc_final: 0.7760 (tmm) REVERT: F 69 GLU cc_start: 0.9379 (mp0) cc_final: 0.8746 (mp0) REVERT: F 158 MET cc_start: 0.6541 (mmp) cc_final: 0.6311 (mmm) REVERT: G 3 ASN cc_start: 0.8434 (p0) cc_final: 0.8028 (p0) REVERT: G 5 MET cc_start: 0.6735 (mmt) cc_final: 0.6278 (mmm) REVERT: G 83 TYR cc_start: 0.8362 (m-80) cc_final: 0.7985 (m-10) REVERT: G 99 ARG cc_start: 0.8531 (mtt-85) cc_final: 0.8080 (mmm-85) REVERT: H 4 MET cc_start: 0.6687 (tpt) cc_final: 0.5924 (tpp) REVERT: H 62 GLN cc_start: 0.8716 (mp10) cc_final: 0.8291 (mp10) REVERT: H 120 MET cc_start: 0.8301 (tmm) cc_final: 0.7957 (tmm) REVERT: I 58 LEU cc_start: 0.9588 (mt) cc_final: 0.9264 (tp) REVERT: I 62 ASN cc_start: 0.9225 (m110) cc_final: 0.8886 (m110) REVERT: J 71 ASN cc_start: 0.9279 (m110) cc_final: 0.8966 (m-40) REVERT: J 96 GLU cc_start: 0.8410 (pp20) cc_final: 0.7964 (pp20) REVERT: J 170 MET cc_start: 0.8505 (mtp) cc_final: 0.8139 (mtp) REVERT: L 45 MET cc_start: 0.2352 (mmm) cc_final: 0.2007 (mmm) REVERT: L 93 MET cc_start: 0.8274 (mtt) cc_final: 0.8031 (mtt) REVERT: L 139 MET cc_start: 0.8088 (ttp) cc_final: 0.7856 (tmm) REVERT: M 71 ARG cc_start: 0.9050 (mmm-85) cc_final: 0.8557 (mmm-85) REVERT: M 74 MET cc_start: 0.9061 (mtp) cc_final: 0.8818 (mtp) REVERT: M 83 MET cc_start: 0.8940 (tpp) cc_final: 0.8363 (tpt) REVERT: M 91 MET cc_start: 0.8351 (mmp) cc_final: 0.7723 (mmp) REVERT: M 158 MET cc_start: 0.8028 (mtt) cc_final: 0.7751 (mtt) REVERT: N 50 MET cc_start: 0.8514 (ptm) cc_final: 0.8172 (ptp) REVERT: N 127 MET cc_start: 0.7789 (ttt) cc_final: 0.7311 (ttt) REVERT: V 71 PHE cc_start: 0.8505 (m-10) cc_final: 0.8125 (m-80) REVERT: V 94 ARG cc_start: 0.8584 (ptt180) cc_final: 0.8104 (ptt180) REVERT: V 239 HIS cc_start: 0.8445 (m90) cc_final: 0.8183 (m90) REVERT: W 205 ASP cc_start: 0.8395 (m-30) cc_final: 0.8066 (p0) REVERT: X 5 TYR cc_start: 0.8046 (m-80) cc_final: 0.7805 (m-10) REVERT: Y 77 THR cc_start: 0.7629 (m) cc_final: 0.7103 (m) REVERT: Y 86 ARG cc_start: 0.8462 (mtm180) cc_final: 0.8220 (mtm180) REVERT: Y 114 LEU cc_start: 0.8540 (mt) cc_final: 0.8303 (mt) REVERT: Z 69 GLU cc_start: 0.8783 (tt0) cc_final: 0.8554 (tt0) REVERT: Z 81 LEU cc_start: 0.8870 (tp) cc_final: 0.8543 (tt) REVERT: Z 86 LYS cc_start: 0.9368 (mttm) cc_final: 0.8891 (tppt) REVERT: Z 90 ASP cc_start: 0.9129 (m-30) cc_final: 0.8657 (m-30) REVERT: Z 98 ASN cc_start: 0.8962 (m-40) cc_final: 0.8633 (m-40) REVERT: Z 133 MET cc_start: 0.7136 (ttt) cc_final: 0.6845 (tpp) REVERT: Z 203 LYS cc_start: 0.9281 (tttt) cc_final: 0.8974 (tptt) REVERT: a 41 LYS cc_start: 0.9228 (tttt) cc_final: 0.8723 (ptpt) REVERT: a 62 LYS cc_start: 0.8678 (mmmt) cc_final: 0.8459 (mtpt) REVERT: a 94 ASP cc_start: 0.8964 (m-30) cc_final: 0.8755 (m-30) REVERT: b 75 MET cc_start: 0.8396 (tpt) cc_final: 0.7938 (tpp) REVERT: b 89 ASP cc_start: 0.9324 (m-30) cc_final: 0.8931 (p0) REVERT: b 93 GLU cc_start: 0.9048 (pt0) cc_final: 0.8065 (pp20) REVERT: b 97 ASN cc_start: 0.9118 (m-40) cc_final: 0.8234 (m-40) REVERT: b 150 MET cc_start: 0.7082 (ttm) cc_final: 0.6534 (tmm) REVERT: O 96 TYR cc_start: 0.8016 (m-80) cc_final: 0.7609 (m-80) REVERT: O 131 MET cc_start: 0.8746 (mmm) cc_final: 