Starting phenix.real_space_refine on Fri Dec 27 10:20:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v5g_31724/12_2024/7v5g_31724.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v5g_31724/12_2024/7v5g_31724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v5g_31724/12_2024/7v5g_31724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v5g_31724/12_2024/7v5g_31724.map" model { file = "/net/cci-nas-00/data/ceres_data/7v5g_31724/12_2024/7v5g_31724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v5g_31724/12_2024/7v5g_31724.cif" } resolution = 4.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 299 5.16 5 C 30449 2.51 5 N 8235 2.21 5 O 9167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 21.07, per 1000 atoms: 0.44 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.85 Conformation dependent library (CDL) restraints added in 4.6 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: 4.87 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: 15.28 Time building geometry restraints manager: 10.39 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: 0.00 - 2.34: 65796 2.34 - 4.67: 372 4.67 - 7.01: 45 7.01 - 9.34: 7 9.34 - 11.68: 2 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 3.120 nonbonded pdb=" O SER P 151 " pdb=" OG SER Q 81 " model vdw 2.218 3.040 nonbonded pdb=" O THR L 44 " pdb=" OG1 THR L 99 " model vdw 2.218 3.040 nonbonded pdb=" O THR E 44 " pdb=" OG1 THR E 99 " model vdw 2.221 3.040 nonbonded pdb=" O LYS P 38 " pdb=" OH TYR P 177 " model vdw 2.227 3.040 ... (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 Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'V' } ncs_group { reference = chain 'P' selection = chain 'W' } ncs_group { reference = (chain 'Q' and resid 2 through 248) selection = chain 'X' } ncs_group { reference = chain 'R' selection = chain 'Y' } ncs_group { reference = chain 'S' selection = chain 'Z' } ncs_group { reference = chain 'T' selection = chain 'a' } ncs_group { reference = chain 'U' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 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: 0.040 Extract box with map and model: 1.310 Check model and map are aligned: 0.260 Set scattering table: 0.330 Process input model: 79.070 Find NCS groups from input model: 2.580 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 49014 Z= 0.123 Angle : 0.502 11.679 66222 Z= 0.306 Chirality : 0.043 0.389 7441 Planarity : 0.004 0.110 8531 Dihedral : 7.724 81.561 18146 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.69 % Favored : 94.18 % Rotamer: Outliers : 0.08 % Allowed : 0.14 % Favored : 99.79 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.09), residues: 6137 helix: -3.36 (0.07), residues: 2045 sheet: -0.84 (0.12), residues: 1408 loop : -0.92 (0.11), residues: 2684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP V 102 HIS 0.004 0.001 HIS U 72 PHE 0.018 0.001 PHE K 171 TYR 0.029 0.001 TYR O 103 ARG 0.005 0.000 ARG N 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1809 residues out of total 5143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1805 time to evaluate : 4.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 THR cc_start: 0.9106 (p) cc_final: 0.8798 (t) REVERT: C 27 PHE cc_start: 0.8041 (t80) cc_final: 0.7808 (t80) REVERT: C 71 ASN cc_start: 0.8888 (m-40) cc_final: 0.7801 (m110) REVERT: C 170 MET cc_start: 0.8558 (mmp) cc_final: 0.8243 (mmm) REVERT: C 185 ILE cc_start: 0.8471 (mt) cc_final: 0.7941 (mt) REVERT: D 186 ASN cc_start: 0.9120 (m-40) cc_final: 0.8710 (m-40) REVERT: E 71 LYS cc_start: 0.8788 (mttt) cc_final: 0.7859 (mtmm) REVERT: F 75 TYR cc_start: 0.7765 (t80) cc_final: 0.6723 (t80) REVERT: F 213 ASP cc_start: 0.2921 (m-30) cc_final: 0.2238 (t70) REVERT: G 39 ILE cc_start: 0.7550 (mt) cc_final: 0.7006 (mt) REVERT: G 73 ASP cc_start: 0.7948 (m-30) cc_final: 0.7271 (m-30) REVERT: H 148 THR cc_start: 0.8887 (p) cc_final: 0.8018 (t) REVERT: H 165 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7857 (pt0) REVERT: I 58 LEU cc_start: 0.9379 (mt) cc_final: 0.9117 (tp) REVERT: J 84 TYR cc_start: 0.8142 (t80) cc_final: 0.7922 (t80) REVERT: J 148 MET cc_start: 0.9156 (mmm) cc_final: 0.8494 (mmm) REVERT: J 170 MET cc_start: 0.8778 (mmp) cc_final: 0.8539 (mmm) REVERT: K 52 ASP cc_start: 0.7763 (m-30) cc_final: 0.6812 (m-30) REVERT: K 53 THR cc_start: 0.8262 (m) cc_final: 0.7979 (p) REVERT: K 68 LYS cc_start: 0.9472 (tttt) cc_final: 0.8806 (ttmt) REVERT: L 51 ASP cc_start: 0.8404 (m-30) cc_final: 0.8141 (m-30) REVERT: N 61 GLN cc_start: 0.8210 (mt0) cc_final: 0.7721 (mt0) REVERT: N 64 LYS cc_start: 0.9008 (mttt) cc_final: 0.8713 (tmmt) REVERT: N 83 TYR cc_start: 0.6717 (m-80) cc_final: 0.5858 (m-80) REVERT: N 117 ASP cc_start: 0.8410 (m-30) cc_final: 0.7943 (m-30) REVERT: N 188 GLN cc_start: 0.7909 (mm110) cc_final: 0.7637 (mm110) REVERT: V 17 PHE cc_start: 0.6119 (m-10) cc_final: 0.5903 (m-10) REVERT: V 106 TYR cc_start: 0.6931 (m-10) cc_final: 0.5856 (m-10) REVERT: V 126 TYR cc_start: 0.7994 (m-10) cc_final: 0.7218 (m-10) REVERT: W 20 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7510 (tp-100) REVERT: W 99 VAL cc_start: 0.9036 (t) cc_final: 0.8756 (p) REVERT: X 45 LEU cc_start: 0.7952 (pp) cc_final: 0.7216 (mt) REVERT: X 82 ASP cc_start: 0.8139 (m-30) cc_final: 0.7666 (t70) REVERT: X 101 TYR cc_start: 0.7999 (m-80) cc_final: 0.7793 (m-80) REVERT: X 124 PHE cc_start: 0.7879 (p90) cc_final: 0.7568 (p90) REVERT: X 155 ASN cc_start: 0.8253 (m-40) cc_final: 0.7993 (m110) REVERT: X 194 ILE cc_start: 0.9283 (mt) cc_final: 0.9016 (tp) REVERT: X 240 HIS cc_start: 0.8194 (t70) cc_final: 0.7985 (t-170) REVERT: Y 77 THR cc_start: 0.6006 (m) cc_final: 0.5265 (m) REVERT: Y 88 ARG cc_start: 0.7870 (mtt180) cc_final: 0.6754 (mtt180) REVERT: Y 114 LEU cc_start: 0.8995 (mt) cc_final: 0.8787 (mt) REVERT: Y 192 ILE cc_start: 0.9465 (mt) cc_final: 0.9061 (pt) REVERT: Y 219 ILE cc_start: 0.7946 (mt) cc_final: 0.7571 (tp) REVERT: Z 86 LYS cc_start: 0.9111 (mttm) cc_final: 0.8906 (tppt) REVERT: Z 99 HIS cc_start: 0.7534 (t-90) cc_final: 0.7280 (t-90) REVERT: Z 112 VAL cc_start: 0.9092 (t) cc_final: 0.8790 (t) REVERT: Z 119 LEU cc_start: 0.8973 (mt) cc_final: 0.8547 (tt) REVERT: Z 166 ASP cc_start: 0.7181 (m-30) cc_final: 0.6774 (m-30) REVERT: Z 203 LYS cc_start: 0.9073 (tttt) cc_final: 0.8615 (tppt) REVERT: a 41 LYS cc_start: 0.8855 (tttt) cc_final: 0.8632 (mtmm) REVERT: a 69 HIS cc_start: 0.8055 (p-80) cc_final: 0.7825 (p90) REVERT: a 80 ASP cc_start: 0.8571 (m-30) cc_final: 0.8103 (m-30) REVERT: a 94 ASP cc_start: 0.9103 (m-30) cc_final: 0.8653 (m-30) REVERT: a 115 LYS cc_start: 0.9382 (mmtp) cc_final: 0.9129 (mmtm) REVERT: a 123 TYR cc_start: 0.6987 (t80) cc_final: 0.6663 (t80) REVERT: a 128 TYR cc_start: 0.6965 (m-80) cc_final: 0.6664 (m-80) REVERT: a 154 PHE cc_start: 0.8612 (m-10) cc_final: 0.7547 (m-80) REVERT: a 225 ASP cc_start: 0.8534 (p0) cc_final: 0.8073 (p0) REVERT: a 227 ASP cc_start: 0.8781 (m-30) cc_final: 0.8326 (m-30) REVERT: b 75 MET cc_start: 0.8253 (ttm) cc_final: 0.7770 (ttm) REVERT: b 97 ASN cc_start: 0.9122 (m-40) cc_final: 0.8909 (m-40) REVERT: b 150 MET cc_start: 0.6602 (ttm) cc_final: 0.5754 (ttm) REVERT: O 16 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.6087 (m-80) REVERT: O 73 THR cc_start: 0.8712 (p) cc_final: 0.8240 (t) REVERT: O 104 LYS cc_start: 0.8218 (mttt) cc_final: 0.7721 (tmmt) REVERT: O 196 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8278 (tp30) REVERT: P 102 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7223 (mt-10) REVERT: P 112 ARG cc_start: 0.7658 (mtt-85) cc_final: 0.7455 (mtt90) REVERT: P 139 ASN cc_start: 0.6620 (m110) cc_final: 0.6107 (t0) REVERT: Q 61 PHE cc_start: 0.6755 (m-10) cc_final: 0.6333 (t80) REVERT: Q 91 ARG cc_start: 0.9201 (mtt180) cc_final: 0.8275 (mtt90) REVERT: Q 136 TYR cc_start: 0.7468 (m-80) cc_final: 0.7232 (m-80) REVERT: Q 201 MET cc_start: 0.8165 (tpt) cc_final: 0.7665 (tpt) REVERT: R 66 ASP cc_start: 0.7428 (p0) cc_final: 0.7140 (p0) REVERT: R 70 CYS cc_start: 0.7927 (m) cc_final: 0.7544 (p) REVERT: R 77 THR cc_start: 0.6970 (m) cc_final: 0.6519 (m) REVERT: R 110 TYR cc_start: 0.7592 (m-10) cc_final: 0.7368 (m-10) REVERT: R 211 MET cc_start: 0.7384 (ttp) cc_final: 0.7115 (tpp) REVERT: R 221 ASN cc_start: 0.9262 (m-40) cc_final: 0.8850 (m-40) REVERT: S 84 ASP cc_start: 0.8039 (m-30) cc_final: 0.7729 (m-30) REVERT: S 88 LEU cc_start: 0.9452 (mt) cc_final: 0.8935 (mt) REVERT: S 98 ASN cc_start: 0.8861 (m-40) cc_final: 0.8407 (m-40) REVERT: S 105 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7529 (mm-30) REVERT: S 201 ILE cc_start: 0.9360 (mt) cc_final: 0.9133 (tp) REVERT: T 49 LEU cc_start: 0.8693 (tp) cc_final: 0.8261 (tt) REVERT: T 67 ASP cc_start: 0.8626 (t0) cc_final: 0.8383 (t70) REVERT: T 215 VAL cc_start: 0.8450 (p) cc_final: 0.7505 (p) REVERT: U 97 ASN cc_start: 0.9060 (m-40) cc_final: 0.8860 (t0) REVERT: U 111 LEU cc_start: 0.8770 (tp) cc_final: 0.8468 (mt) REVERT: U 147 GLN cc_start: 0.7073 (mm-40) cc_final: 0.5825 (mm-40) outliers start: 4 outliers final: 0 residues processed: 1809 average time/residue: 0.5629 time to fit residues: 1565.0323 Evaluate side-chains 882 residues out of total 5143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 880 time to evaluate : 4.201 ------------------------------------------------------------------------------- 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: 8.9990 chunk 255 optimal weight: 0.4980 chunk 157 optimal weight: 30.0000 chunk 310 optimal weight: 4.9990 chunk 246 optimal weight: 20.0000 chunk 476 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 289 optimal weight: 40.0000 chunk 354 optimal weight: 7.9990 chunk 552 