Starting phenix.real_space_refine (version: dev) on Sat Apr 9 17:42:38 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5g_31724/04_2022/7v5g_31724.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5g_31724/04_2022/7v5g_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_31724/04_2022/7v5g_31724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5g_31724/04_2022/7v5g_31724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5g_31724/04_2022/7v5g_31724.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5g_31724/04_2022/7v5g_31724.pdb" } resolution = 4.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4553/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: 25.86, per 1000 atoms: 0.54 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: 18.90 Conformation dependent library (CDL) restraints added in 7.1 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: 2.65 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: 18.75 Time building geometry restraints manager: 20.36 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 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. 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 6.890 Check model and map are aligned: 0.680 Convert atoms to be neutral: 0.420 Process input model: 115.990 Find NCS groups from input model: 4.710 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 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 : 9.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.69 % Favored : 94.18 % Rotamer Outliers : 0.08 % 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 *********************** 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 : 5.981 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 outliers start: 4 outliers final: 0 residues processed: 1809 average time/residue: 0.7185 time to fit residues: 2016.3574 Evaluate side-chains 851 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 851 time to evaluate : 5.864 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.7833 ------------------------------------------------------------------------------- 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: 30.0000 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: 20.0000 chunk 552 optimal weight: 20.0000 overall best weight: 12.7994 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS E 175 ASN F 36 HIS F 79 ASN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 71 ASN H 106 GLN ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 GLN ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN K 63 ASN K 87 ASN M 108 ASN ** M 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 151 GLN 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 119 GLN X 146 GLN X 155 ASN ** X 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 94 HIS ** Z 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 143 ASN O 12 HIS ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 150 GLN P 51 GLN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 188 HIS P 206 ASN Q 88 ASN ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 240 HIS ** R 54 GLN ** 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: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.088 49014 Z= 0.521 Angle : 0.874 12.620 66222 Z= 0.461 Chirality : 0.050 0.316 7441 Planarity : 0.007 0.151 8531 Dihedral : 5.380 36.424 6803 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 25.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.24 % Favored : 96.69 % Rotamer Outliers : 0.12 % 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: -1.59 (0.10), residues: 6137 helix: -1.45 (0.10), residues: 2139 sheet: -0.61 (0.12), residues: 1460 loop : -0.71 (0.12), residues: 2538 *********************** 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 948 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 942 time to evaluate : 5.552 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 outliers start: 6 outliers final: 0 residues processed: 946 average time/residue: 0.6549 time to fit residues: 991.3297 Evaluate side-chains 621 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 621 time to evaluate : 6.026 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.9389 ------------------------------------------------------------------------------- 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: 0.0570 chunk 171 optimal weight: 7.9990 chunk 459 optimal weight: 8.9990 chunk 375 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 553 optimal weight: 8.9990 chunk 597 optimal weight: 7.9990 chunk 492 optimal weight: 0.7980 chunk 548 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 443 optimal weight: 30.0000 overall best weight: 3.3704 ------------------------------------------------------------------------------- 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 193 ASN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 ASN F 79 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN H 106 GLN ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 ASN ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 ASN K 101 ASN ** N 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 102 GLN X 155 ASN Y 18 GLN ** Y 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 116 GLN Y 120 GLN ** Z 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 114 GLN ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 227 HIS ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 GLN O 92 GLN ** P 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 88 ASN ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 102 GLN Q 240 HIS ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 HIS ** T 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 105 ASN U 143 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 49014 Z= 0.212 Angle : 0.608 11.454 66222 Z= 0.319 Chirality : 0.044 0.231 7441 Planarity : 0.005 0.082 8531 Dihedral : 4.865 31.579 6803 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.02 % Rotamer Outliers : 0.06 % 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: -0.87 (0.10), residues: 6137 helix: -0.47 (0.11), residues: 2150 sheet: -0.32 (0.13), residues: 1452 loop : -0.62 (0.12), residues: 2535 *********************** 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 896 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 893 time to evaluate : 5.959 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 outliers start: 3 outliers final: 0 residues processed: 895 average time/residue: 0.6457 time to fit residues: 935.0583 Evaluate side-chains 620 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 620 time to evaluate : 6.195 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.5096 ------------------------------------------------------------------------------- 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: 30.0000 chunk 415 optimal weight: 9.9990 chunk 287 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 263 optimal weight: 9.9990 chunk 371 optimal weight: 30.0000 chunk 555 optimal weight: 30.0000 chunk 587 optimal weight: 20.0000 chunk 290 optimal weight: 30.0000 chunk 526 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 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 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS D 55 GLN ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 HIS F 79 ASN F 131 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 GLN ** 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 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN K 71 ASN ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 ASN ** 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 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 155 ASN ** X 240 HIS ** 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** ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 