Starting phenix.real_space_refine on Tue Sep 15 11:19:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6fki_4272/09_2026/6fki_4272.cif Found real_map, /net/cci-nas-00/data/ceres_data/6fki_4272/09_2026/6fki_4272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6fki_4272/09_2026/6fki_4272.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6fki_4272/09_2026/6fki_4272.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6fki_4272/09_2026/6fki_4272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6fki_4272/09_2026/6fki_4272.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6fki_4272/09_2026/6fki_4272.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6fki_4272/09_2026/6fki_4272.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 129 5.16 5 C 24906 2.51 5 N 6683 2.21 5 O 7495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39231 Number of models: 1 Model: "" Number of chains: 31 Chain: "a" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1741 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "b" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1299 Classifications: {'peptide': 161} Link IDs: {'TRANS': 160} Chain: "d" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1383 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain: "p" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1124 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "g" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2497 Classifications: {'peptide': 321} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 308} Chain: "S" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "N" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "O" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "P" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Q" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "M" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "T" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "G" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "H" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "L" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "K" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "J" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "I" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "E" Number of atoms: 3827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3827 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 480} Chain: "F" Number of atoms: 3627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3627 Classifications: {'peptide': 479} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 452} Chain: "A" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3849 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "B" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3619 Classifications: {'peptide': 478} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 451} Chain: "C" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3851 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} Chain: "D" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3636 Classifications: {'peptide': 480} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 453} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.88, per 1000 atoms: 0.20 Number of scatterers: 39231 At special positions: 0 Unit cell: (128.466, 142.155, 235.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 129 16.00 P 13 15.00 Mg 5 11.99 O 7495 8.00 N 6683 7.00 C 24906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 240 " - pdb=" SG CYS g 246 " distance=2.70 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=26, symmetry=0 Links applied TRANS " PHE a 26 " - " SER p 82 " " LEU p 83 " - " HIS a 25 " " SER p 134 " - " ALA b 74 " Number of additional bonds: simple=26, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.84 Conformation dependent library (CDL) restraints added in 1.9 seconds 10294 Ramachandran restraints generated. 5147 Oldfield, 0 Emsley, 5147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9452 Finding SS restraints... Secondary structure from input PDB file: 190 helices and 28 sheets defined 61.8% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'a' and resid 37 through 59 removed outlier: 4.035A pdb=" N ARG a 59 " --> pdb=" O ALA a 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 68 through 88 removed outlier: 4.135A pdb=" N PHE a 72 " --> pdb=" O GLY a 68 " (cutoff:3.500A) Processing helix chain 'a' and resid 94 through 115 removed outlier: 3.573A pdb=" N ILE a 105 " --> pdb=" O MET a 101 " (cutoff:3.500A) Processing helix chain 'a' and resid 133 through 156 removed outlier: 4.073A pdb=" N THR a 137 " --> pdb=" O ASP a 133 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS a 156 " --> pdb=" O GLY a 152 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 170 No H-bonds generated for 'chain 'a' and resid 168 through 170' Processing helix chain 'a' and resid 171 through 208 removed outlier: 3.751A pdb=" N PHE a 180 " --> pdb=" O ILE a 176 " (cutoff:3.500A) Proline residue: a 183 - end of helix removed outlier: 4.054A pdb=" N LEU a 190 " --> pdb=" O LEU a 186 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU a 207 " --> pdb=" O VAL a 203 " (cutoff:3.500A) Processing helix chain 'a' and resid 213 through 244 removed outlier: 3.515A pdb=" N GLY a 225 " --> pdb=" O LEU a 221 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE a 226 " --> pdb=" O PHE a 222 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA a 228 " --> pdb=" O SER a 224 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 159 removed outlier: 3.592A pdb=" N VAL b 36 " --> pdb=" O ILE b 32 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL b 37 " --> pdb=" O ASN b 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN b 66 " --> pdb=" O ASN b 62 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL b 97 " --> pdb=" O ASP b 93 " (cutoff:3.500A) Processing helix chain 'b' and resid 163 through 182 Processing helix chain 'd' and resid 73 through 90 Processing helix chain 'd' and resid 91 through 107 removed outlier: 3.534A pdb=" N ASP d 98 " --> pdb=" O ALA d 94 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG d 104 " --> pdb=" O GLU d 100 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE d 105 " --> pdb=" O LYS d 101 " (cutoff:3.500A) Processing helix chain 'd' and resid 108 through 117 Processing helix chain 'd' and resid 121 through 137 Processing helix chain 'd' and resid 139 through 152 Processing helix chain 'd' and resid 153 through 156 removed outlier: 4.088A pdb=" N ASN d 156 " --> pdb=" O GLU d 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 153 through 156' Processing helix chain 'd' and resid 157 through 174 removed outlier: 3.761A pdb=" N GLU d 166 " --> pdb=" O LEU d 162 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP d 167 " --> pdb=" O ASN d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 203 removed outlier: 3.525A pdb=" N LEU d 191 " --> pdb=" O GLU d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 237 through 249 removed outlier: 3.934A pdb=" N LEU d 248 " --> pdb=" O ILE d 244 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU d 249 " --> pdb=" O ALA d 245 " (cutoff:3.500A) Processing helix chain 'p' and resid 88 through 108 Processing helix chain 'p' and resid 108 through 202 Processing helix chain 'p' and resid 203 through 219 removed outlier: 3.551A pdb=" N ILE p 207 " --> pdb=" O LEU p 203 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE p 214 " --> pdb=" O LEU p 210 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL p 215 " --> pdb=" O SER p 211 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS p 216 " --> pdb=" O ASP p 212 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS p 217 " --> pdb=" O ASP p 213 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU p 219 " --> pdb=" O VAL p 215 " (cutoff:3.500A) Processing helix chain 'e' and resid 88 through 106 Processing helix chain 'e' and resid 108 through 130 removed outlier: 3.899A pdb=" N ILE e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR e 124 " --> pdb=" O ARG e 120 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG e 125 " --> pdb=" O ARG e 121 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL e 126 " --> pdb=" O ALA e 122 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU e 127 " --> pdb=" O ARG e 123 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA e 128 " --> pdb=" O THR e 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 82 removed outlier: 3.611A pdb=" N GLY g 82 " --> pdb=" O ALA g 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 82 through 101 removed outlier: 3.666A pdb=" N GLN g 101 " --> pdb=" O ASN g 97 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 152 removed outlier: 3.526A pdb=" N ARG g 144 " --> pdb=" O LYS g 140 " (cutoff:3.500A) Processing helix chain 'g' and resid 161 through 171 removed outlier: 3.590A pdb=" N ARG g 170 " --> pdb=" O THR g 166 " (cutoff:3.500A) Processing helix chain 'g' and resid 187 through 204 removed outlier: 3.615A pdb=" N ALA g 193 " --> pdb=" O LYS g 189 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE g 194 " --> pdb=" O GLU g 190 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER g 204 " --> pdb=" O SER g 200 " (cutoff:3.500A) Processing helix chain 'g' and resid 287 through 362 Proline residue: g 297 - end of helix Processing helix chain 'S' and resid 4 through 21 removed outlier: 3.867A pdb=" N VAL S 17 " --> pdb=" O ALA S 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER S 21 " --> pdb=" O VAL S 17 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 42 removed outlier: 3.761A pdb=" N GLY S 29 " --> pdb=" O GLY S 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY S 38 " --> pdb=" O GLN S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 76 removed outlier: 3.605A pdb=" N GLY S 51 " --> pdb=" O GLY S 47 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR S 52 " --> pdb=" O LYS S 48 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU S 63 " --> pdb=" O PHE S 59 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR S 64 " --> pdb=" O MET S 60 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 21 removed outlier: 3.866A pdb=" N VAL N 17 " --> pdb=" O ALA N 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER N 21 " --> pdb=" O VAL N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 21 through 42 removed outlier: 3.761A pdb=" N GLY N 29 " --> pdb=" O GLY N 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY N 38 " --> pdb=" O GLN N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 76 removed outlier: 3.604A pdb=" N GLY N 51 " --> pdb=" O GLY N 47 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR N 52 " --> pdb=" O LYS N 48 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU N 63 " --> pdb=" O PHE N 59 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 21 removed outlier: 3.866A pdb=" N VAL O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER O 21 " --> pdb=" O VAL O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 42 removed outlier: 3.761A pdb=" N GLY O 29 " --> pdb=" O GLY O 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY O 38 " --> pdb=" O GLN O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 76 removed outlier: 3.604A pdb=" N GLY O 51 " --> pdb=" O GLY O 47 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR O 52 " --> pdb=" O LYS O 48 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU O 63 " --> pdb=" O PHE O 59 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 21 removed outlier: 3.866A pdb=" N VAL P 17 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER P 21 " --> pdb=" O VAL P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 42 removed outlier: 3.760A pdb=" N GLY P 29 " --> pdb=" O GLY P 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY P 38 " --> pdb=" O GLN P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 76 removed outlier: 3.603A pdb=" N GLY P 51 " --> pdb=" O GLY P 47 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR P 52 " --> pdb=" O LYS P 48 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU P 63 " --> pdb=" O PHE P 59 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY P 67 " --> pdb=" O LEU P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 21 removed outlier: 3.867A pdb=" N VAL Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER Q 21 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 42 removed outlier: 3.760A pdb=" N GLY Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY Q 38 " --> pdb=" O GLN Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 76 removed outlier: 3.603A pdb=" N GLY Q 51 " --> pdb=" O GLY Q 47 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR Q 52 " --> pdb=" O LYS Q 48 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU Q 63 " --> pdb=" O PHE Q 59 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR Q 64 " --> pdb=" O MET Q 60 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY Q 67 " --> pdb=" O LEU Q 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 21 removed outlier: 3.866A pdb=" N VAL R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER R 21 " --> pdb=" O VAL R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 42 removed outlier: 3.760A pdb=" N GLY R 29 " --> pdb=" O GLY R 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY R 38 " --> pdb=" O GLN R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 76 removed outlier: 3.603A pdb=" N GLY R 51 " --> pdb=" O GLY R 47 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR R 52 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU R 63 " --> pdb=" O PHE R 59 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR R 64 " --> pdb=" O MET R 60 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 21 removed outlier: 3.867A pdb=" N VAL M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER M 21 " --> pdb=" O VAL M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 42 removed outlier: 3.760A pdb=" N GLY M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY M 38 " --> pdb=" O GLN M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 76 removed outlier: 3.604A pdb=" N GLY M 51 " --> pdb=" O GLY M 47 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR M 52 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU M 63 " --> pdb=" O PHE M 59 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR M 64 " --> pdb=" O MET M 60 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY M 67 " --> pdb=" O LEU M 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 21 removed outlier: 3.866A pdb=" N VAL T 17 " --> pdb=" O ALA T 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER T 21 " --> pdb=" O VAL T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 21 through 42 removed outlier: 3.761A pdb=" N GLY T 29 " --> pdb=" O GLY T 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY T 38 " --> pdb=" O GLN T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 76 removed outlier: 3.604A pdb=" N GLY T 51 " --> pdb=" O GLY T 47 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR T 52 " --> pdb=" O LYS T 48 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU T 63 " --> pdb=" O PHE T 59 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR T 64 " --> pdb=" O MET T 60 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 21 removed outlier: 3.866A pdb=" N VAL G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER G 21 " --> pdb=" O VAL G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 42 removed outlier: 3.760A pdb=" N GLY G 29 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY G 38 " --> pdb=" O GLN G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 76 removed outlier: 3.603A pdb=" N GLY G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR G 52 " --> pdb=" O LYS G 48 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU G 63 " --> pdb=" O PHE G 59 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR G 64 " --> pdb=" O MET G 60 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 21 removed outlier: 3.866A pdb=" N VAL H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 42 removed outlier: 3.760A pdb=" N GLY H 29 " --> pdb=" O GLY H 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY H 38 " --> pdb=" O GLN H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 76 removed outlier: 3.605A pdb=" N GLY H 51 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR H 52 " --> pdb=" O LYS H 48 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU H 63 " --> pdb=" O PHE H 59 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR H 64 " --> pdb=" O MET H 60 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY H 67 " --> pdb=" O LEU H 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 21 removed outlier: 3.867A pdb=" N VAL L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER L 21 " --> pdb=" O VAL L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 42 removed outlier: 3.760A pdb=" N GLY L 29 " --> pdb=" O GLY L 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY L 38 " --> pdb=" O GLN L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 76 removed outlier: 3.604A pdb=" N GLY L 51 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR L 52 " --> pdb=" O LYS L 48 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU L 63 " --> pdb=" O PHE L 59 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR L 64 " --> pdb=" O MET L 60 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 21 removed outlier: 3.866A pdb=" N VAL K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER K 21 " --> pdb=" O VAL K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 42 removed outlier: 3.758A pdb=" N GLY K 29 " --> pdb=" O GLY K 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY K 38 " --> pdb=" O GLN K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 76 removed outlier: 3.604A pdb=" N GLY K 51 " --> pdb=" O GLY K 47 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR K 52 " --> pdb=" O LYS K 48 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU K 63 " --> pdb=" O PHE K 59 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR K 64 " --> pdb=" O MET K 60 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 21 removed outlier: 3.865A pdb=" N VAL J 17 " --> pdb=" O ALA J 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER J 21 " --> pdb=" O VAL J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 42 removed outlier: 3.761A pdb=" N GLY J 29 " --> pdb=" O GLY J 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY J 38 " --> pdb=" O GLN J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 76 removed outlier: 3.604A pdb=" N GLY J 51 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR J 52 " --> pdb=" O LYS J 48 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU J 63 " --> pdb=" O PHE J 59 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR J 64 " --> pdb=" O MET J 60 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY J 67 " --> pdb=" O LEU J 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 21 removed outlier: 3.867A pdb=" N VAL I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER I 21 " --> pdb=" O VAL I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 42 removed outlier: 3.760A pdb=" N GLY I 29 " --> pdb=" O GLY I 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY I 38 " --> pdb=" O GLN I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 76 removed outlier: 3.604A pdb=" N GLY I 51 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR I 52 " --> pdb=" O LYS I 48 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU I 63 " --> pdb=" O PHE I 59 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR I 64 " --> pdb=" O MET I 60 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY I 67 " --> pdb=" O LEU I 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 25 removed outlier: 3.722A pdb=" N GLU E 23 " --> pdb=" O GLY E 19 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL E 24 " --> pdb=" O TYR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 105 removed outlier: 3.872A pdb=" N TYR E 104 " --> pdb=" O SER E 101 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU E 105 " --> pdb=" O GLU E 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 101 through 105' Processing helix chain 'E' and resid 151 through 158 removed outlier: 3.721A pdb=" N MET E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 187 removed outlier: 3.745A pdb=" N GLN E 187 " --> pdb=" O THR E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 216 Processing helix chain 'E' and resid 217 through 220 Processing helix chain 'E' and resid 232 through 252 Proline residue: E 240 - end of helix removed outlier: 3.609A pdb=" N PHE E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 278 removed outlier: 3.707A pdb=" N ALA E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 287 Processing helix chain 'E' and resid 289 through 301 removed outlier: 4.536A pdb=" N TYR E 293 " --> pdb=" O GLY E 289 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG E 301 " --> pdb=" O ARG E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 326 Processing helix chain 'E' and resid 329 through 339 Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 367 through 371 removed outlier: 3.632A pdb=" N ALA E 370 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 393 removed outlier: 3.598A pdb=" N VAL E 379 " --> pdb=" O ALA E 375 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 403 removed outlier: 4.096A pdb=" N GLN E 398 " --> pdb=" O ALA E 395 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA E 400 " --> pdb=" O ALA E 397 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N SER E 401 " --> pdb=" O GLN E 398 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU E 403 " --> pdb=" O ALA E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 422 removed outlier: 3.675A pdb=" N ARG E 416 " --> pdb=" O ALA E 412 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU E 421 " --> pdb=" O LEU E 417 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS E 422 " --> pdb=" O ARG E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 443 removed outlier: 3.663A pdb=" N ASN E 443 " --> pdb=" O TYR E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 469 removed outlier: 4.086A pdb=" N ARG E 455 " --> pdb=" O LEU E 451 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS E 456 " --> pdb=" O ASP E 452 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E 459 " --> pdb=" O ARG E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 480 removed outlier: 4.373A pdb=" N GLN E 473 " --> pdb=" O LYS E 469 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU E 474 " --> pdb=" O PRO E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 504 Processing helix chain 'F' and resid 153 through 159 Processing helix chain 'F' and resid 177 through 193 removed outlier: 3.746A pdb=" N ALA F 190 " --> pdb=" O ILE F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 219 removed outlier: 3.610A pdb=" N LYS F 217 " --> pdb=" O TYR F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 248 removed outlier: 3.531A pdb=" N ARG F 246 " --> pdb=" O PRO F 242 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET F 247 " --> pdb=" O PRO F 243 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG F 248 " --> pdb=" O GLY F 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 242 through 248' Processing helix chain 'F' and resid 248 through 263 removed outlier: 3.945A pdb=" N PHE F 260 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP F 262 " --> pdb=" O GLU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 290 removed outlier: 3.667A pdb=" N PHE F 278 " --> pdb=" O ASN F 274 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL F 279 " --> pdb=" O ILE F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 298 removed outlier: 3.765A pdb=" N TYR F 298 " --> pdb=" O ALA F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 311 removed outlier: 3.522A pdb=" N LEU F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 333 Processing helix chain 'F' and resid 336 through 346 removed outlier: 4.142A pdb=" N HIS F 345 " --> pdb=" O THR F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 360 removed outlier: 3.841A pdb=" N ALA F 357 " --> pdb=" O SER F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 381 through 413 removed outlier: 4.700A pdb=" N ASP F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU F 410 " --> pdb=" O ALA F 406 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N ASP F 411 " --> pdb=" O ILE F 407 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU F 412 " --> pdb=" O LEU F 408 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU F 413 " --> pdb=" O GLY F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 432 removed outlier: 3.703A pdb=" N SER F 432 " --> pdb=" O GLU F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 443 Processing helix chain 'F' and resid 450 through 463 removed outlier: 3.575A pdb=" N LEU F 460 " --> pdb=" O ARG F 