optimal weight: 20.0000 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 77 HIS ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 165 ASN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 ASN ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 GLN K 101 ASN M 108 ASN ** M 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN W 87 HIS ** W 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 95 GLN ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 206 ASN ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 94 HIS ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 114 GLN ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 143 ASN O 12 HIS O 92 GLN O 150 GLN P 51 GLN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 GLN Q 102 GLN ** R 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 98 ASN ** T 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 49014 Z= 0.291 Angle : 0.684 11.079 66222 Z= 0.362 Chirality : 0.046 0.261 7441 Planarity : 0.005 0.092 8531 Dihedral : 4.626 32.911 6803 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.79 % Favored : 97.16 % Rotamer: Outliers : 0.08 % Allowed : 1.77 % Favored : 98.15 % 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: -1.35 (0.10), residues: 6137 helix: -1.33 (0.10), residues: 2097 sheet: -0.45 (0.12), residues: 1460 loop : -0.54 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP V 190 HIS 0.013 0.002 HIS U 224 PHE 0.034 0.002 PHE W 172 TYR 0.042 0.002 TYR O 103 ARG 0.012 0.001 ARG E 73 *********************** 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 1073 residues out of total 5143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1069 time to evaluate : 4.427 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: A 62 GLN cc_start: 0.9196 (pt0) cc_final: 0.8990 (pm20) REVERT: A 95 MET cc_start: 0.7881 (tmm) cc_final: 0.7504 (tmm) REVERT: B 145 ASP cc_start: 0.6883 (t0) cc_final: 0.6682 (t0) REVERT: B 149 GLU cc_start: 0.8747 (tp30) cc_final: 0.8531 (tm-30) REVERT: B 204 CYS cc_start: 0.7696 (m) cc_final: 0.7080 (m) REVERT: C 27 PHE cc_start: 0.8176 (t80) cc_final: 0.7936 (t80) REVERT: C 68 PHE cc_start: 0.7977 (t80) cc_final: 0.7571 (t80) REVERT: C 84 TYR cc_start: 0.8058 (t80) cc_final: 0.7547 (t80) REVERT: C 130 MET cc_start: 0.7177 (ttm) cc_final: 0.6613 (ttp) REVERT: C 161 HIS cc_start: 0.8159 (m-70) cc_final: 0.7531 (m-70) REVERT: C 185 ILE cc_start: 0.8614 (mt) cc_final: 0.8339 (mm) REVERT: D 38 MET cc_start: 0.7776 (mtp) cc_final: 0.6542 (tpp) REVERT: D 139 THR cc_start: 0.9100 (p) cc_final: 0.8786 (p) REVERT: E 62 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8558 (mp10) REVERT: E 97 MET cc_start: 0.6926 (tmm) cc_final: 0.6425 (tmm) REVERT: F 19 ASP cc_start: 0.7812 (p0) cc_final: 0.7449 (p0) REVERT: F 158 MET cc_start: 0.6971 (mmp) cc_final: 0.6393 (mmm) REVERT: G 73 ASP cc_start: 0.7815 (m-30) cc_final: 0.7582 (m-30) REVERT: G 127 MET cc_start: 0.8115 (ptp) cc_final: 0.7280 (pmm) REVERT: G 156 LYS cc_start: 0.8728 (ptpp) cc_final: 0.8356 (mtpp) REVERT: H 62 GLN cc_start: 0.8779 (mp10) cc_final: 0.8456 (mp10) REVERT: I 58 LEU cc_start: 0.9607 (mt) cc_final: 0.9293 (tp) REVERT: I 62 ASN cc_start: 0.9233 (m-40) cc_final: 0.8949 (m110) REVERT: J 69 ARG cc_start: 0.9088 (mtt180) cc_final: 0.8838 (mtt180) REVERT: J 148 MET cc_start: 0.8723 (mmm) cc_final: 0.8332 (mmm) REVERT: J 157 MET cc_start: 0.7763 (mmm) cc_final: 0.6784 (mmm) REVERT: J 170 MET cc_start: 0.8930 (mmp) cc_final: 0.8667 (mmm) REVERT: L 97 MET cc_start: 0.6606 (tpp) cc_final: 0.6213 (tpp) REVERT: L 100 MET cc_start: 0.5877 (mpp) cc_final: 0.5519 (mpp) REVERT: M 31 GLU cc_start: 0.8465 (pp20) cc_final: 0.8255 (pm20) REVERT: M 169 ASP cc_start: 0.8592 (p0) cc_final: 0.8390 (p0) REVERT: M 172 MET cc_start: 0.8715 (mmp) cc_final: 0.8485 (mmm) REVERT: N 26 MET cc_start: 0.7547 (mpp) cc_final: 0.5671 (mpp) REVERT: N 50 MET cc_start: 0.8058 (ttp) cc_final: 0.7722 (tmm) REVERT: N 59 ASP cc_start: 0.6306 (p0) cc_final: 0.5826 (p0) REVERT: V 17 PHE cc_start: 0.6560 (m-10) cc_final: 0.6316 (m-10) REVERT: V 106 TYR cc_start: 0.7322 (m-10) cc_final: 0.6952 (m-10) REVERT: V 126 TYR cc_start: 0.8508 (m-10) cc_final: 0.7982 (m-10) REVERT: V 132 MET cc_start: 0.7789 (ttp) cc_final: 0.7257 (ttp) REVERT: W 117 MET cc_start: 0.8049 (tpp) cc_final: 0.7114 (tpp) REVERT: X 19 TYR cc_start: 0.7671 (m-80) cc_final: 0.7114 (m-80) REVERT: X 45 LEU cc_start: 0.7945 (pp) cc_final: 0.7144 (mt) REVERT: X 82 ASP cc_start: 0.8862 (m-30) cc_final: 0.8611 (m-30) REVERT: X 87 THR cc_start: 0.8728 (m) cc_final: 0.8259 (p) REVERT: X 124 PHE cc_start: 0.7992 (p90) cc_final: 0.7451 (p90) REVERT: X 155 ASN cc_start: 0.8863 (m-40) cc_final: 0.8398 (m110) REVERT: X 194 ILE cc_start: 0.9331 (mt) cc_final: 0.9025 (tp) REVERT: Y 77 THR cc_start: 0.7315 (m) cc_final: 0.7020 (p) REVERT: Y 86 ARG cc_start: 0.7982 (mtm180) cc_final: 0.7240 (mtm180) REVERT: Z 69 GLU cc_start: 0.8812 (tt0) cc_final: 0.8508 (tm-30) REVERT: Z 86 LYS cc_start: 0.9310 (mttm) cc_final: 0.8873 (tppt) REVERT: Z 98 ASN cc_start: 0.9196 (m-40) cc_final: 0.8720 (m-40) REVERT: Z 203 LYS cc_start: 0.9019 (tttt) cc_final: 0.8666 (tppt) REVERT: a 41 LYS cc_start: 0.8952 (tttt) cc_final: 0.8697 (ptpp) REVERT: a 90 GLN cc_start: 0.8122 (pp30) cc_final: 0.7753 (pp30) REVERT: a 94 ASP cc_start: 0.9095 (m-30) cc_final: 0.8653 (m-30) REVERT: a 123 TYR cc_start: 0.7384 (t80) cc_final: 0.7025 (t80) REVERT: a 154 PHE cc_start: 0.8092 (m-10) cc_final: 0.7223 (m-80) REVERT: a 215 VAL cc_start: 0.8656 (p) cc_final: 0.8391 (p) REVERT: b 68 ASN cc_start: 0.7674 (m-40) cc_final: 0.7461 (m-40) REVERT: b 75 MET cc_start: 0.7686 (ttm) cc_final: 0.7416 (ttm) REVERT: b 87 LEU cc_start: 0.8683 (pp) cc_final: 0.8411 (pp) REVERT: b 93 GLU cc_start: 0.9200 (pt0) cc_final: 0.8560 (pt0) REVERT: b 97 ASN cc_start: 0.9192 (m-40) cc_final: 0.8814 (m-40) REVERT: b 101 ASN cc_start: 0.7979 (m-40) cc_final: 0.7535 (m-40) REVERT: b 150 MET cc_start: 0.7166 (ttm) cc_final: 0.6883 (ttm) REVERT: b 181 MET cc_start: 0.9233 (pmm) cc_final: 0.8793 (pmm) REVERT: O 53 GLN cc_start: 0.8171 (tt0) cc_final: 0.7960 (tp40) REVERT: O 96 TYR cc_start: 0.8119 (m-80) cc_final: 0.7730 (m-80) REVERT: O 159 TYR cc_start: 0.7345 (m-10) cc_final: 0.7104 (m-10) REVERT: O 196 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8092 (mm-30) REVERT: P 92 LEU cc_start: 0.8082 (mt) cc_final: 0.7662 (mt) REVERT: P 104 ILE cc_start: 0.8103 (tt) cc_final: 0.7556 (tt) REVERT: Q 61 PHE cc_start: 0.6674 (m-10) cc_final: 0.6406 (t80) REVERT: Q 84 ASN cc_start: 0.9277 (t0) cc_final: 0.8739 (m110) REVERT: Q 95 GLN cc_start: 0.9046 (mp10) cc_final: 0.8541 (mm-40) REVERT: Q 201 MET cc_start: 0.8155 (tpt) cc_final: 0.7680 (tpt) REVERT: R 21 TYR cc_start: 0.7225 (m-10) cc_final: 0.6979 (m-10) REVERT: R 77 THR cc_start: 0.7252 (m) cc_final: 0.6863 (m) REVERT: R 91 CYS cc_start: 0.8797 (m) cc_final: 0.8402 (m) REVERT: R 92 GLN cc_start: 0.8471 (mp10) cc_final: 0.7940 (mp10) REVERT: R 219 ILE cc_start: 0.7653 (tp) cc_final: 0.7219 (tp) REVERT: S 66 LYS cc_start: 0.7710 (mtpt) cc_final: 0.7213 (mtpt) REVERT: S 98 ASN cc_start: 0.9102 (m110) cc_final: 0.8754 (m110) REVERT: S 201 ILE cc_start: 0.9618 (mt) cc_final: 0.9374 (tp) REVERT: T 49 LEU cc_start: 0.8663 (tp) cc_final: 0.8415 (tt) REVERT: T 67 ASP cc_start: 0.8571 (t0) cc_final: 0.8319 (t70) REVERT: T 99 PHE cc_start: 0.7096 (m-10) cc_final: 0.6469 (m-10) REVERT: U 97 ASN cc_start: 0.8979 (m-40) cc_final: 0.8760 (m110) outliers start: 4 outliers final: 1 residues processed: 1071 average time/residue: 0.5209 time to fit residues: 886.2527 Evaluate side-chains 709 residues out of total 5143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 708 time to evaluate : 4.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 306 optimal weight: 20.0000 chunk 171 optimal weight: 8.9990 chunk 459 optimal weight: 6.9990 chunk 375 optimal weight: 30.0000 chunk 152 optimal weight: 10.0000 chunk 553 optimal weight: 20.0000 chunk 597 optimal weight: 9.9990 chunk 492 optimal weight: 40.0000 chunk 548 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 443 optimal weight: 0.0870 overall best weight: 6.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN B 193 ASN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 ASN D 65 GLN F 79 ASN F 131 GLN F 146 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 GLN I 193 ASN ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 ASN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN ** M 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN ** W 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 95 GLN X 119 GLN ** X 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 GLN Y 92 GLN Y 120 GLN ** Z 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 59 HIS O 92 GLN P 87 HIS ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 188 HIS ** T 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 GLN ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 49014 Z= 0.292 Angle : 0.649 11.229 66222 Z= 0.343 Chirality : 0.045 0.379 7441 Planarity : 0.005 0.098 8531 Dihedral : 4.769 31.776 6803 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.98 % Favored : 96.99 % Rotamer: Outliers : 0.08 % Allowed : 2.72 % Favored : 97.20 % 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: -0.86 (0.10), residues: 6137 helix: -0.56 (0.10), residues: 2131 sheet: -0.35 (0.13), residues: 1482 loop : -0.49 (0.12), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N 107 HIS 0.011 0.002 HIS I 66 PHE 0.026 0.002 PHE Q 124 TYR 0.033 0.002 TYR P 100 ARG 0.009 0.001 ARG E 61 *********************** 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 902 residues out of