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 98 ASN S 182 GLN T 21 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.6187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.092 49014 Z= 0.304 Angle : 0.647 11.068 66222 Z= 0.340 Chirality : 0.044 0.406 7441 Planarity : 0.005 0.072 8531 Dihedral : 4.948 32.184 6803 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.42 % Favored : 96.53 % Rotamer Outliers : 0.04 % 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: -0.79 (0.10), residues: 6137 helix: -0.28 (0.11), residues: 2148 sheet: -0.35 (0.13), residues: 1498 loop : -0.65 (0.12), residues: 2491 *********************** 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 770 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 768 time to evaluate : 5.906 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 outliers start: 2 outliers final: 0 residues processed: 769 average time/residue: 0.6423 time to fit residues: 802.9221 Evaluate side-chains 573 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 573 time to evaluate : 6.130 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.3700 ------------------------------------------------------------------------------- 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: 20.0000 chunk 8 optimal weight: 9.9990 chunk 437 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 chunk 501 optimal weight: 6.9990 chunk 406 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 300 optimal weight: 7.9990 chunk 527 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 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** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 ASN K 101 ASN ** M 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 HIS ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 168 ASN X 69 ASN X 155 ASN ** X 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 98 ASN ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 110 HIS ** b 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 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 182 GLN ** 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: 0.7648 moved from start: 0.6477 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 : 0.612 10.015 66222 Z= 0.322 Chirality : 0.044 0.307 7441 Planarity : 0.005 0.067 8531 Dihedral : 4.885 32.818 6803 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.47 % Favored : 96.50 % Rotamer Outliers : 0.02 % 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: -0.67 (0.10), residues: 6137 helix: -0.04 (0.11), residues: 2156 sheet: -0.41 (0.13), residues: 1557 loop : -0.63 (0.13), residues: 2424 *********************** 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 765 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 764 time to evaluate : 6.042 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 outliers start: 1 outliers final: 1 residues processed: 765 average time/residue: 0.6209 time to fit residues: 777.2960 Evaluate side-chains 573 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 572 time to evaluate : 5.888 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4749 time to fit residues: 8.5827 ------------------------------------------------------------------------------- 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: 5.9990 chunk 529 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 345 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 588 optimal weight: 5.9990 chunk 488 optimal weight: 20.0000 chunk 272 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 chunk 308 optimal weight: 0.9990 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** ** C 92 ASN ** 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** ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 128 GLN ** V 194 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 155 ASN ** X 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** b 224 HIS ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 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 S 118 ASN ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.6705 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= 0.261 Angle : 0.620 11.437 66222 Z= 0.323 Chirality : 0.044 0.434 7441 Planarity : 0.005 0.084 8531 Dihedral : 4.867 33.778 6803 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.20 % Rotamer Outliers : 0.02 % 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: -0.65 (0.10), residues: 6137 helix: -0.00 (0.11), residues: 2188 sheet: -0.34 (0.13), residues: 1491 loop : -0.70 (0.12), residues: 2458 *********************** 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 753 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 752 time to evaluate : 6.302 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 outliers start: 1 outliers final: 0 residues processed: 753 average time/residue: 0.6187 time to fit residues: 766.0233 Evaluate side-chains 568 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 568 time to evaluate : 5.417 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.0838 ------------------------------------------------------------------------------- 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: 40.0000 chunk 66 optimal weight: 20.0000 chunk 335 optimal weight: 6.9990 chunk 429 optimal weight: 9.9990 chunk 332 optimal weight: 20.0000 chunk 495 optimal weight: 20.0000 chunk 328 optimal weight: 8.9990 chunk 586 optimal weight: 20.0000 chunk 366 optimal weight: 8.9990 chunk 357 optimal weight: 2.9990 chunk 270 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 71 ASN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 HIS ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 13 HIS ** V 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 194 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 ** W 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 155 ASN ** X 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 120 GLN ** Y 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 152 GLN ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 21 GLN b 97 ASN O 90 GLN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 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 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.7050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 49014 Z= 0.320 Angle : 0.667 11.992 66222 Z= 0.349 Chirality : 0.045 0.270 7441 Planarity : 0.005 0.089 8531 Dihedral : 5.057 32.998 6803 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 23.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.37 % Favored : 95.60 % Rotamer Outliers : 0.00 % 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: -0.80 (0.10), residues: 6137 helix: -0.12 (0.11), residues: 2163 sheet: -0.45 (0.13), residues: 1535 loop : -0.77 (0.13), residues: 2439 *********************** 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 713 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 713 time to evaluate : 6.269 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 outliers start: 0 outliers final: 0 residues processed: 713 average time/residue: 0.6221 time to fit residues: 723.5732 Evaluate side-chains 543 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 543 time to evaluate : 6.015 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.7567 ------------------------------------------------------------------------------- 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: 8.9990 chunk 349 optimal weight: 8.9990 chunk 176 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 113 optimal weight: 0.6980 chunk 372 optimal weight: 30.0000 chunk 399 optimal weight: 10.0000 chunk 289 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 460 optimal weight: 6.