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 474 Processing helix chain 'F' and resid 479 through 496 removed outlier: 3.551A pdb=" N ALA F 483 " --> pdb=" O ASN F 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 18 removed outlier: 4.447A pdb=" N SER A 10 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LYS A 11 " --> pdb=" O ASP A 7 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 17 " --> pdb=" O ILE A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.690A pdb=" N TYR A 104 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 175 through 186 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 232 through 252 Proline residue: A 240 - end of helix removed outlier: 3.855A pdb=" N PHE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 288 through 289 No H-bonds generated for 'chain 'A' and resid 288 through 289' Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.623A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.502A pdb=" N SER A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 373 through 395 removed outlier: 4.053A pdb=" N LYS A 382 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 383 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 385 " --> pdb=" O GLY A 381 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 404 through 422 removed outlier: 3.898A pdb=" N GLN A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 443 Processing helix chain 'A' and resid 450 through 468 removed outlier: 4.633A pdb=" N ARG A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LYS A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 459 " --> pdb=" O ARG A 455 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 460 " --> pdb=" O LYS A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 removed outlier: 3.570A pdb=" N GLU A 474 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 503 removed outlier: 3.803A pdb=" N ALA A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 503 " --> pdb=" O GLU A 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.743A pdb=" N LEU B 142 " --> pdb=" O PHE B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.519A pdb=" N ALA B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 193 removed outlier: 4.457A pdb=" N LYS B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 242 through 264 removed outlier: 4.048A pdb=" N ARG B 248 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLY B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU B 251 " --> pdb=" O MET B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 290 removed outlier: 3.718A pdb=" N PHE B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 312 removed outlier: 3.866A pdb=" N ARG B 312 " --> pdb=" O SER B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 333 Processing helix chain 'B' and resid 336 through 346 removed outlier: 3.541A pdb=" N THR B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N HIS B 345 " --> pdb=" O THR B 341 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 346 " --> pdb=" O THR B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 360 Processing helix chain 'B' and resid 376 through 408 removed outlier: 7.564A pdb=" N GLU B 382 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N GLU B 383 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N HIS B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 390 " --> pdb=" O GLU B 386 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP B 403 " --> pdb=" O LYS B 399 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.949A pdb=" N GLU B 412 " --> pdb=" O GLY B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 432 removed outlier: 3.657A pdb=" N SER B 432 " --> pdb=" O GLU B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 470 through 474 Processing helix chain 'B' and resid 479 through 493 removed outlier: 3.640A pdb=" N ALA B 483 " --> pdb=" O ASN B 479 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 19 Processing helix chain 'C' and resid 101 through 105 removed outlier: 4.063A pdb=" N TYR C 104 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU C 105 " --> pdb=" O GLU C 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 101 through 105' Processing helix chain 'C' and resid 151 through 158 removed outlier: 3.695A pdb=" N MET C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 186 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 232 through 252 Proline residue: C 240 - end of helix removed outlier: 3.544A pdb=" N PHE C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.645A pdb=" N ALA C 286 " --> pdb=" O GLY C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 289 No H-bonds generated for 'chain 'C' and resid 288 through 289' Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.540A pdb=" N HIS C 295 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 326 Processing helix chain 'C' and resid 329 through 339 removed outlier: 3.598A pdb=" N SER C 337 " --> pdb=" O THR C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 removed outlier: 3.742A pdb=" N ALA C 352 " --> pdb=" O ASP C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.878A pdb=" N ALA C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN C 372 " --> pdb=" O SER C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 381 Processing helix chain 'C' and resid 382 through 395 removed outlier: 3.603A pdb=" N LEU C 393 " --> pdb=" O GLN C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 421 removed outlier: 3.937A pdb=" N GLN C 410 " --> pdb=" O ALA C 406 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C 419 " --> pdb=" O GLN C 415 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 443 removed outlier: 3.544A pdb=" N THR C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 468 removed outlier: 3.882A pdb=" N ARG C 455 " --> pdb=" O LEU C 451 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS C 456 " --> pdb=" O ASP C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 479 removed outlier: 4.131A pdb=" N GLN C 473 " --> pdb=" O LYS C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 504 Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 177 through 193 Processing helix chain 'D' and resid 205 through 219 Processing helix chain 'D' and resid 242 through 247 Processing helix chain 'D' and