total 5143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 898 time to evaluate : 4.211 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: A 62 GLN cc_start: 0.9303 (pt0) cc_final: 0.8891 (pm20) REVERT: A 95 MET cc_start: 0.7958 (tmm) cc_final: 0.7520 (tmm) REVERT: A 116 MET cc_start: 0.7103 (pmm) cc_final: 0.6768 (pmm) REVERT: A 134 TYR cc_start: 0.8920 (m-80) cc_final: 0.8689 (m-80) REVERT: B 30 ASN cc_start: 0.7738 (t0) cc_final: 0.7502 (t0) REVERT: B 42 TYR cc_start: 0.8163 (m-80) cc_final: 0.7889 (m-80) REVERT: B 149 GLU cc_start: 0.8793 (tp30) cc_final: 0.8589 (tm-30) REVERT: C 25 ARG cc_start: 0.7024 (mmm-85) cc_final: 0.6633 (mmm-85) REVERT: C 68 PHE cc_start: 0.8295 (t80) cc_final: 0.8058 (t80) REVERT: C 84 TYR cc_start: 0.7922 (t80) cc_final: 0.7494 (t80) REVERT: C 96 GLU cc_start: 0.8204 (pp20) cc_final: 0.7716 (pp20) REVERT: C 130 MET cc_start: 0.6923 (ttm) cc_final: 0.6158 (ttm) REVERT: C 161 HIS cc_start: 0.8174 (m-70) cc_final: 0.7543 (m-70) REVERT: C 182 MET cc_start: 0.6899 (mmp) cc_final: 0.6647 (mmp) REVERT: C 185 ILE cc_start: 0.8605 (mt) cc_final: 0.8325 (mm) REVERT: D 38 MET cc_start: 0.7944 (mtp) cc_final: 0.6810 (mmt) REVERT: D 63 ASN cc_start: 0.9112 (m-40) cc_final: 0.8908 (m110) REVERT: D 69 MET cc_start: 0.7748 (ttm) cc_final: 0.7237 (tpp) REVERT: E 67 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8094 (mm-30) REVERT: F 74 MET cc_start: 0.9009 (mtt) cc_final: 0.8664 (mtp) REVERT: F 76 LYS cc_start: 0.9156 (mmtt) cc_final: 0.8626 (mmtm) REVERT: F 107 TYR cc_start: 0.8104 (m-80) cc_final: 0.7847 (m-10) REVERT: F 158 MET cc_start: 0.6962 (mmp) cc_final: 0.6683 (mmm) REVERT: G 3 ASN cc_start: 0.8547 (p0) cc_final: 0.8290 (p0) REVERT: G 83 TYR cc_start: 0.8524 (m-10) cc_final: 0.8279 (m-10) REVERT: G 127 MET cc_start: 0.8184 (ptp) cc_final: 0.7418 (pmm) REVERT: H 62 GLN cc_start: 0.8890 (mp10) cc_final: 0.8528 (mp10) REVERT: H 119 MET cc_start: 0.8809 (ptt) cc_final: 0.8571 (ptp) REVERT: H 120 MET cc_start: 0.8329 (tmm) cc_final: 0.7889 (tmm) REVERT: H 136 TYR cc_start: 0.7501 (m-10) cc_final: 0.7284 (m-10) REVERT: I 58 LEU cc_start: 0.9597 (mt) cc_final: 0.9299 (tp) REVERT: I 62 ASN cc_start: 0.9231 (m-40) cc_final: 0.8869 (m110) REVERT: J 27 PHE cc_start: 0.7436 (t80) cc_final: 0.7225 (t80) REVERT: J 69 ARG cc_start: 0.9007 (mtt180) cc_final: 0.8757 (mtt180) REVERT: J 71 ASN cc_start: 0.9001 (m-40) cc_final: 0.8278 (m-40) REVERT: J 96 GLU cc_start: 0.8438 (pp20) cc_final: 0.7821 (pp20) REVERT: J 148 MET cc_start: 0.8788 (mmm) cc_final: 0.8332 (mmm) REVERT: J 170 MET cc_start: 0.8882 (mmp) cc_final: 0.8643 (mmm) REVERT: K 28 MET cc_start: 0.7300 (ttt) cc_final: 0.7059 (ttt) REVERT: K 62 LYS cc_start: 0.9254 (tptt) cc_final: 0.8892 (tptt) REVERT: L 45 MET cc_start: 0.4872 (tpp) cc_final: 0.4456 (mmm) REVERT: L 100 MET cc_start: 0.5903 (mpp) cc_final: 0.4687 (mpp) REVERT: M 31 GLU cc_start: 0.8545 (pp20) cc_final: 0.8142 (pm20) REVERT: M 83 MET cc_start: 0.8911 (tpp) cc_final: 0.8370 (mmm) REVERT: M 158 MET cc_start: 0.8761 (mtp) cc_final: 0.8325 (mtp) REVERT: N 26 MET cc_start: 0.7126 (mpp) cc_final: 0.6919 (mpp) REVERT: N 50 MET cc_start: 0.8147 (ttp) cc_final: 0.7879 (ptt) REVERT: N 56 ASP cc_start: 0.7831 (t0) cc_final: 0.7473 (t0) REVERT: N 59 ASP cc_start: 0.6553 (p0) cc_final: 0.5827 (p0) REVERT: V 17 PHE cc_start: 0.7125 (m-10) cc_final: 0.6411 (m-10) REVERT: V 101 ASN cc_start: 0.8424 (t0) cc_final: 0.8179 (t0) REVERT: W 78 MET cc_start: 0.8389 (ttt) cc_final: 0.8181 (ttm) REVERT: W 117 MET cc_start: 0.7982 (tpp) cc_final: 0.7071 (tpp) REVERT: X 11 ILE cc_start: 0.7241 (pt) cc_final: 0.7031 (pt) REVERT: X 19 TYR cc_start: 0.7957 (m-80) cc_final: 0.7664 (m-80) REVERT: X 82 ASP cc_start: 0.9062 (m-30) cc_final: 0.8761 (m-30) REVERT: X 87 THR cc_start: 0.8697 (m) cc_final: 0.8122 (p) REVERT: X 124 PHE cc_start: 0.8157 (p90) cc_final: 0.7800 (p90) REVERT: X 155 ASN cc_start: 0.8865 (m-40) cc_final: 0.8476 (m-40) REVERT: X 174 MET cc_start: 0.9081 (mmp) cc_final: 0.8876 (mmm) REVERT: Y 77 THR cc_start: 0.7312 (m) cc_final: 0.7052 (p) REVERT: Z 69 GLU cc_start: 0.8869 (tt0) cc_final: 0.8504 (tm-30) REVERT: Z 86 LYS cc_start: 0.9398 (mttm) cc_final: 0.8950 (tppt) REVERT: Z 98 ASN cc_start: 0.9180 (m-40) cc_final: 0.8828 (m-40) REVERT: Z 122 GLN cc_start: 0.7431 (mt0) cc_final: 0.7096 (mt0) REVERT: Z 166 ASP cc_start: 0.5050 (t0) cc_final: 0.4798 (t0) REVERT: Z 203 LYS cc_start: 0.9169 (tttt) cc_final: 0.8861 (tptt) REVERT: a 41 LYS cc_start: 0.9072 (tttt) cc_final: 0.8700 (ptpt) REVERT: a 92 CYS cc_start: 0.9185 (m) cc_final: 0.8966 (m) REVERT: a 94 ASP cc_start: 0.9088 (m-30) cc_final: 0.8489 (m-30) REVERT: a 123 TYR cc_start: 0.7595 (t80) cc_final: 0.7216 (t80) REVERT: a 154 PHE cc_start: 0.8242 (m-10) cc_final: 0.7564 (m-80) REVERT: a 161 ILE cc_start: 0.8725 (mp) cc_final: 0.8450 (tp) REVERT: b 89 ASP cc_start: 0.9100 (m-30) cc_final: 0.8380 (p0) REVERT: b 93 GLU cc_start: 0.9266 (pt0) cc_final: 0.8494 (pt0) REVERT: b 125 TYR cc_start: 0.7177 (m-10) cc_final: 0.6794 (m-10) REVERT: O 53 GLN cc_start: 0.8223 (tt0) cc_final: 0.8005 (tp40) REVERT: O 96 TYR cc_start: 0.8192 (m-80) cc_final: 0.7657 (m-80) REVERT: P 118 GLN cc_start: 0.8222 (tp40) cc_final: 0.7934 (tp40) REVERT: Q 84 ASN cc_start: 0.9268 (t0) cc_final: 0.8843 (m110) REVERT: Q 201 MET cc_start: 0.8465 (tpt) cc_final: 0.8209 (tpt) REVERT: S 69 GLU cc_start: 0.8374 (tt0) cc_final: 0.7744 (tm-30) REVERT: S 93 ARG cc_start: 0.9077 (mtt-85) cc_final: 0.8557 (mtt-85) REVERT: S 98 ASN cc_start: 0.9146 (m110) cc_final: 0.8772 (m110) REVERT: S 201 ILE cc_start: 0.9610 (mt) cc_final: 0.9348 (tp) REVERT: S 206 MET cc_start: 0.8252 (mmt) cc_final: 0.7934 (mmm) REVERT: T 26 MET cc_start: 0.7617 (mmp) cc_final: 0.7009 (mmm) REVERT: U 135 PHE cc_start: 0.7535 (p90) cc_final: 0.7301 (p90) outliers start: 4 outliers final: 2 residues processed: 902 average time/residue: 0.5109 time to fit residues: 745.2462 Evaluate side-chains 656 residues out of total 5143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 654 time to evaluate : 4.223 ------------------------------------------------------------------------------- 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: 10.0000 chunk 415 optimal weight: 10.0000 chunk 287 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 263 optimal weight: 5.9990 chunk 371 optimal weight: 20.0000 chunk 555 optimal weight: 30.0000 chunk 587 optimal weight: 20.0000 chunk 290 optimal weight: 5.9990 chunk 526 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN C 156 ASN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN ** N 61 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** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN ** Q 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 HIS S 118 ASN ** T 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 49014 Z= 0.244 Angle : 0.611 11.150 66222 Z= 0.322 Chirality : 0.044 0.274 7441 Planarity : 0.005 0.083 8531 Dihedral : 4.727 32.616 6803 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.10 % Rotamer: Outliers : 0.02 % Allowed : 2.16 % Favored : 97.82 % 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: -0.66 (0.10), residues: 6137 helix: -0.22 (0.11), residues: 2184 sheet: -0.28 (0.13), residues: 1492 loop : -0.53 (0.12), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP b 215 HIS 0.010 0.002 HIS I 66 PHE 0.025 0.002 PHE Y 138 TYR 0.019 0.002 TYR P 100 ARG 0.011 0.001 ARG W 83 *********************** 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 859 residues out of total 5143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 858 time to evaluate : 4.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.7112 (pmm) cc_final: 0.6394 (pmm) REVERT: A 134 TYR cc_start: 0.8826 (m-80) cc_final: 0.8466 (m-80) REVERT: B 149 GLU cc_start: 0.8798 (tp30) cc_final: 0.8575 (tm-30) REVERT: C 25 ARG cc_start: 0.6785 (mmm-85) cc_final: 0.6448 (mmm-85) REVERT: C 72 LEU cc_start: 0.9255 (mt) cc_final: 0.9017 (mt) REVERT: C 79 ARG cc_start: 0.7913 (mmt-90) cc_final: 0.6654 (mmt180) REVERT: C 84 TYR cc_start: 0.7890 (t80) cc_final: 0.7473 (t80) REVERT: C 96 GLU cc_start: 0.8234 (pp20) cc_final: 0.7758 (pp20) REVERT: C 130 MET cc_start: 0.6654 (ttm) cc_final: 0.5897 (ttm) REVERT: C 157 MET cc_start: 0.7964 (mmp) cc_final: 0.7641 (mmp) REVERT: C 161 HIS cc_start: 0.8377 (m-70) cc_final: 0.8156 (t-170) REVERT: C 185 ILE cc_start: 0.8554 (mt) cc_final: 0.8308 (mm) REVERT: D 28 MET cc_start: 0.6497 (ptm) cc_final: 0.6281 (ptp) REVERT: D 38 MET cc_start: 0.8042 (mtp) cc_final: 0.7077 (tpp) REVERT: D 62 LYS cc_start: 0.9142 (tttp) cc_final: 0.8936 (tttp) REVERT: D 63 ASN cc_start: 0.9156 (m-40) cc_final: 0.8953 (m110) REVERT: E 45 MET cc_start: 0.6579 (ttt) cc_final: 0.6037 (ttt) REVERT: E 65 ILE cc_start: 0.9585 (mm) cc_final: 0.9194 (pt) REVERT: E 67 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8252 (mm-30) REVERT: E 93 MET cc_start: 0.8177 (mtt) cc_final: 0.7635 (mtm) REVERT: F 74 MET cc_start: 0.9031 (mtt) cc_final: 0.8650 (mtp) REVERT: F 76 LYS cc_start: 0.9198 (mmtt) cc_final: 0.8846 (mmtm) REVERT: F 83 MET cc_start: 0.6792 (ttt) cc_final: 0.6376 (ttt) REVERT: F 158 MET cc_start: 0.6932 (mmp) cc_final: 0.6717 (mmm) REVERT: F 213 ASP cc_start: 0.3904 (m-30) cc_final: 0.3509 (m-30) REVERT: G 83 TYR cc_start: 0.8551 (m-10) cc_final: 0.8277 (m-80) REVERT: G 127 MET cc_start: 0.8208 (ptp) cc_final: 0.7392 (pmm) REVERT: H 4 MET cc_start: 0.7207 (tpt) cc_final: 0.6492 (tpp) REVERT: H 62 GLN cc_start: 0.8902 (mp10) cc_final: 0.8505 (mp10) REVERT: H 119 MET cc_start: 0.8717 (ptt) cc_final: 0.8484 (ptp) REVERT: H 120 MET cc_start: 0.8313 (tmm) cc_final: 0.7858 (tmm) REVERT: I 30 ASN