0.8257 (mmm) REVERT: P 109 LEU cc_start: 0.8797 (tt) cc_final: 0.8334 (tp) REVERT: Q 84 ASN cc_start: 0.9371 (t0) cc_final: 0.9049 (m110) REVERT: Q 201 MET cc_start: 0.8374 (tpt) cc_final: 0.8084 (tpt) REVERT: Q 228 LEU cc_start: 0.9175 (mt) cc_final: 0.8831 (mp) REVERT: R 77 THR cc_start: 0.7718 (m) cc_final: 0.7351 (m) REVERT: S 101 PHE cc_start: 0.7314 (m-80) cc_final: 0.6765 (m-80) REVERT: S 103 TYR cc_start: 0.8356 (m-80) cc_final: 0.7745 (m-80) REVERT: S 201 ILE cc_start: 0.9580 (mt) cc_final: 0.9292 (tp) REVERT: S 206 MET cc_start: 0.8683 (mmt) cc_final: 0.7995 (mmm) REVERT: T 26 MET cc_start: 0.7322 (mmp) cc_final: 0.6567 (mmm) REVERT: T 185 ASN cc_start: 0.9016 (m-40) cc_final: 0.8815 (m-40) REVERT: U 135 PHE cc_start: 0.8003 (p90) cc_final: 0.7599 (p90) outliers start: 0 outliers final: 0 residues processed: 738 average time/residue: 0.6110 time to fit residues: 736.0554 Evaluate side-chains 581 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 581 time to evaluate : 6.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 358 optimal weight: 50.0000 chunk 577 optimal weight: 9.9990 chunk 352 optimal weight: 6.9990 chunk 273 optimal weight: 1.9990 chunk 401 optimal weight: 20.0000 chunk 605 optimal weight: 0.0470 chunk 557 optimal weight: 0.8980 chunk 482 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 372 optimal weight: 20.0000 chunk 295 optimal weight: 8.9990 overall best weight: 3.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 148 GLN ** W 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 21 GLN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 GLN ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 190 HIS U 22 GLN U 105 ASN ** U 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.6982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 49014 Z= 0.207 Angle : 0.609 12.088 66222 Z= 0.314 Chirality : 0.044 0.221 7441 Planarity : 0.004 0.097 8531 Dihedral : 4.720 32.862 6803 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.73 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.11), residues: 6137 helix: 0.32 (0.11), residues: 2203 sheet: -0.26 (0.13), residues: 1534 loop : -0.66 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP N 91 HIS 0.010 0.001 HIS Y 94 PHE 0.031 0.002 PHE O 187 TYR 0.029 0.001 TYR O 103 ARG 0.014 0.001 ARG R 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 765 time to evaluate : 5.871 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: symmetry clash revert: 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 119 MET cc_start: 0.7619 (ptp) cc_final: 0.7400 (ptp) REVERT: A 134 TYR cc_start: 0.8833 (m-80) cc_final: 0.8426 (m-80) REVERT: C 74 GLU cc_start: 0.8662 (tp30) cc_final: 0.8322 (tp30) REVERT: C 130 MET cc_start: 0.6628 (ttm) cc_final: 0.5839 (ttm) REVERT: C 161 HIS cc_start: 0.8041 (m-70) cc_final: 0.7630 (m170) REVERT: D 60 ILE cc_start: 0.9317 (pt) cc_final: 0.9097 (pt) REVERT: D 87 ASN cc_start: 0.8952 (m-40) cc_final: 0.8535 (m-40) REVERT: E 62 GLN cc_start: 0.9235 (mm-40) cc_final: 0.8889 (mm-40) REVERT: E 63 CYS cc_start: 0.8775 (t) cc_final: 0.8141 (t) REVERT: E 65 ILE cc_start: 0.9322 (pt) cc_final: 