resid 248 through 263 Processing helix chain 'D' and resid 274 through 287 removed outlier: 3.947A pdb=" N PHE D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY D 282 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 285 " --> pdb=" O ALA D 281 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 298 removed outlier: 3.799A pdb=" N TYR D 298 " --> pdb=" O ALA D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 313 removed outlier: 3.512A pdb=" N GLY D 307 " --> pdb=" O SER D 303 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG D 312 " --> pdb=" O SER D 308 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 333 Processing helix chain 'D' and resid 336 through 346 removed outlier: 3.726A pdb=" N THR D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N HIS D 345 " --> pdb=" O THR D 341 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU D 346 " --> pdb=" O THR D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 359 Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 381 through 409 removed outlier: 3.602A pdb=" N LYS D 392 " --> pdb=" O ALA D 388 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASP D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 413 Processing helix chain 'D' and resid 414 through 432 removed outlier: 3.980A pdb=" N SER D 432 " --> pdb=" O GLU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.521A pdb=" N ILE D 461 " --> pdb=" O GLY D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 474 Processing helix chain 'D' and resid 479 through 496 Processing sheet with id=A, first strand: chain 'a' and resid 28 through 30 Processing sheet with id=B, first strand: chain 'd' and resid 206 through 213 removed outlier: 3.628A pdb=" N PHE d 221 " --> pdb=" O MET d 235 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'e' and resid 4 through 8 removed outlier: 3.651A pdb=" N GLU e 73 " --> pdb=" O GLY e 70 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'e' and resid 31 through 34 removed outlier: 3.625A pdb=" N ILE e 22 " --> pdb=" O VAL e 33 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU e 53 " --> pdb=" O GLN e 56 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'e' and resid 46 through 48 removed outlier: 3.514A pdb=" N LEU e 62 " --> pdb=" O GLY e 47 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'g' and resid 155 through 160 removed outlier: 6.865A pdb=" N VAL g 118 " --> pdb=" O THR g 156 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE g 158 " --> pdb=" O VAL g 118 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU g 120 " --> pdb=" O ILE g 158 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ILE g 160 " --> pdb=" O LEU g 120 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL g 122 " --> pdb=" O ILE g 160 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU g 211 " --> pdb=" O MET g 121 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N VAL g 123 " --> pdb=" O GLU g 211 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU g 213 " --> pdb=" O VAL g 123 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'g' and resid 251 through 259 removed outlier: 4.179A pdb=" N ASP g 252 " --> pdb=" O ILE g 271 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'E' and resid 61 through 63 removed outlier: 6.537A pdb=" N ARG E 41 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL E 35 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE E 39 " --> pdb=" O VAL E 35 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'E' and resid 97 through 100 removed outlier: 3.703A pdb=" N GLU E 126 " --> pdb=" O VAL E 100 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'E' and resid 341 through 345 removed outlier: 3.531A pdb=" N GLY E 170 " --> pdb=" O VAL E 320 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'E' and resid 315 through 318 removed outlier: 5.830A pdb=" N ILE E 193 " --> pdb=" O LEU E 258 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE E 260 " --> pdb=" O ILE E 193 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL E 195 " --> pdb=" O ILE E 260 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASP E 262 " --> pdb=" O VAL E 195 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL E 197 " --> pdb=" O ASP E 262 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'F' and resid 58 through 64 removed outlier: 4.636A pdb=" N GLU F 90 " --> pdb=" O LYS F 50 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASN F 19 " --> pdb=" O ASP F 93 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL F 77 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N VAL F 65 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=N, first strand: chain 'F' and resid 348 through 350 removed outlier: 8.829A pdb=" N ILE F 168 " --> pdb=" O ILE F 321 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER F 323 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU F 170 " --> pdb=" O SER F 323 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLN F 325 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE F 272 " --> pdb=" O ILE F 324 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.973A pdb=" N ILE A 61 " --> pdb=" O MET A 77 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU A 67 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N HIS A 43 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N VAL A 32 " --> pdb=" O HIS A 43 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'A' and resid 97 through 100 removed outlier: 3.691A pdb=" N GLU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain 'A' and resid 341 through 345 Processing sheet with id=R, first strand: chain 'A' and resid 223 through 226 removed outlier: 6.167A pdb=" N SER A 313 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE A 259 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR A 315 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N TYR A 261 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU A 317 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'B' and resid 61 through 64 removed outlier: 4.152A pdb=" N VAL B 61 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 32 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE B 26 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 30 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 