cc_start: 0.7693 (t0) cc_final: 0.7479 (t0) REVERT: I 54 MET cc_start: 0.8461 (mmp) cc_final: 0.8217 (mmm) REVERT: I 58 LEU cc_start: 0.9572 (mt) cc_final: 0.9266 (tp) REVERT: I 62 ASN cc_start: 0.9251 (m-40) cc_final: 0.8836 (m110) REVERT: J 93 LEU cc_start: 0.9506 (tt) cc_final: 0.9294 (tt) REVERT: J 96 GLU cc_start: 0.8489 (pp20) cc_final: 0.7875 (pp20) REVERT: J 148 MET cc_start: 0.8755 (mmm) cc_final: 0.8376 (mmm) REVERT: J 170 MET cc_start: 0.8900 (mmp) cc_final: 0.8657 (mmm) REVERT: K 38 MET cc_start: 0.8085 (mmp) cc_final: 0.7865 (mmm) REVERT: K 68 LYS cc_start: 0.8872 (mmtt) cc_final: 0.8636 (mmtm) REVERT: L 45 MET cc_start: 0.3418 (tpp) cc_final: 0.3077 (mmm) REVERT: L 100 MET cc_start: 0.5929 (mpp) cc_final: 0.4756 (mpp) REVERT: M 31 GLU cc_start: 0.8441 (pp20) cc_final: 0.7922 (pm20) REVERT: M 83 MET cc_start: 0.9103 (tpp) cc_final: 0.8431 (mmm) REVERT: M 158 MET cc_start: 0.8748 (mtp) cc_final: 0.8326 (mtp) REVERT: N 56 ASP cc_start: 0.7881 (t0) cc_final: 0.7438 (t0) REVERT: N 59 ASP cc_start: 0.6383 (p0) cc_final: 0.5410 (p0) REVERT: N 91 TRP cc_start: 0.8711 (t-100) cc_final: 0.8483 (t-100) REVERT: X 11 ILE cc_start: 0.7183 (pt) cc_final: 0.6980 (pt) REVERT: X 82 ASP cc_start: 0.8975 (m-30) cc_final: 0.8706 (m-30) REVERT: X 155 ASN cc_start: 0.8684 (m-40) cc_final: 0.8308 (m-40) REVERT: Y 77 THR cc_start: 0.7407 (m) cc_final: 0.7168 (p) REVERT: Y 211 MET cc_start: 0.7769 (tpt) cc_final: 0.7392 (tpp) REVERT: Z 66 LYS cc_start: 0.7986 (mtpt) cc_final: 0.6954 (mtpp) REVERT: Z 78 MET cc_start: 0.8150 (tmm) cc_final: 0.7793 (tmm) REVERT: Z 86 LYS cc_start: 0.9385 (mttm) cc_final: 0.8886 (tppt) REVERT: Z 107 MET cc_start: 0.6711 (tpt) cc_final: 0.6352 (tpt) REVERT: Z 112 VAL cc_start: 0.9058 (t) cc_final: 0.8832 (t) REVERT: Z 203 LYS cc_start: 0.9243 (tttt) cc_final: 0.8895 (tptt) REVERT: a 41 LYS cc_start: 0.9082 (tttt) cc_final: 0.8644 (ptpt) REVERT: a 62 LYS cc_start: 0.8680 (mmmt) cc_final: 0.8225 (mtpt) REVERT: a 94 ASP cc_start: 0.8884 (m-30) cc_final: 0.8585 (m-30) REVERT: a 152 ASN cc_start: 0.8996 (t0) cc_final: 0.8724 (t0) REVERT: a 154 PHE cc_start: 0.8074 (m-10) cc_final: 0.7460 (m-80) REVERT: a 161 ILE cc_start: 0.8709 (mp) cc_final: 0.8421 (tp) REVERT: a 208 LYS cc_start: 0.9094 (pptt) cc_final: 0.8838 (pptt) REVERT: b 89 ASP cc_start: 0.9156 (m-30) cc_final: 0.8544 (p0) REVERT: b 93 GLU cc_start: 0.9132 (pt0) cc_final: 0.8271 (pp20) REVERT: b 97 ASN cc_start: 0.9171 (m110) cc_final: 0.8159 (m-40) REVERT: b 150 MET cc_start: 0.7219 (ttp) cc_final: 0.6265 (tmm) REVERT: b 181 MET cc_start: 0.9186 (pmm) cc_final: 0.8864 (pmm) REVERT: O 53 GLN cc_start: 0.8183 (tt0) cc_final: 0.7961 (tp40) REVERT: O 96 TYR cc_start: 0.8047 (m-80) cc_final: 0.7712 (m-80) REVERT: O 131 MET cc_start: 0.8775 (mmm) cc_final: 0.7770 (mmm) REVERT: P 118 GLN cc_start: 0.8173 (tp40) cc_final: 0.7872 (tp40) REVERT: Q 84 ASN cc_start: 0.9244 (t0) cc_final: 0.8868 (m110) REVERT: Q 174 MET cc_start: 0.8218 (tpp) cc_final: 0.7998 (tpp) REVERT: Q 201 MET cc_start: 0.8469 (tpt) cc_final: 0.8182 (tpt) REVERT: R 77 THR cc_start: 0.7624 (m) cc_final: 0.7085 (m) REVERT: S 69 GLU cc_start: 0.8393 (tt0) cc_final: 0.8081 (tm-30) REVERT: S 98 ASN cc_start: 0.9261 (m110) cc_final: 0.9029 (m-40) REVERT: S 107 MET cc_start: 0.9014 (ttt) cc_final: 0.8081 (ttt) REVERT: S 201 ILE cc_start: 0.9566 (mt) cc_final: 0.9263 (tp) REVERT: S 206 MET cc_start: 0.8348 (mmt) cc_final: 0.7814 (mmm) REVERT: T 26 MET cc_start: 0.7383 (mmp) cc_final: 0.6683 (mmm) REVERT: U 135 PHE cc_start: 0.7320 (p90) cc_final: 0.6768 (p90) outliers start: 1 outliers final: 1 residues processed: 859 average time/residue: 0.4981 time to fit residues: 691.1576 Evaluate side-chains 641 residues out of total 5143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 640 time to evaluate : 4.185 ------------------------------------------------------------------------------- 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: 8.9990 chunk 333 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 437 optimal weight: 20.0000 chunk 242 optimal weight: 3.9990 chunk 501 optimal weight: 10.0000 chunk 406 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 300 optimal weight: 6.9990 chunk 527 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN D 87 ASN F 36 HIS ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN K 101 ASN ** M 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 61 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** W 168 ASN Y 92 GLN ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 152 GLN ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN ** b 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 220 ASN ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN T 21 GLN U 105 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.6152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 49014 Z= 0.253 Angle : 0.610 10.399 66222 Z= 0.321 Chirality : 0.044 0.188 7441 Planarity : 0.005 0.100 8531 Dihedral : 4.735 33.767 6803 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.72 % Rotamer: Outliers : 0.04 % Allowed : 1.94 % Favored : 98.02 % 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: -0.58 (0.10), residues: 6137 helix: -0.07 (0.11), residues: 2184 sheet: -0.29 (0.13), residues: 1540 loop : -0.52 (0.13), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP N 91 HIS 0.010 0.001 HIS a 190 PHE 0.023 0.002 PHE T 87 TYR 0.023 0.002 TYR O 103 ARG 0.018 0.001 ARG S 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 5143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 810 time to evaluate : 4.438 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: A 116 MET cc_start: 0.7177 (pmm) cc_final: 0.6479 (pmm) REVERT: A 134 TYR cc_start: 0.8829 (m-80) cc_final: 0.8498 (m-80) REVERT: C 65 ARG cc_start: 0.8906 (mtp85) cc_final: 0.8702 (mmm-85) REVERT: C 68 PHE cc_start: 0.8320 (t80) cc_final: 0.8061 (t80) REVERT: C 72 LEU cc_start: 0.9388 (mt) cc_final: 0.9175 (mt) REVERT: C 96 GLU cc_start: 0.8244 (pp20) cc_final: 0.7680 (pp20) REVERT: C 130 MET cc_start: 0.7019 (ttm) cc_final: 0.6303 (ttm) REVERT: C 170 MET cc_start: 0.8648 (mmm) cc_final: 0.8399 (mtp) REVERT: C 185 ILE cc_start: 0.8655 (mt) cc_final: 0.8376 (mm) REVERT: D 62 LYS cc_start: 0.9094 (tttp) cc_final: 0.8838 (tttp) REVERT: D 69 MET cc_start: 0.7684 (ttm) cc_final: 0.7179 (tpp) REVERT: E 45 MET cc_start: 0.6707 (ttt) cc_final: 0.6425 (ttt) REVERT: E 67 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8228 (mm-30) REVERT: F 74 MET cc_start: 0.9164 (mtt) cc_final: 0.8790 (mtp) REVERT: F 76 LYS cc_start: 0.9090 (mmtt) cc_final: 0.8850 (mmtm) REVERT: G 5 MET cc_start: 0.7047 (mmm) cc_final: 0.6618 (mmm) REVERT: G 83 TYR cc_start: 0.8530 (m-10) cc_final: 0.8244 (m-80) REVERT: G 127 MET cc_start: 0.8192 (ptp) cc_final: 0.7332 (pmm) REVERT: H 4 MET cc_start: 0.7062 (tpt) cc_final: 0.6278 (tpp) REVERT: H 62 GLN cc_start: 0.8932 (mp10) cc_final: 0.8494 (mp10) REVERT: H 120 MET cc_start: 0.8382 (tmm) cc_final: 0.7888 (tmm) REVERT: I 30 ASN cc_start: 0.7845 (t0) cc_final: 0.7631 (t0) REVERT: I 58 LEU cc_start: 0.9584 (mt) cc_final: 0.9273 (tp) REVERT: I 62 ASN cc_start: 0.9225 (m-40) cc_final: 0.8810 (m110) REVERT: J 96 GLU cc_start: 0.8489 (pp20) cc_final: 0.7992 (pp20) REVERT: J 148 MET cc_start: 0.8772 (mmm) cc_final: 0.8405 (mmm) REVERT: K 38 MET cc_start: 0.8228 (mmp) cc_final: 0.7543 (mmm) REVERT: K 68 LYS cc_start: 0.8761 (mmtt) cc_final: 0.8352 (mmtm) REVERT: L 45 MET cc_start: 0.3739 (tpp) cc_final: 0.3490 (mmm) REVERT: L 100 MET cc_start: 0.5929 (mpp) cc_final: 0.4796 (mpp) REVERT: M 31 GLU cc_start: 0.8468 (pp20) cc_final: 0.7924 (pm20) REVERT: M 83 MET cc_start: 0.9052 (tpp) cc_final: 0.8448 (mmm) REVERT: M 91 MET cc_start: 0.8339 (mmp) cc_final: 0.7857 (mmm) REVERT: M 158 MET cc_start: 0.8762 (mtp) cc_final: 0.8323 (mtp) REVERT: N 50 MET cc_start: 0.8456 (ptm) cc_final: 0.7756 (ppp) REVERT: N 56 ASP cc_start: 0.7701 (t0) cc_final: 0.7306 (t0) REVERT: N 59 ASP cc_start: 0.6376 (p0) cc_final: 0.5515 (p0) REVERT: V 71 PHE cc_start: 0.8435 (m-10) cc_final: 0.8205 (m-80) REVERT: V 106 TYR cc_start: 0.7547 (m-10) cc_final: 0.7327 (m-10) REVERT: W 90 ARG cc_start: 0.7488 (mtt180) cc_final: 0.7156 (mtt180) REVERT: X 11 ILE cc_start: 0.7406 (pt) cc_final: 0.7205 (pt) REVERT: X 155 ASN cc_start: 0.8740 (m-40) cc_final: 0.8443 (m-40) REVERT: Z 69 GLU cc_start: 0.8910 (tt0) cc_final: 0.8646 (tt0) REVERT: Z 86 LYS cc_start: 0.9384 (mttm) cc_final: 0.8841 (tppt) REVERT: Z 90 ASP cc_start: 0.8902 (m-30) cc_final: 0.8657 (m-30) REVERT: Z 98 ASN cc_start: 0.9083 (m-40) cc_final: 0.8853 (m-40) REVERT: Z 107 MET cc_start: 0.6795 (tpt) cc_final: 0.5361 (tpt) REVERT: Z 112 VAL cc_start: 0.9158 (t) cc_final: 0.8874 (t) REVERT: Z 133 MET cc_start: 0.6353 (ttp) cc_final: 0.5862 (tmm) REVERT: Z 203 LYS cc_start: 0.9256 (tttt) cc_final: 0.8921 (tptt) REVERT: a 41 LYS cc_start: 0.9083 (tttt) cc_final: 0.8532 (mtmm) REVERT: a 62 LYS cc_start: 0.8650 (mmmt) cc_final: 0.8259 (mtpt) REVERT: a 94 ASP cc_start: 0.8860 (m-30) cc_final: 0.8567 (m-30) REVERT: a 152 ASN cc_start: 0.8783 (t0) cc_final: 0.8553 (t0) REVERT: a 154 PHE cc_start: 0.8197 (m-10) cc_final: 0.7774 (m-80) REVERT: a 161 ILE cc_start: 0.8747 (mp) cc_final: 0.8431 (tp) REVERT: a 180 MET cc_start: 0.8670 (tpt) cc_final: 0.8398 (tpp) REVERT: a 208 LYS cc_start: 0.9031 (pptt) cc_final: 0.8758 (pptt) REVERT: b 89 ASP cc_start: 0.9149 (m-30) cc_final: 0.8573 (p0) REVERT: b 93 GLU cc_start: 0.9028 (pt0) cc_final: 0.8212 (pp20) REVERT: b 97 ASN cc_start: 0.9138 (m110) cc_final: 0.8166 (m-40) REVERT: b 150 MET cc_start: 0.7142 (ttp) cc_final: 0.6239 (tmm) REVERT: O 53 GLN cc_start: 0.8195 (tt0) cc_final: 