0.8769 (pt) REVERT: E 69 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.8218 (ptt180) REVERT: E 97 MET cc_start: 0.6003 (tmm) cc_final: 0.5635 (tmm) REVERT: E 139 MET cc_start: 0.8218 (tmm) cc_final: 0.7822 (tmm) REVERT: F 69 GLU cc_start: 0.9335 (mp0) cc_final: 0.8993 (mp0) REVERT: F 74 MET cc_start: 0.9154 (mtp) cc_final: 0.8936 (mtp) REVERT: G 3 ASN cc_start: 0.8451 (p0) cc_final: 0.8020 (p0) REVERT: G 5 MET cc_start: 0.6882 (mmt) cc_final: 0.6512 (mmm) REVERT: G 99 ARG cc_start: 0.8405 (mtt-85) cc_final: 0.7970 (mmm-85) REVERT: H 4 MET cc_start: 0.6596 (tpt) cc_final: 0.5874 (tpp) REVERT: H 62 GLN cc_start: 0.8812 (mp10) cc_final: 0.8334 (mp10) REVERT: H 119 MET cc_start: 0.8180 (ptp) cc_final: 0.7952 (ptm) REVERT: H 120 MET cc_start: 0.8269 (tmm) cc_final: 0.7913 (tmm) REVERT: I 54 MET cc_start: 0.8438 (mmp) cc_final: 0.8038 (mmm) REVERT: I 58 LEU cc_start: 0.9575 (mt) cc_final: 0.9219 (tp) REVERT: I 62 ASN cc_start: 0.9251 (m110) cc_final: 0.8834 (m110) REVERT: J 84 TYR cc_start: 0.8220 (t80) cc_final: 0.7969 (t80) REVERT: J 87 MET cc_start: 0.8011 (mmm) cc_final: 0.7439 (mmm) REVERT: J 96 GLU cc_start: 0.8370 (pp20) cc_final: 0.7797 (pp20) REVERT: J 170 MET cc_start: 0.8583 (mtp) cc_final: 0.8115 (mtp) REVERT: K 38 MET cc_start: 0.8205 (mmm) cc_final: 0.7440 (tpt) REVERT: L 45 MET cc_start: 0.2533 (mmm) cc_final: 0.2157 (mmm) REVERT: L 93 MET cc_start: 0.8239 (mtt) cc_final: 0.8013 (mtt) REVERT: L 139 MET cc_start: 0.8048 (ttp) cc_final: 0.7756 (tmm) REVERT: M 71 ARG cc_start: 0.9095 (mmm-85) cc_final: 0.8581 (mmm-85) REVERT: M 74 MET cc_start: 0.9012 (mtp) cc_final: 0.8783 (mtp) REVERT: M 83 MET cc_start: 0.8912 (tpp) cc_final: 0.8337 (tpt) REVERT: M 91 MET cc_start: 0.8292 (mmp) cc_final: 0.7753 (mmp) REVERT: M 158 MET cc_start: 0.8030 (mtt) cc_final: 0.7637 (mtt) REVERT: N 50 MET cc_start: 0.8541 (ptm) cc_final: 0.8187 (ptp) REVERT: V 71 PHE cc_start: 0.8549 (m-10) cc_final: 0.8168 (m-80) REVERT: V 94 ARG cc_start: 0.8630 (ptt180) cc_final: 0.8102 (ptt180) REVERT: V 239 HIS cc_start: 0.8405 (m90) cc_final: 0.8169 (m90) REVERT: W 205 ASP cc_start: 0.8107 (m-30) cc_final: 0.7847 (p0) REVERT: X 5 TYR cc_start: 0.8101 (m-80) cc_final: 0.7875 (m-10) REVERT: X 100 GLN cc_start: 0.8593 (mm110) cc_final: 0.8052 (mm-40) REVERT: Y 77 THR cc_start: 0.7576 (m) cc_final: 0.7049 (m) REVERT: Z 81 LEU cc_start: 0.8884 (tp) cc_final: 0.8624 (tt) REVERT: Z 86 LYS cc_start: 0.9374 (mttm) cc_final: 0.8887 (tppt) REVERT: Z 90 ASP cc_start: 0.9152 (m-30) cc_final: 0.8480 (m-30) REVERT: Z 98 ASN cc_start: 0.8850 (m-40) cc_final: 0.8542 (m-40) REVERT: Z 107 MET cc_start: 0.6663 (tpt) cc_final: 0.5986 (tpt) REVERT: Z 112 VAL cc_start: 0.9140 (t) cc_final: 0.8928 (t) REVERT: Z 133 MET cc_start: 0.7254 (ttt) cc_final: 0.5702 (tmm) REVERT: Z 203 LYS cc_start: 0.9277 (tttt) cc_final: 0.8850 (tptp) REVERT: a 41 LYS cc_start: 0.9185 (tttt) cc_final: 0.8692 (ptpt) REVERT: a 62 LYS cc_start: 0.8636 (mmmt) cc_final: 0.8413 (mtpt) REVERT: a 94 ASP cc_start: 0.8935 (m-30) cc_final: 0.8731 (m-30) REVERT: b 75 MET cc_start: 0.8359 (tpt) cc_final: 0.8002 (tpp) REVERT: b 89 ASP cc_start: 0.9355 (m-30) cc_final: 0.8873 (p0) REVERT: b 93 GLU cc_start: 0.9022 (pt0) cc_final: 0.8093 (pp20) REVERT: b 97 ASN cc_start: 0.9093 (m-40) cc_final: 0.8190 (m-40) REVERT: b 150 MET cc_start: 0.7015 (ttm) cc_final: 0.6528 (tmm) REVERT: O 96 TYR cc_start: 0.8006 (m-80) cc_final: 0.7576 (m-80) REVERT: O 131 MET cc_start: 0.8795 (mmm) cc_final: 0.8260 (mmm) REVERT: Q 84 ASN cc_start: 0.9314 (t0) cc_final: 0.8978 (m110) REVERT: Q 201 MET cc_start: 0.8321 (tpt) cc_final: 0.8068 (tpt) REVERT: Q 228 LEU cc_start: 0.9150 (mt) cc_final: 0.8800 (mp) REVERT: R 77 THR cc_start: 0.7668 (m) cc_final: 0.7258 (m) REVERT: S 101 PHE cc_start: 0.7221 (m-80) cc_final: 0.6713 (m-80) REVERT: S 103 TYR cc_start: 0.8298 (m-80) cc_final: 0.7667 (m-80) REVERT: S 201 ILE cc_start: 0.9554 (mt) cc_final: 0.9251 (tp) REVERT: S 206 MET cc_start: 0.8641 (mmt) cc_final: 0.7992 (mmm) REVERT: T 26 MET cc_start: 0.7298 (mmp) cc_final: 0.6527 (mmm) REVERT: T 49 LEU cc_start: 0.8386 (tp) cc_final: 0.7976 (tt) REVERT: U 135 PHE cc_start: 0.7846 (p90) cc_final: 0.7493 (p90) REVERT: U 150 MET cc_start: 0.6494 (tpp) cc_final: 0.6071 (tpp) outliers start: 0 outliers final: 0 residues processed: 765 average time/residue: 0.6514 time to fit residues: 815.5649 Evaluate side-chains 592 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 592 time to evaluate : 6.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 383 optimal weight: 6.9990 chunk 513 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 444 optimal weight: 40.0000 chunk 71 optimal weight: 20.0000 chunk 134 optimal weight: 20.0000 chunk 483 optimal weight: 7.9990 chunk 202 optimal weight: 9.9990 chunk 496 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 88 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 HIS F 79 ASN ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 ASN J 92 ASN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 GLN ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 227 HIS ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 105 ASN ** U 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 224 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.057124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.048354 restraints weight = 283465.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.049955 restraints weight = 170254.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.051106 restraints weight = 114673.598| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.7161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 49014 Z= 0.259 Angle : 0.638 12.776 66222 Z= 0.329 Chirality : 0.044 0.244 7441 Planarity : 0.004 0.076 8531 Dihedral : 4.812 33.061 6803 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.22 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.11), residues: 6137 helix: 0.21 (0.11), residues: 2200 sheet: -0.38 (0.13), residues: 1555 loop : -0.69 (0.13), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP N 107 HIS 0.010 0.001 HIS H 66 PHE 0.034 0.002 PHE S 101 TYR 0.032 0.002 TYR J 95 ARG 0.012 0.001 ARG b 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13921.21 seconds wall clock time: 251 minutes 10.53 seconds (15070.53 seconds total)