77 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL B 65 " --> pdb=" O VAL B 77 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain 'B' and resid 99 through 101 Processing sheet with id=U, first strand: chain 'B' and resid 348 through 351 Processing sheet with id=V, first strand: chain 'C' and resid 88 through 90 removed outlier: 6.484A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=W, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.909A pdb=" N GLU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain 'C' and resid 342 through 344 removed outlier: 6.545A pdb=" N LEU C 167 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY C 170 " --> pdb=" O VAL C 320 " (cutoff:3.500A) Processing sheet with id=Y, first strand: chain 'C' and resid 313 through 318 Processing sheet with id=Z, first strand: chain 'D' and resid 20 through 22 removed outlier: 4.936A pdb=" N GLU D 90 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG D 75 " --> pdb=" O GLN D 66 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU D 68 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ARG D 73 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ALA D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ILE D 23 " --> pdb=" O ALA D 34 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'D' and resid 99 through 101 Processing sheet with id=AB, first strand: chain 'D' and resid 348 through 351 removed outlier: 7.897A pdb=" N ILE D 168 " --> pdb=" O ILE D 321 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER D 323 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU D 170 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLN D 325 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLY D 172 " --> pdb=" O GLN D 325 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL D 327 " --> pdb=" O GLY D 172 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL D 268 " --> pdb=" O THR D 322 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE D 324 " --> pdb=" O VAL D 268 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU D 270 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ALA D 326 " --> pdb=" O LEU D 270 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE D 272 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N TYR D 328 " --> pdb=" O ILE D 272 " (cutoff:3.500A) 2442 hydrogen bonds defined for protein. 7176 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: 8.74 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.23: 2177 1.23 - 1.48: 20531 1.48 - 1.74: 16823 1.74 - 1.99: 246 1.99 - 2.25: 1 Bond restraints: 39778 Sorted by residual: bond pdb=" C GLN b 77 " pdb=" N LEU b 78 " ideal model delta sigma weight residual 1.335 2.248 -0.913 1.25e-02 6.40e+03 5.34e+03 bond pdb=" C PHE F 276 " pdb=" N ARG F 277 " ideal model delta sigma weight residual 1.335 0.970 0.365 1.31e-02 5.83e+03 7.76e+02 bond pdb=" C GLY A 30 " pdb=" N THR A 31 " ideal model delta sigma weight residual 1.330 1.525 -0.195 1.32e-02 5.74e+03 2.19e+02 bond pdb=" N PRO g 84 " pdb=" CD PRO g 84 " ideal model delta sigma weight residual 1.473 1.652 -0.179 1.40e-02 5.10e+03 1.63e+02 bond pdb=" C ASP p 105 " pdb=" N LYS p 106 " ideal model delta sigma weight residual 1.333 1.170 0.162 1.37e-02 5.33e+03 1.40e+02 ... (remaining 39773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.74: 52444 3.74 - 7.48: 1370 7.48 - 11.22: 118 11.22 - 14.96: 10 14.96 - 18.70: 1 Bond angle restraints: 53943 Sorted by residual: angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 125.12 14.75 1.00e+00 1.00e+00 2.17e+02 angle pdb=" PB ATP E 600 " pdb=" O3B ATP E 600 " pdb=" PG ATP E 600 " ideal model delta sigma weight residual 139.87 125.59 14.28 1.00e+00 1.00e+00 2.04e+02 angle pdb=" C VAL a 212 " pdb=" N PRO a 213 " pdb=" CA PRO a 213 " ideal model delta sigma weight residual 119.87 133.74 -13.87 1.04e+00 9.25e-01 1.78e+02 angle pdb=" C GLY C 30 " pdb=" N THR C 31 " pdb=" CA THR C 31 " ideal model delta sigma weight residual 121.42 140.12 -18.70 1.43e+00 4.89e-01 1.71e+02 angle pdb=" O GLU b 181 " pdb=" C GLU b 181 " pdb=" N ILE b 182 " ideal model delta sigma weight residual 122.07 109.79 12.28 1.03e+00 9.43e-01 1.42e+02 ... (remaining 53938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.84: 23476 26.84 - 53.68: 590 53.68 - 80.52: 58 80.52 - 107.36: 6 107.36 - 134.20: 4 Dihedral angle restraints: 24134 sinusoidal: 9376 harmonic: 14758 Sorted by residual: dihedral pdb=" CA ASP E 262 " pdb=" C ASP E 262 " pdb=" N ASP E 263 " pdb=" CA ASP E 263 " ideal model delta harmonic sigma weight residual -180.00 -49.91 -130.09 0 5.00e+00 4.00e-02 6.77e+02 dihedral pdb=" CA ASP C 262 " pdb=" C ASP C 262 " pdb=" N ASP C 263 " pdb=" CA ASP C 263 " ideal model delta harmonic sigma weight residual -180.00 -51.16 -128.84 0 5.00e+00 4.00e-02 6.64e+02 dihedral pdb=" CA ALA b 74 " pdb=" C ALA b 74 " pdb=" N SER p 134 " pdb=" CA SER p 134 " ideal model delta harmonic sigma weight residual 180.00 64.27 115.73 0 5.00e+00 4.00e-02 5.36e+02 ... (remaining 24131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 5860 0.146 - 0.292: 506 0.292 - 0.437: 69 0.437 - 0.583: 6 0.583 - 0.729: 15 Chirality restraints: 6456 Sorted by residual: chirality pdb=" CB VAL O 81 " pdb=" CA VAL O 81 " pdb=" CG1 VAL O 81 " pdb=" CG2 VAL O 81 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CB VAL T 81 " pdb=" CA VAL T 81 " pdb=" CG1 VAL T 81 " pdb=" CG2 VAL T 81 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CB VAL N 81 " pdb=" CA VAL N 81 " pdb=" CG1 VAL N 81 " pdb=" CG2 VAL N 81 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.32e+01 ... (remaining 6453 not shown) Planarity restraints: 6964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS a 25 " 0.036 2.00e-02 2.50e+03 1.81e-01 3.28e+02 pdb=" C HIS a 25 " -0.302 2.00e-02 2.50e+03 pdb=" O HIS a 25 " 0.089 2.00e-02 2.50e+03 pdb=" N LEU p 83 " 0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N PHE a 26 " -0.171 2.00e-02 2.50e+03 1.45e-01 2.11e+02 pdb=" CA SER p 82 " -0.059 2.00e-02 2.50e+03 pdb=" C SER p 82 " 0.227 2.00e-02 2.50e+03 pdb=" O SER p 82 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU b 181 " 0.067 2.00e-02 2.50e+03 1.24e-01 1.55e+02 pdb=" C GLU b 181 " -0.215 2.00e-02 2.50e+03 