0.7972 (tp40) REVERT: O 96 TYR cc_start: 0.8188 (m-80) cc_final: 0.7881 (m-80) REVERT: O 131 MET cc_start: 0.8814 (mmm) cc_final: 0.7813 (mmm) REVERT: P 118 GLN cc_start: 0.8204 (tp40) cc_final: 0.7920 (tp40) REVERT: Q 84 ASN cc_start: 0.9263 (t0) cc_final: 0.8908 (m110) REVERT: Q 95 GLN cc_start: 0.9025 (mp10) cc_final: 0.8698 (mp10) REVERT: Q 201 MET cc_start: 0.8362 (tpt) cc_final: 0.8068 (tpt) REVERT: R 77 THR cc_start: 0.7722 (m) cc_final: 0.7203 (m) REVERT: S 69 GLU cc_start: 0.8336 (tt0) cc_final: 0.8086 (tm-30) REVERT: S 201 ILE cc_start: 0.9586 (mt) cc_final: 0.9297 (tp) REVERT: S 206 MET cc_start: 0.8470 (mmt) cc_final: 0.7818 (mmm) REVERT: U 135 PHE cc_start: 0.7612 (p90) cc_final: 0.7245 (p90) outliers start: 2 outliers final: 1 residues processed: 811 average time/residue: 0.4981 time to fit residues: 654.2645 Evaluate side-chains 614 residues out of total 5143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 613 time to evaluate : 4.169 ------------------------------------------------------------------------------- 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: 9.9990 chunk 529 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 345 optimal weight: 9.9990 chunk 145 optimal weight: 20.0000 chunk 588 optimal weight: 10.0000 chunk 488 optimal weight: 7.9990 chunk 272 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 308 optimal weight: 0.0170 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 25 GLN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 194 GLN ** W 94 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** Y 94 HIS ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 143 ASN ** b 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 224 HIS ** O 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 98 ASN S 99 HIS S 118 ASN T 59 HIS U 105 ASN U 143 ASN ** U 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.6377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 49014 Z= 0.233 Angle : 0.607 12.562 66222 Z= 0.315 Chirality : 0.044 0.304 7441 Planarity : 0.005 0.076 8531 Dihedral : 4.692 33.215 6803 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.31 % Favored : 96.66 % Rotamer: Outliers : 0.02 % Allowed : 1.36 % Favored : 98.62 % 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: -0.45 (0.10), residues: 6137 helix: 0.12 (0.11), residues: 2177 sheet: -0.31 (0.13), residues: 1538 loop : -0.48 (0.13), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP b 215 HIS 0.010 0.001 HIS U 110 PHE 0.028 0.002 PHE a 87 TYR 0.025 0.002 TYR J 95 ARG 0.017 0.001 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 5143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 791 time to evaluate : 4.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.7322 (pmm) cc_final: 0.6653 (pmm) REVERT: A 119 MET cc_start: 0.7660 (ptp) cc_final: 0.7405 (ptp) REVERT: A 134 TYR cc_start: 0.8837 (m-80) cc_final: 0.8440 (m-80) REVERT: A 164 MET cc_start: 0.7740 (mmp) cc_final: 0.7518 (mmp) REVERT: B 24 MET cc_start: 0.7779 (mmm) cc_final: 0.7363 (mmp) REVERT: C 68 PHE cc_start: 0.8184 (t80) cc_final: 0.7925 (t80) REVERT: C 74 GLU cc_start: 0.8360 (tp30) cc_final: 0.8072 (tp30) REVERT: C 130 MET cc_start: 0.6976 (ttm) cc_final: 0.5968 (ttm) REVERT: C 157 MET cc_start: 0.7908 (mmp) cc_final: 0.7487 (mmp) REVERT: D 28 MET cc_start: 0.6449 (ptm) cc_final: 0.6243 (ptp) REVERT: D 62 LYS cc_start: 0.9004 (tttp) cc_final: 0.8757 (tttp) REVERT: D 69 MET cc_start: 0.7530 (ttm) cc_final: 0.6985 (tpp) REVERT: E 45 MET cc_start: 0.6722 (ttt) cc_final: 0.6464 (ttt) REVERT: E 67 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8319 (mm-30) REVERT: F 69 GLU cc_start: 0.9253 (mp0) cc_final: 0.8513 (mp0) REVERT: F 74 MET cc_start: 0.9169 (mtt) cc_final: 0.8791 (mtp) REVERT: F 76 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8834 (mmtm) REVERT: F 158 MET cc_start: 0.6965 (mmp) cc_final: 0.6604 (mmm) REVERT: F 213 ASP cc_start: 0.3856 (m-30) cc_final: 0.3502 (m-30) REVERT: G 5 MET cc_start: 0.6570 (mmm) cc_final: 0.6158 (mmm) REVERT: G 30 TYR cc_start: 0.7950 (t80) cc_final: 0.7039 (t80) REVERT: G 83 TYR cc_start: 0.8502 (m-10) cc_final: 0.8236 (m-80) REVERT: G 127 MET cc_start: 0.8179 (ptp) cc_final: 0.7305 (pmm) REVERT: H 4 MET cc_start: 0.6956 (tpt) cc_final: 0.6067 (tpp) REVERT: H 62 GLN cc_start: 0.8892 (mp10) cc_final: 0.8416 (mp10) REVERT: H 120 MET cc_start: 0.8398 (tmm) cc_final: 0.7955 (tmm) REVERT: I 30 ASN cc_start: 0.7673 (t0) cc_final: 0.7389 (t0) REVERT: I 31 CYS cc_start: 0.6622 (t) cc_final: 0.6304 (t) REVERT: I 58 LEU cc_start: 0.9623 (mt) cc_final: 0.9227 (tp) REVERT: I 62 ASN cc_start: 0.9293 (m-40) cc_final: 0.8803 (m110) REVERT: J 87 MET cc_start: 0.8413 (mmm) cc_final: 0.7988 (mmm) REVERT: J 96 GLU cc_start: 0.8401 (pp20) cc_final: 0.7937 (pp20) REVERT: J 148 MET cc_start: 0.8868 (mmm) cc_final: 0.8581 (mmm) REVERT: K 38 MET cc_start: 0.8260 (mmp) cc_final: 0.7471 (mmm) REVERT: K 62 LYS cc_start: 0.9017 (tptt) cc_final: 0.8744 (tptt) REVERT: K 68 LYS cc_start: 0.8774 (mmtt) cc_final: 0.8269 (mmtm) REVERT: K 118 MET cc_start: 0.4782 (ttm) cc_final: 0.4464 (ttp) REVERT: L 45 MET cc_start: 0.3739 (tpp) cc_final: 0.3480 (mmm) REVERT: L 100 MET cc_start: 0.5911 (mpp) cc_final: 0.4792 (mpp) REVERT: M 31 GLU cc_start: 0.8494 (pp20) cc_final: 0.7855 (pm20) REVERT: M 83 MET cc_start: 0.9124 (tpp) cc_final: 0.8415 (tpp) REVERT: M 91 MET cc_start: 0.8327 (mmp) cc_final: 0.7791 (mmp) REVERT: M 158 MET cc_start: 0.8718 (mtp) cc_final: 0.8342 (mtp) REVERT: N 50 MET cc_start: 0.8421 (ptm) cc_final: 0.7665 (ppp) REVERT: N 56 ASP cc_start: 0.7727 (t0) cc_final: 0.7184 (t0) REVERT: N 59 ASP cc_start: 0.6426 (p0) cc_final: 0.5496 (p0) REVERT: N 126 ASP cc_start: 0.8240 (t70) cc_final: 0.7685 (t0) REVERT: V 71 PHE cc_start: 0.8415 (m-10) cc_final: 0.8118 (m-80) REVERT: W 90 ARG cc_start: 0.7388 (mtt180) cc_final: 0.7097 (mtt180) REVERT: X 5 TYR cc_start: 0.7810 (m-80) cc_final: 0.7473 (m-10) REVERT: X 11 ILE cc_start: 0.7376 (pt) cc_final: 0.7170 (pt) REVERT: Y 77 THR cc_start: 0.7073 (p) cc_final: 0.6139 (p) REVERT: Z 59 MET cc_start: 0.8335 (mtm) cc_final: 0.8087 (mpp) REVERT: Z 86 LYS cc_start: 0.9363 (mttm) cc_final: 0.8807 (tppt) REVERT: Z 90 ASP cc_start: 0.9027 (m-30) cc_final: 0.8756 (m-30) REVERT: Z 107 MET cc_start: 0.6993 (tpt) cc_final: 0.6051 (tpt) REVERT: Z 112 VAL cc_start: 0.9135 (t) cc_final: 0.8910 (t) REVERT: Z 133 MET cc_start: 0.6500 (ttp) cc_final: 0.5884 (tmm) REVERT: Z 203 LYS cc_start: 0.9257 (tttt) cc_final: 0.8927 (tptt) REVERT: a 41 LYS cc_start: 0.9056 (tttt) cc_final: 0.8489 (mtmm) REVERT: a 62 LYS cc_start: 0.8616 (mmmt) cc_final: 0.8262 (mtpt) REVERT: a 94 ASP cc_start: 0.8877 (m-30) cc_final: 0.8559 (m-30) REVERT: a 152 ASN cc_start: 0.8776 (t0) cc_final: 0.8560 (t0) REVERT: a 154 PHE cc_start: 0.8312 (m-10) cc_final: 0.7958 (m-80) REVERT: a 161 ILE cc_start: 0.8721 (mp) cc_final: 0.8427 (tp) REVERT: a 180 MET cc_start: 0.8679 (tpt) cc_final: 0.8429 (tpp) REVERT: a 208 LYS cc_start: 0.9013 (pptt) cc_final: 0.8745 (pptt) REVERT: b 89 ASP cc_start: 0.9135 (m-30) cc_final: 0.8575 (p0) REVERT: b 93 GLU cc_start: 0.8997 (pt0) cc_final: 0.8288 (pp20) REVERT: b 97 ASN cc_start: 0.9206 (m110) cc_final: 0.8257 (m-40) REVERT: b 150 MET cc_start: 0.7075 (ttp) cc_final: 0.6285 (tmm) REVERT: O 96 TYR cc_start: 0.8298 (m-80) cc_final: 0.7789 (m-80) REVERT: O 131 MET cc_start: 0.8750 (mmm) cc_final: 0.7703 (mmm) REVERT: Q 84 ASN cc_start: 0.9259 (t0) cc_final: 0.8872 (m110) REVERT: Q 201 MET cc_start: 0.8355 (tpt) cc_final: 0.8074 (tpt) REVERT: R 77 THR cc_start: 0.7661 (m) cc_final: 0.7207 (m) REVERT: R 92 GLN cc_start: 0.9020 (mp10) cc_final: 0.8762 (mp10) REVERT: S 69 GLU cc_start: 0.8301 (tt0) cc_final: 0.8065 (tm-30) REVERT: S 201 ILE cc_start: 0.9566 (mt) cc_final: 0.9286 (tp) REVERT: S 206 MET cc_start: 0.8572 (mmt) cc_final: 0.7821 (mmm) REVERT: T 26 MET cc_start: 0.7341 (mmp) cc_final: 0.6522 (mmm) REVERT: U 97 ASN cc_start: 0.8926 (m-40) cc_final: 0.8455 (t0) REVERT: U 101 ASN cc_start: 0.8046 (m-40) cc_final: 0.7694 (m-40) REVERT: U 135 PHE cc_start: 0.7615 (p90) cc_final: 0.7387 (p90) outliers start: 1 outliers final: 1 residues processed: 792 average time/residue: 0.4984 time to fit residues: 641.1526 Evaluate side-chains 600 residues out of total 5143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 599 time to evaluate : 4.204 ------------------------------------------------------------------------------- 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: 20.0000 chunk 66 optimal weight: 20.0000 chunk 335 optimal weight: 20.0000 chunk 429 optimal weight: 8.9990 chunk 332 optimal weight: 3.9990 chunk 495 optimal weight: 30.0000 chunk 328 optimal weight: 7.9990 chunk 586 optimal weight: 20.0000 chunk 366 optimal weight: 9.9990 chunk 357 optimal weight: 8.9990 chunk 270 optimal weight: 3.9990 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 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 13 HIS ** W 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 206 ASN ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 143 ASN ** b 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 GLN ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN U 105 ASN ** U 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.6714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 49014 Z= 0.298 Angle : 0.658 10.676 66222 Z= 0.344 Chirality : 0.045 0.359 7441 Planarity : 0.005 0.091 8531 Dihedral : 4.851 33.189 6803 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.14 % Favored : 95.83 % Rotamer: Outliers : 0.02 % Allowed : 1.21 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.11), residues: 6137 helix: 0.06 (0.11), residues: 2164 sheet: -0.34 (0.13), residues: 1544 loop : -0.63 (0.13), residues: 2429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP N 107 HIS 0.010 0.002 HIS b 110 PHE 0.024 0.002 PHE V 188 TYR 0.021 0.002 TYR O 103 ARG 0.014 0.001 ARG E 180 *********************** 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 771 residues out of total 5143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 770 time to evaluate : 4.239 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: A 95 MET cc_start: 0.7454 (tmm) cc_final: 0.6692 (tmm) REVERT: A 119 MET cc_start: 0.7716 (ptp) cc_final: 0.7436 (ptp) REVERT: A 134 TYR cc_start: 0.8904 (m-80) cc_final: 0.8517 (m-80) REVERT: B 24 MET cc_start: 0.7773 (mmm) cc_final: 0.7165 (mmp) REVERT: C 13 MET cc_start: 0.6953 (mmm) cc_final: 0.6707 (mmm) REVERT: C 68 PHE cc_start: 0.8108 (t80) cc_final: 0.7789 (t80) REVERT: C 74 GLU cc_start: 0.8533 (tp30) cc_final: 0.8233 (tp30) REVERT: C 93 LEU cc_start: 0.9413 (tt) cc_final: 0.8728 (tt) REVERT: C 130 MET cc_start: 0.6109 (ttm) cc_final: 0.5364 (ttm) REVERT: D 69 MET cc_start: 0.7760 (ttm) cc_final: 0.7215 (tpp) REVERT: E 45 MET cc_start: 0.6992 (ttt) cc_final: 0.6764 (ttt) REVERT: F 74 MET cc_start: 0.9207 (mtt) cc_final: 0.8816 (mtp) REVERT: F 158 MET cc_start: 0.6868 (mmp) cc_final: 0.6659 (mmm) REVERT: F 213 ASP cc_start: 0.4058 (m-30) cc_final: 0.3689 (m-30) REVERT: G 83 TYR cc_start: 0.8431 (m-10) cc_final: 0.8127 (m-80) REVERT: G 127 MET cc_start: 0.8207 (ptp) cc_final: 0.7875 (pmm) REVERT: H 4 MET cc_start: 0.6911 (tpt) cc_final: 0.6263 (tpp) REVERT: H 62 GLN cc_start: 0.8900 (mp10) cc_final: 0.8435 (mp10) REVERT: H 88 TYR cc_start: 0.8264 (t80) cc_final: 0.8057 (t80) REVERT: H 120 MET cc_start: 0.8513 (tmm) cc_final: 0.8052 (tmm) REVERT: I 30 ASN cc_start: 0.7806 (t0) cc_final: 0.7481 (t0) REVERT: I 31 CYS cc_start: 0.6758 (t) cc_final: 0.6413 (t) REVERT: I 58 LEU cc_start: 0.9636 (mt) cc_final: 0.9245 (tp) REVERT: I 62 ASN cc_start: 0.9312 (m-40) cc_final: 0.8807 (m110) REVERT: J 69 ARG cc_start: 0.8986 (mtt180) cc_final: 0.8711 (mtt180) REVERT: J 87 MET cc_start: 0.8379 (mmm) cc_final: 0.8000 (mmm) REVERT: J 96 GLU cc_start: 0.8503 (pp20) cc_final: 0.8045 (pp20) REVERT: J 157 MET cc_start: 0.8349 (mmm) cc_final: 0.8128 (mmm) REVERT: K 38 MET cc_start: 0.8449 (mmp) cc_final: 0.8071 (mmm) REVERT: K 68 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8261 (mmtm) REVERT: K 186 ASN cc_start: 0.9501 (m-40) cc_final: 0.9288 (m-40) REVERT: L 45 MET cc_start: 0.3814 (tpp) cc_final: 0.3528 (mmm) REVERT: L 93 MET cc_start: 0.8425 (mtt) cc_final: 0.8181 (mtt) REVERT: L 100 MET cc_start: 0.5721 (mpp) cc_final: 0.4608 (mpp) REVERT: M 31 GLU cc_start: 0.8451 (pp20) cc_final: 0.7839 (pm20) REVERT: M 91 MET cc_start: 0.8360 (mmp) cc_final: 0.7516 (mmp) REVERT: M 158 MET cc_start: 0.8757 (mtp) cc_final: 0.8276 (mtp) REVERT: N 50 MET cc_start: 0.8586 (ptm) cc_final: 0.7871 (ppp) REVERT: N 56 ASP cc_start: 0.7862 (t0) cc_final: 0.7358 (t70) REVERT: N 59 ASP cc_start: 0.6617 (p0) cc_final: 0.5993 (p0) REVERT: V 71 PHE cc_start: 0.8374 (m-10) cc_final: 0.8044 (m-80) REVERT: V 239 HIS cc_start: 0.8362 (m90) cc_final: 0.8105 (m90) REVERT: X 5 TYR cc_start: 0.8149 (m-80) cc_final: 0.7764 (m-10) REVERT: X 11 ILE cc_start: 0.7525 (pt) cc_final: 0.7294 (pt) REVERT: X 82 ASP cc_start: 0.9004 (m-30) cc_final: 0.8723 (m-30) REVERT: X 155 ASN cc_start: 0.8518 (m-40) cc_final: 0.8310 (m110) REVERT: Y 77 THR cc_start: 0.7482 (p) cc_final: 0.6755 (p) REVERT: Y 86 ARG cc_start: 0.8336 (mtm180) cc_final: 0.8120 (mtm180) REVERT: Z 86 LYS cc_start: 0.9348 (mttm) cc_final: 0.8769 (tppt) REVERT: Z 90 ASP cc_start: 0.9070 (m-30) cc_final: 0.8568 (m-30) REVERT: Z 98 ASN cc_start: 0.9006 (m-40) cc_final: 0.8762 (m-40) REVERT: Z 107 MET cc_start: 0.7067 (tpt) cc_final: 0.6046 (tpt) REVERT: Z 133 MET cc_start: 0.6693 (ttp) cc_final: 0.5814 (tmm) REVERT: Z 203 LYS cc_start: 0.9272 (tttt) cc_final: 0.8945 (tptt) REVERT: a 41 LYS cc_start: 0.9207 (tttt) cc_final: 0.8741 (ptpt) REVERT: a 62 LYS cc_start: 0.8684 (mmmt) cc_final: 0.8386 (mtpt) REVERT: a 92 CYS cc_start: 0.9248 (m) cc_final: 0.9018 (m) REVERT: a 94 ASP cc_start: 0.8675 (m-30) cc_final: 0.8426 (m-30) REVERT: a 208 LYS cc_start: 0.9056 (pptt) cc_final: 0.8854 (pptt) REVERT: b 57 LEU cc_start: 0.8772 (mt) cc_final: 0.8386 (mp) REVERT: b 93 GLU cc_start: 0.8949 (pt0) cc_final: 0.8166 (pp20) REVERT: b 97 ASN cc_start: 0.9080 (m110) cc_final: 0.7873 (m-40) REVERT: b 150 MET cc_start: 0.7045 (ttp) cc_final: 0.6113 (tmm) REVERT: O 95 ARG cc_start: 0.8630 (mtt180) cc_final: 0.8327 (mtt180) REVERT: O 96 TYR cc_start: 0.8192 (m-80) cc_final: 0.7673 (m-80) REVERT: O 131 MET cc_start: 0.8786 (mmm) cc_final: 0.7756 (mmm) REVERT: O 196 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8037 (tp30) REVERT: Q 84 ASN cc_start: 0.9281 (t0) cc_final: 0.8933 (m110) REVERT: Q 201 MET cc_start: 0.8328 (tpt) cc_final: 0.8041 (tpt) REVERT: R 77 THR cc_start: 0.7703 (m) cc_final: 0.7293 (m) REVERT: R 91 CYS cc_start: 0.8813 (m) cc_final: 0.8530 (m) REVERT: R 92 GLN cc_start: 0.9112 (mp10) cc_final: 0.8865 (mp10) REVERT: S 103 TYR cc_start: 0.8373 (m-80) cc_final: 0.7924 (m-80) REVERT: S 201 ILE cc_start: 0.9587 (mt) cc_final: 0.9312 (tp) REVERT: T 26 MET cc_start: 0.7306 (mmp) cc_final: 0.6651 (mmm) REVERT: U 135 PHE cc_start: 0.7828 (p90) cc_final: 0.7324 (p90) outliers start: 1 outliers final: 1 residues processed: 771 average time/residue: 0.4973 time to fit residues: 623.5569 Evaluate side-chains 582 residues out of total 5143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 581 time to evaluate : 4.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 362 optimal weight: 20.0000 chunk 234 optimal weight: 10.0000 chunk 349 optimal weight: 30.0000 chunk 176 optimal weight: 0.8980 chunk 115 optimal weight: 0.0570 chunk 113 optimal weight: 1.9990 chunk 372 optimal weight: 10.0000 chunk 399 optimal weight: 7.9990 chunk 289 optimal weight: 30.0000 chunk 54 optimal weight: 9.9990 chunk 460 optimal weight: 8.9990 overall best weight: 3.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 HIS ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 95 GLN ** W 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 GLN ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN ** b 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 GLN ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 227 HIS U 105 ASN U 224 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.6834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 49014 Z= 0.218 Angle : 0.624 10.672 66222 Z= 0.323 Chirality : 0.044 0.295 7441 Planarity : 0.004 0.067 8531 Dihedral : 4.738 33.279 6803 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.39 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: -0.45 (0.11), residues: 6137 helix: 0.19 (0.11), residues: 2206 sheet: -0.30 (0.13), residues: 1552 loop : -0.57 (0.13), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP N 91 HIS 0.023 0.001 HIS C 161 PHE 0.025 0.002 PHE V 188 TYR 0.023 0.002 TYR U 160 ARG 0.013 0.001 ARG R 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 5143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 769 time to evaluate : 4.215 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: A 4 MET cc_start: 0.7637 (tpt) cc_final: 0.7084 (tpt) REVERT: A 116 MET cc_start: 0.7437 (pmm) cc_final: 0.7153 (pmm) REVERT: A 119 MET cc_start: 0.7634 (ptp) cc_final: 0.7360 (ptp) REVERT: A 134 TYR cc_start: 0.8876 (m-80) cc_final: 0.8493 (m-80) REVERT: B 24 MET cc_start: 0.7723 (mmm) cc_final: 0.7213 (mmp) REVERT: C 68 PHE cc_start: 0.8115 (t80) cc_final: 0.7768 (t80) REVERT: C 74 GLU cc_start: 0.8610 (tp30) cc_final: 0.8358 (tp30) REVERT: C 93 LEU cc_start: 0.9390 (tt) cc_final: 0.8802 (tt) REVERT: C 130 MET cc_start: 0.6251 (ttm) cc_final: 0.5414 (ttm) REVERT: E 45 MET cc_start: 0.6953 (ttt) cc_final: 0.6673 (ttt) REVERT: E 97 MET cc_start: 0.5680 (tmm) cc_final: 0.5195 (tmm) REVERT: E 139 MET cc_start: 0.8150 (tmm) cc_final: 0.7846 (tmm) REVERT: F 69 GLU cc_start: 0.9268 (mp0) cc_final: 0.8596 (mp0) REVERT: F 74 MET cc_start: 0.9252 (mtt) cc_final: 0.8948 (mtp) REVERT: F 76 LYS cc_start: 0.9154 (mmtt) cc_final: 0.8858 (mppt) REVERT: F 91 MET cc_start: 0.8262 (mmm) cc_final: 0.7851 (mmm) REVERT: F 130 TYR cc_start: 0.7972 (t80) cc_final: 0.7647 (t80) REVERT: F 213 ASP cc_start: 0.3717 (m-30) cc_final: 0.3456 (m-30) REVERT: G 81 HIS cc_start: 0.8093 (m90) cc_final: 0.7591 (m90) REVERT: G 83 TYR cc_start: 0.8438 (m-10) cc_final: 0.8118 (m-10) REVERT: G 127 MET cc_start: 0.7865 (ptp) cc_final: 0.7612 (pmm) REVERT: H 4 MET cc_start: 0.6707 (tpt) cc_final: 0.6078 (tpp) REVERT: H 62 GLN cc_start: 0.8863 (mp10) cc_final: 0.8366 (mp10) REVERT: H 120 MET cc_start: 0.8437 (tmm) cc_final: 0.8222 (tmm) REVERT: I 30 ASN cc_start: 0.7643 (t0) cc_final: 0.7383 (t0) REVERT: I 31 CYS cc_start: 0.6571 (t) cc_final: 0.6275 (t) REVERT: I 58 LEU cc_start: 0.9628 (mt) cc_final: 0.9416 (mm) REVERT: I 62 ASN cc_start: 0.9358 (m-40) cc_final: 0.9063 (m110) REVERT: J 87 MET cc_start: 0.8322 (mmm) cc_final: 0.7916 (mmm) REVERT: J 96 GLU cc_start: 0.8403 (pp20) cc_final: 0.7976 (pp20) REVERT: J 170 MET cc_start: 0.8191 (mtt) cc_final: 0.7620 (mtt) REVERT: K 38 MET cc_start: 0.8357 (mmp) cc_final: 0.7950 (mmm) REVERT: K 62 LYS cc_start: 0.8952 (tptt) cc_final: 0.8707 (tptt) REVERT: K 68 LYS cc_start: 0.8752 (mmtt) cc_final: 0.8212 (mmtm) REVERT: L 45 MET cc_start: 0.3809 (tpp) cc_final: 0.3512 (mmm) REVERT: L 93 MET cc_start: 0.8409 (mtt) cc_final: 0.8183 (mtt) REVERT: L 97 MET cc_start: 0.6524 (tpp) cc_final: 0.6140 (tpp) REVERT: L 100 MET cc_start: 0.5693 (mpp) cc_final: 0.4640 (mpp) REVERT: M 31 GLU cc_start: 0.8396 (pp20) cc_final: 0.7776 (pm20) REVERT: M 91 MET cc_start: 0.8318 (mmp) cc_final: 0.7667 (mmp) REVERT: M 158 MET cc_start: 0.8670 (mtp) cc_final: 0.8232 (mtp) REVERT: N 50 MET cc_start: 0.8486 (ptm) cc_final: 0.6911 (ppp) REVERT: N 56 ASP cc_start: 0.7455 (t0) cc_final: 0.6855 (t70) REVERT: N 59 ASP cc_start: 0.6758 (p0) cc_final: 0.6079 (p0) REVERT: N 127 MET cc_start: 0.8089 (ttt) cc_final: 0.7563 (ttt) REVERT: V 71 PHE cc_start: 0.8385 (m-10) cc_final: 0.8050 (m-80) REVERT: V 106 TYR cc_start: 0.7533 (m-10) cc_final: 0.7031 (m-10) REVERT: V 126 TYR cc_start: 0.8451 (m-10) cc_final: 0.8167 (m-10) REVERT: V 132 MET cc_start: 0.7574 (tpt) cc_final: 0.7008 (mmm) REVERT: V 239 HIS cc_start: 0.8351 (m90) cc_final: 0.8124 (m90) REVERT: W 83 ARG cc_start: 0.8850 (ptp-170) cc_final: 0.8559 (ptp-170) REVERT: X 5 TYR cc_start: 0.8074 (m-80) cc_final: 0.7602 (m-10) REVERT: X 11 ILE cc_start: 0.7370 (pt) cc_final: 0.7139 (pt) REVERT: X 82 ASP cc_start: 0.8967 (m-30) cc_final: 0.8756 (m-30) REVERT: X 155 ASN cc_start: 0.8554 (m-40) cc_final: 0.8310 (m110) REVERT: Y 77 THR cc_start: 0.7383 (p) cc_final: 0.6706 (p) REVERT: Z 86 LYS cc_start: 0.9339 (mttm) cc_final: 0.8764 (tppt) REVERT: Z 90 ASP cc_start: 0.9035 (m-30) cc_final: 0.8412 (m-30) REVERT: Z 98 ASN cc_start: 0.8961 (m-40) cc_final: 0.8729 (m-40) REVERT: Z 107 MET cc_start: 0.7276 (tpt) cc_final: 0.5988 (tpt) REVERT: Z 133 MET cc_start: 0.6654 (ttp) cc_final: 0.5714 (tmm) REVERT: Z 203 LYS cc_start: 0.9268 (tttt) cc_final: 0.8948 (tptt) REVERT: a 41 LYS cc_start: 0.9158 (tttt) cc_final: 0.8567 (mtmm) REVERT: a 62 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8388 (mtpt) REVERT: a 92 CYS cc_start: 0.9216 (m) cc_final: 0.9013 (m) REVERT: b 57 LEU cc_start: 0.8736 (mt) cc_final: 0.8519 (mp) REVERT: b 67 PHE cc_start: 0.8572 (m-10) cc_final: 0.8149 (m-80) REVERT: b 75 MET cc_start: 0.7187 (ttm) cc_final: 0.6652 (ttp) REVERT: b 89 ASP cc_start: 0.9247 (m-30) cc_final: 0.8751 (p0) REVERT: b 93 GLU cc_start: 0.8957 (pt0) cc_final: 0.8190 (pp20) REVERT: b 97 ASN cc_start: 0.9140 (m110) cc_final: 0.8092 (m-40) REVERT: b 150 MET cc_start: 0.7053 (ttp) cc_final: 0.6154 (tmm) REVERT: O 95 ARG cc_start: 0.8697 (mtt180) cc_final: 0.8435 (mtt180) REVERT: O 96 TYR cc_start: 0.8309 (m-80) cc_final: 0.7805 (m-80) REVERT: O 196 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8226 (tp30) REVERT: P 87 HIS cc_start: 0.8547 (m90) cc_final: 0.8328 (m90) REVERT: Q 84 ASN cc_start: 0.9281 (t0) cc_final: 0.8929 (m110) REVERT: Q 201 MET cc_start: 0.8331 (tpt) cc_final: 0.8049 (tpt) REVERT: R 77 THR cc_start: 0.7767 (m) cc_final: 0.7317 (m) REVERT: R 92 GLN cc_start: 0.9139 (mp10) cc_final: 0.8862 (mp10) REVERT: S 103 TYR cc_start: 0.8211 (m-80) cc_final: 0.7729 (m-80) REVERT: S 201 ILE cc_start: 0.9580 (mt) cc_final: 0.9288 (tp) REVERT: T 26 MET cc_start: 0.7319 (mmp) cc_final: 0.6888 (mmm) REVERT: T 49 LEU cc_start: 0.8359 (tp) cc_final: 0.7933 (tt) REVERT: U 93 GLU cc_start: 0.8576 (pm20) cc_final: 0.8366 (pm20) REVERT: U 135 PHE cc_start: 0.7679 (p90) cc_final: 0.7375 (p90) REVERT: U 136 MET cc_start: 0.5076 (mpp) cc_final: 0.4814 (mpp) outliers start: 0 outliers final: 0 residues processed: 769 average time/residue: 0.4935 time to fit residues: 619.2495 Evaluate side-chains 595 residues out of total 5143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 595 time to evaluate : 4.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 533 optimal weight: 30.0000 chunk 561 optimal weight: 10.0000 chunk 512 optimal weight: 20.0000 chunk 546 optimal weight: 9.9990 chunk 328 optimal weight: 9.9990 chunk 237 optimal weight: 3.9990 chunk 428 optimal weight: 8.9990 chunk 167 optimal weight: 30.0000 chunk 493 optimal weight: 10.0000 chunk 516 optimal weight: 30.0000 chunk 544 optimal weight: 8.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 124 GLN ** W 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 120 GLN Z 224 GLN ** a 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 GLN ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN S 155 HIS U 105 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.7123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 49014 Z= 0.347 Angle : 0.704 14.073 66222 Z= 0.367 Chirality : 0.046 0.323 7441 Planarity : 0.005 0.072 8531 Dihedral : 5.004 33.382 6803 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.55 % Favored : 95.44 % Rotamer: Outliers : 0.02 % Allowed : 0.60 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.10), residues: 6137 helix: -0.06 (0.11), residues: 2198 sheet: -0.43 (0.13), residues: 1522 loop : -0.76 (0.13), residues: 2417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP N 91 HIS 0.020 0.002 HIS C 161 PHE 0.026 0.002 PHE V 188 TYR 0.031 0.002 TYR O 103 ARG 0.013 0.001 ARG R 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 5143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 724 time to evaluate : 4.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7525 (tmm) cc_final: 0.6884 (tmm) REVERT: A 119 MET cc_start: 0.7709 (ptp) cc_final: 0.7485 (ptp) REVERT: A 134 TYR cc_start: 0.8823 (m-80) cc_final: 0.8474 (m-80) REVERT: B 24 MET cc_start: 0.7795 (mmm) cc_final: 0.7244 (mmp) REVERT: B 174 ASP cc_start: 0.8115 (m-30) cc_final: 0.7840 (m-30) REVERT: C 68 PHE cc_start: 0.8235 (t80) cc_final: 0.7651 (t80) REVERT: C 74 GLU cc_start: 0.8604 (tp30) cc_final: 0.8226 (tp30) REVERT: C 96 GLU cc_start: 0.8391 (pp20) cc_final: 0.7921 (pp20) REVERT: C 130 MET cc_start: 0.6279 (ttm) cc_final: 0.5676 (ttp) REVERT: C 185 ILE cc_start: 0.8707 (mm) cc_final: 0.8468 (mm) REVERT: D 69 MET cc_start: 0.7841 (ttm) cc_final: 0.7282 (tpp) REVERT: E 45 MET cc_start: 0.7135 (ttt) cc_final: 0.6864 (ttt) REVERT: E 62 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8843 (mm-40) REVERT: E 67 GLU cc_start: 0.8988 (mp0) cc_final: 0.8783 (mp0) REVERT: E 139 MET cc_start: 0.8264 (tmm) cc_final: 0.8023 (tmm) REVERT: F 69 GLU cc_start: 0.9402 (mp0) cc_final: 0.8991 (mp0) REVERT: F 74 MET cc_start: 0.9229 (mtt) cc_final: 0.8901 (mtp) REVERT: F 91 MET cc_start: 0.8265 (mmm) cc_final: 0.7801 (mmm) REVERT: F 213 ASP cc_start: 0.3948 (m-30) cc_final: 0.3622 (m-30) REVERT: G 83 TYR cc_start: 0.8420 (m-10) cc_final: 0.8129 (m-10) REVERT: H 4 MET cc_start: 0.6757 (tpt) cc_final: 0.6331 (tpt) REVERT: H 62 GLN cc_start: 0.8907 (mp10) cc_final: 0.8433 (mp10) REVERT: H 120 MET cc_start: 0.8502 (tmm) cc_final: 0.7918 (tmm) REVERT: I 30 ASN cc_start: 0.7716 (t0) cc_final: 0.7418 (t0) REVERT: I 31 CYS cc_start: 0.6823 (t) cc_final: 0.6593 (t) REVERT: I 54 MET cc_start: 0.8482 (mmp) cc_final: 0.8278 (mmm) REVERT: I 62 ASN cc_start: 0.9344 (m-40) cc_final: 0.9096 (m-40) REVERT: J 87 MET cc_start: 0.8405 (mmm) cc_final: 0.7998 (mmm) REVERT: J 96 GLU cc_start: 0.8537 (pp20) cc_final: 0.8159 (pp20) REVERT: J 170 MET cc_start: 0.8252 (mtt) cc_final: 0.7551 (mtt) REVERT: K 38 MET cc_start: 0.8516 (mmp) cc_final: 0.8198 (mmm) REVERT: K 62 LYS cc_start: 0.8993 (tptt) cc_final: 0.8701 (tptt) REVERT: L 45 MET cc_start: 0.3920 (tpp) cc_final: 0.3552 (mmm) REVERT: L 93 MET cc_start: 0.8527 (mtt) cc_final: 0.8314 (mtt) REVERT: L 100 MET cc_start: 0.5808 (mpp) cc_final: 0.4839 (mpp) REVERT: M 31 GLU cc_start: 0.8419 (pp20) cc_final: 0.7655 (pm20) REVERT: M 83 MET cc_start: 0.8304 (tpt) cc_final: 0.7406 (tpt) REVERT: M 91 MET cc_start: 0.8335 (mmp) cc_final: 0.7813 (mmp) REVERT: M 158 MET cc_start: 0.8700 (mtp) cc_final: 0.8319 (mtp) REVERT: N 50 MET cc_start: 0.8426 (ptm) cc_final: 0.6873 (ppp) REVERT: N 56 ASP cc_start: 0.7562 (t0) cc_final: 0.7228 (t0) REVERT: N 59 ASP cc_start: 0.6723 (p0) cc_final: 0.5399 (p0) REVERT: N 127 MET cc_start: 0.8158 (ttt) cc_final: 0.7579 (ttt) REVERT: V 71 PHE cc_start: 0.8462 (m-10) cc_final: 0.8107 (m-80) REVERT: V 106 TYR cc_start: 0.7602 (m-10) cc_final: 0.7341 (m-10) REVERT: V 239 HIS cc_start: 0.8415 (m90) cc_final: 0.8171 (m90) REVERT: W 83 ARG cc_start: 0.8880 (ptp-170) cc_final: 0.8462 (ptp-170) REVERT: W 90 ARG cc_start: 0.7615 (mtt180) cc_final: 0.7108 (mtt180) REVERT: X 5 TYR cc_start: 0.8176 (m-80) cc_final: 0.7723 (m-10) REVERT: X 11 ILE cc_start: 0.7374 (pt) cc_final: 0.7127 (pt) REVERT: X 82 ASP cc_start: 0.9012 (m-30) cc_final: 0.8775 (m-30) REVERT: X 89 GLU cc_start: 0.8870 (mp0) cc_final: 0.8577 (mp0) REVERT: X 155 ASN cc_start: 0.8480 (m-40) cc_final: 0.8229 (m110) REVERT: Y 77 THR cc_start: 0.7532 (p) cc_final: 0.6857 (p) REVERT: Y 86 ARG cc_start: 0.8396 (mtm180) cc_final: 0.8138 (mtm180) REVERT: Y 114 LEU cc_start: 0.8784 (mt) cc_final: 0.8467 (mt) REVERT: Z 86 LYS cc_start: 0.9417 (mttm) cc_final: 0.8834 (tppt) REVERT: Z 90 ASP cc_start: 0.9101 (m-30) cc_final: 0.8453 (m-30) REVERT: Z 98 ASN cc_start: 0.8890 (m-40) cc_final: 0.8612 (m110) REVERT: Z 133 MET cc_start: 0.6995 (ttp) cc_final: 0.5829 (tmm) REVERT: Z 203 LYS cc_start: 0.9280 (tttt) cc_final: 0.8854 (tppt) REVERT: Z 228 MET cc_start: 0.8479 (mpp) cc_final: 0.8246 (mpp) REVERT: a 62 LYS cc_start: 0.8746 (mmmt) cc_final: 0.8434 (mtpt) REVERT: a 94 ASP cc_start: 0.8847 (m-30) cc_final: 0.8619 (m-30) REVERT: b 67 PHE cc_start: 0.8576 (m-10) cc_final: 0.7526 (m-10) REVERT: b 75 MET cc_start: 0.7195 (ttm) cc_final: 0.6630 (ttp) REVERT: b 89 ASP cc_start: 0.9254 (m-30) cc_final: 0.8775 (p0) REVERT: b 93 GLU cc_start: 0.9023 (pt0) cc_final: 0.8315 (pp20) REVERT: b 97 ASN cc_start: 0.9010 (m110) cc_final: 0.7642 (m-40) REVERT: b 150 MET cc_start: 0.7108 (ttp) cc_final: 0.5924 (tmm) REVERT: O 96 TYR cc_start: 0.8338 (m-80) cc_final: 0.7780 (m-80) REVERT: O 196 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8311 (tp30) REVERT: P 87 HIS cc_start: 