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- 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 66 HIS ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 172 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 194 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 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 120 GLN ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 68 ASN b 97 ASN O 193 GLN ** Q 95 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 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.7186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 49014 Z= 0.262 Angle : 0.639 14.093 66222 Z= 0.332 Chirality : 0.044 0.433 7441 Planarity : 0.005 0.088 8531 Dihedral : 4.989 32.857 6803 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.24 % Favored : 95.75 % Rotamer Outliers : 0.00 % 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: -0.76 (0.11), residues: 6137 helix: -0.02 (0.11), residues: 2191 sheet: -0.46 (0.13), residues: 1541 loop : -0.79 (0.13), residues: 2405 *********************** 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 709 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 709 time to evaluate : 5.932 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 outliers start: 0 outliers final: 0 residues processed: 709 average time/residue: 0.6218 time to fit residues: 723.9549 Evaluate side-chains 539 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 539 time to evaluate : 5.787 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.4981 ------------------------------------------------------------------------------- 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: 4.9990 chunk 561 optimal weight: 10.0000 chunk 512 optimal weight: 2.9990 chunk 546 optimal weight: 5.9990 chunk 328 optimal weight: 2.9990 chunk 237 optimal weight: 20.0000 chunk 428 optimal weight: 7.9990 chunk 167 optimal weight: 7.9990 chunk 493 optimal weight: 10.0000 chunk 516 optimal weight: 20.0000 chunk 544 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN B 66 HIS ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 ASN M 163 HIS ** 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 ** W 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 84 ASN ** X 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 120 GLN ** Z 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 97 ASN ** O 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 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 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 22 GLN U 105 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.7275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 49014 Z= 0.239 Angle : 0.634 16.242 66222 Z= 0.328 Chirality : 0.044 0.277 7441 Planarity : 0.005 0.091 8531 Dihedral : 4.944 32.154 6803 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.20 % Favored : 95.78 % Rotamer Outliers : 0.02 % 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: -0.65 (0.11), residues: 6137 helix: 0.08 (0.11), residues: 2178 sheet: -0.38 (0.13), residues: 1523 loop : -0.78 (0.13), residues: 2436 *********************** 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 714 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 713 time to evaluate : 5.887 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 outliers start: 1 outliers final: 0 residues processed: 713 average time/residue: 0.6262 time to fit residues: 731.7360 Evaluate side-chains 549 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 549 time to evaluate : 5.817 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.8417 ------------------------------------------------------------------------------- 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: 20.0000 chunk 352 optimal weight: 7.9990 chunk 273 optimal weight: 7.9990 chunk 401 optimal weight: 6.9990 chunk 605 optimal weight: 30.0000 chunk 557 optimal weight: 8.9990 chunk 482 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 372 optimal weight: 0.0970 chunk 295 optimal weight: 20.0000 overall best weight: 6.0186 ------------------------------------------------------------------------------- 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 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 ASN ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 ASN ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 128 GLN ** W 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 111 GLN ** W 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 155 ASN ** X 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 120 GLN ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 68 ASN b 97 ASN ** O 123 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 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.7434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 49014 Z= 0.273 Angle : 0.665 12.154 66222 Z= 0.343 Chirality : 0.045 0.302 7441 Planarity : 0.005 0.096 8531 Dihedral : 5.009 31.463 6803 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 22.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.66 % Favored : 95.32 % Rotamer Outliers : 0.00 % 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: -0.70 (0.11), residues: 6137 helix: 0.04 (0.11), residues: 2191 sheet: -0.38 (0.13), residues: 1507 loop : -0.83 (0.13), residues: 2439 ********************** 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 704 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 704 time to evaluate : 6.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 704 average time/residue: 0.6298 time to fit residues: 726.0556 Evaluate side-chains 529 residues out of total 5143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 529 time to evaluate : 5.952 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.7486 ------------------------------------------------------------------------------- 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: 8.9990 chunk 513 optimal weight: 20.0000 chunk 147 optimal weight: 8.9990 chunk 444 optimal weight: 0.5980 chunk 71 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 483 optimal weight: 20.0000 chunk 202 optimal weight: 5.9990 chunk 496 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- 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 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 HIS ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 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 111 GLN ** X 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 155 ASN ** X 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 120 GLN ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 186 HIS Z 224 GLN b 97 ASN ** O 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 ASN ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 146 GLN ** Q 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 190 HIS U 105 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.056602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.047850 restraints weight = 283135.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.049447 restraints weight = 170103.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.050585 restraints weight = 114542.918| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.7514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 49014 Z= 0.243 Angle : 0.647 12.898 66222 Z= 0.334 Chirality : 0.045 0.270 7441 Planarity : 0.005 0.066 8531 Dihedral : 4.986 31.395 6803 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 0.02 % 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: -0.67 (0.11), residues: 6137 helix: 0.09 (0.11), residues: 2181 sheet: -0.35 (0.13), residues: 1505 loop : -0.84 (0.13), residues: 2451 =============================================================================== Job complete usr+sys time: 12911.15 seconds wall clock time: 234 minutes 44.50 seconds (14084.50 seconds total)