0.8759 (m90) cc_final: 0.8448 (m90) REVERT: Q 84 ASN cc_start: 0.9312 (t0) cc_final: 0.8921 (m110) REVERT: Q 201 MET cc_start: 0.8337 (tpt) cc_final: 0.8024 (tpt) REVERT: R 77 THR cc_start: 0.7725 (m) cc_final: 0.7274 (m) REVERT: R 92 GLN cc_start: 0.9125 (mp10) cc_final: 0.8905 (mp10) REVERT: S 103 TYR cc_start: 0.8318 (m-80) cc_final: 0.7705 (m-80) REVERT: S 201 ILE cc_start: 0.9587 (mt) cc_final: 0.9278 (tp) REVERT: S 206 MET cc_start: 0.8549 (mmt) cc_final: 0.7856 (mmm) REVERT: T 49 LEU cc_start: 0.8370 (tp) cc_final: 0.8137 (tp) outliers start: 1 outliers final: 0 residues processed: 725 average time/residue: 0.4936 time to fit residues: 581.7886 Evaluate side-chains 559 residues out of total 5143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 559 time to evaluate : 4.298 ------------------------------------------------------------------------------- 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: 9.9990 chunk 273 optimal weight: 1.9990 chunk 401 optimal weight: 1.9990 chunk 605 optimal weight: 1.9990 chunk 557 optimal weight: 7.9990 chunk 482 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 372 optimal weight: 9.9990 chunk 295 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 GLN ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 HIS ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 40 ASN Y 85 ASN Y 120 GLN ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN ** b 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 GLN U 22 GLN U 105 ASN U 224 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.7147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 49014 Z= 0.204 Angle : 0.637 12.358 66222 Z= 0.329 Chirality : 0.045 0.267 7441 Planarity : 0.005 0.066 8531 Dihedral : 4.853 32.465 6803 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.73 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -0.56 (0.11), residues: 6137 helix: 0.14 (0.11), residues: 2227 sheet: -0.41 (0.13), residues: 1529 loop : -0.65 (0.13), residues: 2381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP G 91 HIS 0.010 0.001 HIS A 77 PHE 0.026 0.002 PHE V 188 TYR 0.028 0.002 TYR Y 106 ARG 0.014 0.001 ARG R 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12274 Ramachandran restraints generated. 6137 Oldfield, 0 Emsley, 6137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 5143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 756 time to evaluate : 4.320 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: A 95 MET cc_start: 0.7478 (tmm) cc_final: 0.6796 (tmm) REVERT: A 119 MET cc_start: 0.7512 (ptp) cc_final: 0.7112 (ptp) REVERT: A 134 TYR cc_start: 0.8855 (m-80) cc_final: 0.8501 (m-80) REVERT: B 24 MET cc_start: 0.7731 (mmm) cc_final: 0.7304 (mmp) REVERT: C 68 PHE cc_start: 0.8177 (t80) cc_final: 0.7795 (t80) REVERT: C 74 GLU cc_start: 0.8672 (tp30) cc_final: 0.8336 (tp30) REVERT: C 130 MET cc_start: 0.6206 (ttm) cc_final: 0.5523 (ttp) REVERT: C 185 ILE cc_start: 0.8766 (mm) cc_final: 0.8236 (mm) REVERT: D 62 LYS cc_start: 0.8923 (tttp) cc_final: 0.8667 (tttp) REVERT: D 68 LYS cc_start: 0.9095 (mtmt) cc_final: 0.8682 (mttt) REVERT: D 118 MET cc_start: 0.5588 (ptp) cc_final: 0.5333 (ptp) REVERT: E 62 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8832 (mm-40) REVERT: E 139 MET cc_start: 0.8264 (tmm) cc_final: 0.8021 (tmm) REVERT: F 69 GLU cc_start: 0.9328 (mp0) cc_final: 0.8985 (mp0) REVERT: F 76 LYS cc_start: 0.9153 (mmtt) cc_final: 0.8927 (mmtm) REVERT: F 130 TYR cc_start: 0.7979 (t80) cc_final: 0.7742 (t80) REVERT: F 213 ASP cc_start: 0.3769 (m-30) cc_final: 0.3568 (m-30) REVERT: G 5 MET cc_start: 0.7080 (tpp) cc_final: 0.5767 (tpp) REVERT: G 127 MET cc_start: 0.7277 (pmm) cc_final: 0.7019 (pmm) REVERT: H 4 MET cc_start: 0.6758 (tpt) cc_final: 0.6345 (tpt) REVERT: H 62 GLN cc_start: 0.8842 (mp10) cc_final: 0.8340 (mp10) REVERT: H 120 MET cc_start: 0.8483 (tmm) cc_final: 0.8034 (tmm) REVERT: I 30 ASN cc_start: 0.7731 (t0) cc_final: 0.7421 (t0) REVERT: I 31 CYS cc_start: 0.6576 (t) cc_final: 0.6329 (t) REVERT: I 54 MET cc_start: 0.8515 (mmp) cc_final: 0.8213 (mmm) REVERT: I 62 ASN cc_start: 0.9326 (m-40) cc_final: 0.9076 (m110) REVERT: J 87 MET cc_start: 0.8396 (mmm) cc_final: 0.8164 (mmm) REVERT: J 96 GLU cc_start: 0.8428 (pp20) cc_final: 0.8009 (pp20) REVERT: J 170 MET cc_start: 0.8186 (mtt) cc_final: 0.7475 (mtt) REVERT: K 38 MET cc_start: 0.8614 (mmp) cc_final: 0.7964 (tpp) REVERT: K 62 LYS cc_start: 0.8852 (tptt) cc_final: 0.8573 (tptt) REVERT: L 45 MET cc_start: 0.3768 (tpp) cc_final: 0.3517 (mmm) REVERT: L 93 MET cc_start: 0.8383 (mtt) cc_final: 0.8074 (mtt) REVERT: L 100 MET cc_start: 0.5784 (mpp) cc_final: 0.4692 (mpp) REVERT: L 117 GLU cc_start: 0.8987 (mp0) cc_final: 0.8777 (mp0) REVERT: M 31 GLU cc_start: 0.8347 (pp20) cc_final: 0.7730 (pm20) REVERT: M 83 MET cc_start: 0.8150 (tpt) cc_final: 0.7171 (tpt) REVERT: M 91 MET cc_start: 0.8391 (mmp) cc_final: 0.7823 (mmp) REVERT: N 56 ASP cc_start: 0.7550 (t0) cc_final: 0.7165 (t0) REVERT: N 59 ASP cc_start: 0.6678 (p0) cc_final: 0.5807 (p0) REVERT: N 127 MET cc_start: 0.8034 (ttt) cc_final: 0.7508 (ttt) REVERT: V 71 PHE cc_start: 0.8406 (m-10) cc_final: 0.8103 (m-80) REVERT: V 106 TYR cc_start: 0.7480 (m-10) cc_final: 0.7075 (m-10) REVERT: V 239 HIS cc_start: 0.8277 (m90) cc_final: 0.8027 (m90) REVERT: W 205 ASP cc_start: 0.8673 (m-30) cc_final: 0.8079 (p0) REVERT: X 5 TYR cc_start: 0.7988 (m-80) cc_final: 0.7561 (m-10) REVERT: X 11 ILE cc_start: 0.7318 (pt) cc_final: 0.7114 (pt) REVERT: X 155 ASN cc_start: 0.8664 (m-40) cc_final: 0.8439 (m110) REVERT: Y 77 THR cc_start: 0.7372 (p) cc_final: 0.6676 (p) REVERT: Z 69 GLU cc_start: 0.8801 (tt0) cc_final: 0.8550 (tt0) REVERT: Z 86 LYS cc_start: 0.9381 (mttm) cc_final: 0.8804 (tppt) REVERT: Z 90 ASP cc_start: 0.9084 (m-30) cc_final: 0.8631 (m-30) REVERT: Z 133 MET cc_start: 0.6854 (ttp) cc_final: 0.5659 (tmm) REVERT: Z 203 LYS cc_start: 0.9266 (tttt) cc_final: 0.8844 (tptp) REVERT: Z 228 MET cc_start: 0.8534 (mpp) cc_final: 0.8329 (mpp) REVERT: a 41 LYS cc_start: 0.9119 (tttt) cc_final: 0.8524 (mtmm) REVERT: a 62 LYS cc_start: 0.8632 (mmmt) cc_final: 0.8353 (mtpt) REVERT: a 94 ASP cc_start: 0.8787 (m-30) cc_final: 0.8521 (m-30) REVERT: b 75 MET cc_start: 0.7318 (ttm) cc_final: 0.7031 (ttp) REVERT: b 89 ASP cc_start: 0.9268 (m-30) cc_final: 0.8931 (m-30) REVERT: b 93 GLU cc_start: 0.8963 (pt0) cc_final: 0.8172 (pp20) REVERT: b 97 ASN cc_start: 0.9152 (m110) cc_final: 0.8182 (m-40) REVERT: b 150 MET cc_start: 0.7084 (ttp) cc_final: 0.6053 (tmm) REVERT: O 96 TYR cc_start: 0.8281 (m-80) cc_final: 0.7789 (m-80) REVERT: O 196 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8294 (tp30) REVERT: P 87 HIS cc_start: 0.8630 (m90) cc_final: 0.8357 (m90) REVERT: Q 84 ASN cc_start: 0.9288 (t0) cc_final: 0.8877 (m110) REVERT: Q 201 MET cc_start: 0.8266 (tpt) cc_final: 0.8013 (tpt) REVERT: R 77 THR cc_start: 0.7607 (m) cc_final: 0.7114 (m) REVERT: R 92 GLN cc_start: 0.9075 (mp10) cc_final: 0.8866 (mp10) REVERT: S 20 ARG cc_start: 0.7079 (mmp-170) cc_final: 0.6362 (mmp80) REVERT: S 103 TYR cc_start: 0.8196 (m-80) cc_final: 0.7727 (m-80) REVERT: S 201 ILE cc_start: 0.9569 (mt) cc_final: 0.9252 (tp) REVERT: S 206 MET cc_start: 0.8527 (mmt) cc_final: 0.7908 (mmm) REVERT: T 26 MET cc_start: 0.7677 (mmp) cc_final: 0.7019 (mmm) REVERT: T 49 LEU cc_start: 0.8337 (tp) cc_final: 0.7904 (tt) REVERT: U 93 GLU cc_start: 0.8681 (pm20) cc_final: 0.8397 (pm20) REVERT: U 135 PHE cc_start: 0.8121 (p90) cc_final: 0.7908 (p90) REVERT: U 136 MET cc_start: 0.6118 (mpp) cc_final: 0.5429 (mpp) outliers start: 0 outliers final: 0 residues processed: 756 average time/residue: 0.5127 time to fit residues: 638.2369 Evaluate side-chains 591 residues out of total 5143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 591 time to evaluate : 4.290 ------------------------------------------------------------------------------- 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: 0.0000 chunk 513 optimal weight: 30.0000 chunk 147 optimal weight: 0.0980 chunk 444 optimal weight: 7.9990 chunk 71 optimal weight: 30.0000 chunk 134 optimal weight: 20.0000 chunk 483 optimal weight: 6.9990 chunk 202 optimal weight: 20.0000 chunk 496 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 overall best weight: 7.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 94 GLN ** 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** a 86 ASN ** b 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 123 GLN O 193 GLN ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 227 HIS U 105 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.056417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.047534 restraints weight = 283876.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.049092 restraints weight = 170695.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.050225 restraints weight = 115762.758| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.7355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 49014 Z= 0.308 Angle : 0.693 16.162 66222 Z= 0.359 Chirality : 0.046 0.299 7441 Planarity : 0.005 0.062 8531 Dihedral : 5.016 32.423 6803 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.55 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -0.73 (0.11), residues: 6137 helix: 0.01 (0.11), residues: 2205 sheet: -0.42 (0.13), residues: 1503 loop : -0.81 (0.13), residues: 2429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP N 91 HIS 0.012 0.001 HIS Y 94 PHE 0.031 0.002 PHE D 56 TYR 0.029 0.002 TYR F 75 ARG 0.009 0.001 ARG E 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11138.56 seconds wall clock time: 196 minutes 31.72 seconds (11791.72 seconds total)