pdb=" O GLU b 181 " 0.080 2.00e-02 2.50e+03 pdb=" N ILE b 182 " 0.069 2.00e-02 2.50e+03 ... (remaining 6961 not shown) Histogram of nonbonded interaction distances: 0.35 - 1.26: 94 1.26 - 2.17: 579 2.17 - 3.08: 31085 3.08 - 3.99: 106845 3.99 - 4.90: 203114 Warning: very small nonbonded interaction distances. Nonbonded interactions: 341717 Sorted by model distance: nonbonded pdb=" CB LEU b 78 " pdb=" CA GLU p 136 " model vdw 0.349 3.870 nonbonded pdb=" CG ARG b 71 " pdb=" CA GLY p 129 " model vdw 0.379 3.840 nonbonded pdb=" CA SER b 67 " pdb=" CB LEU p 127 " model vdw 0.511 3.870 nonbonded pdb=" C ARG b 84 " pdb=" CB ALA p 144 " model vdw 0.528 3.690 nonbonded pdb=" C ALA b 81 " pdb=" C LEU p 140 " model vdw 0.541 2.800 ... (remaining 341712 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' and resid 7 through 601) selection = (chain 'C' and (resid 7 through 503 or resid 601 through 602)) selection = (chain 'E' and (resid 7 through 503 or resid 600 through 601)) } ncs_group { reference = (chain 'B' and resid 18 through 494) selection = (chain 'D' and resid 18 through 494) selection = (chain 'F' and resid 18 through 494) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 2.610 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: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 36.180 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 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 : 0.021 1.229 39808 Z= 1.634 Angle : 1.534 72.547 53954 Z= 0.985 Chirality : 0.094 0.729 6456 Planarity : 0.009 0.124 6961 Dihedral : 11.862 134.196 14670 Min Nonbonded Distance : 0.349 Molprobity Statistics. All-atom Clashscore : 58.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.02 % Rotamer: Outliers : 0.15 % Allowed : 5.48 % Favored : 94.37 % Cbeta Deviations : 0.59 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.12), residues: 5147 helix: 0.85 (0.10), residues: 2777 sheet: -1.33 (0.21), residues: 565 loop : -1.12 (0.13), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG F 246 TYR 0.034 0.003 TYR A 287 PHE 0.067 0.003 PHE D 171 TRP 0.045 0.005 TRP a 110 HIS 0.018 0.003 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.01499 / 0.87 (39778) covalent geometry : angle 1.41894 / 0.93 (53943) SS BOND : bond 0.66586 / 35.05 ( 1) SS BOND : angle 39.84707 / 21.48 ( 2) hydrogen bonds : bond 0.24405 / 16.26 ( 2442) hydrogen bonds : angle 8.60654 / 6.31 ( 7176) Misc. bond : bond 0.49770 / 32.97 ( 26) link_TRANS : bond 0.83942 / 36.15 ( 3) link_TRANS : angle 41.05044 / 22.94 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10294 Ramachandran restraints generated. 5147 Oldfield, 0 Emsley, 5147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10294 Ramachandran restraints generated. 5147 Oldfield, 0 Emsley, 5147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1789 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1783 time to evaluate : 1.400 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: a 150 TYR cc_start: 0.6735 (t80) cc_final: 0.5700 (m-80) REVERT: b 141 ARG cc_start: 0.6585 (mtm180) cc_final: 0.6345 (mtm180) REVERT: d 138 LEU cc_start: 0.7814 (mt) cc_final: 0.7545 (mt) REVERT: d 208 ARG cc_start: 0.7464 (mtp180) cc_final: 0.7172 (ttm110) REVERT: e 125 ARG cc_start: 0.7627 (tpt-90) cc_final: 0.7346 (tpt-90) REVERT: g 133 PHE cc_start: 0.7067 (t80) cc_final: 0.6139 (t80) REVERT: g 245 LYS cc_start: 0.8860 (mttt) cc_final: 0.8107 (tmmt) REVERT: g 328 ASP cc_start: 0.8836 (m-30) cc_final: 0.8538 (t0) REVERT: P 60 MET cc_start: 0.6408 (mtm) cc_final: 0.5671 (mmm) REVERT: M 49 ILE cc_start: 0.7341 (mt) cc_final: 0.7007 (mt) REVERT: M 53 LEU cc_start: 0.7554 (tp) cc_final: 0.7190 (tp) REVERT: M 65 ILE cc_start: 0.4624 (tp) cc_final: 0.4419 (tp) REVERT: H 78 ASN cc_start: 0.2692 (t0) cc_final: 0.1859 (t0) REVERT: L 28 GLN cc_start: 0.5907 (mt0) cc_final: 0.5677 (tt0) REVERT: J 59 PHE cc_start: 0.3034 (m-80) cc_final: 0.2337 (m-80) REVERT: J 72 LEU cc_start: 0.7218 (mt) cc_final: 0.6907 (pp) REVERT: I 48 LYS cc_start: 0.4681 (mttt) cc_final: 0.4388 (mttt) REVERT: E 166 GLU cc_start: 0.9150 (tp30) cc_final: 0.8812 (tp30) REVERT: E 185 LEU cc_start: 0.9063 (mt) cc_final: 0.8303 (tt) REVERT: E 192 VAL cc_start: 0.9180 (m) cc_final: 0.8880 (p) REVERT: E 219 MET cc_start: 0.7869 (mmm) cc_final: 0.7326 (mmm) REVERT: E 287 TYR cc_start: 0.8783 (m-80) cc_final: 0.8570 (m-80) REVERT: E 301 ARG cc_start: 0.8364 (mtp180) cc_final: 0.8051 (mtm-85) REVERT: E 326 ASP cc_start: 0.8808 (t0) cc_final: 0.8536 (t0) REVERT: E 342 GLN cc_start: 0.8733 (mp10) cc_final: 0.8241 (mp10) REVERT: E 354 ILE cc_start: 0.8991 (mp) cc_final: 0.8697 (tt) REVERT: E 376 MET cc_start: 0.7944 (tpt) cc_final: 0.7139 (tpp) REVERT: E 393 LEU cc_start: 0.8208 (mt) cc_final: 0.7960 (mt) REVERT: E 402 ASP cc_start: 0.8472 (m-30) cc_final: 0.8045 (t0) REVERT: E 403 LEU cc_start: 0.8203 (mt) cc_final: 0.7912 (tp) REVERT: E 434 GLN cc_start: 0.8838 (mt0) cc_final: 0.8056 (mt0) REVERT: E 447 ASP cc_start: 0.7719 (m-30) cc_final: 0.6537 (t0) REVERT: E 459 VAL cc_start: 0.8984 (t) cc_final: 0.8530 (t) REVERT: E 480 LYS cc_start: 0.9007 (mttt) cc_final: 0.8562 (mmtm) REVERT: F 27 ILE cc_start: 0.9086 (mt) cc_final: 0.8746 (pt) REVERT: F 40 MET cc_start: 0.7465 (tpt) cc_final: 0.7248 (ppp) REVERT: F 49 VAL cc_start: 0.9527 (t) cc_final: 0.9087 (p) REVERT: F 79 MET cc_start: 0.8524 (mmm) cc_final: 0.8046 (mmt) REVERT: F 212 LEU cc_start: 0.9188 (tp) cc_final: 0.8873 (tp) REVERT: F 258 GLU cc_start: 0.8054 (pt0) cc_final: 0.7707 (tt0) REVERT: F 275 ILE cc_start: 0.9226 (tp) cc_final: 0.8887 (tp) REVERT: F 292 MET cc_start: 0.9202 (ttm) cc_final: 0.8965 (ttm) REVERT: F 294 SER cc_start: 0.9528 (t) cc_final: 0.9174 (p) REVERT: F 306 MET cc_start: 0.9289 (tpp) cc_final: 0.8779 (tpp) REVERT: F 313 ILE cc_start: 0.9549 (mt) cc_final: 0.9326 (tp) REVERT: F 321 ILE cc_start: 0.9325 (pt) cc_final: 0.9086 (tt) REVERT: F 322 THR cc_start: 0.9179 (m) cc_final: 0.8893 (p) REVERT: F 336 ASP cc_start: 0.9179 (t0) cc_final: 0.8769 (t0) REVERT: F 362 TYR cc_start: 0.7352 (m-80) cc_final: 0.6957 (m-80) REVERT: A 65 LEU cc_start: 0.9013 (mt) cc_final: 0.8554 (mp) REVERT: A 66 ASN cc_start: 0.8710 (m110) cc_final: 0.8483 (m-40) REVERT: A 122 ILE cc_start: 0.7326 (mt) cc_final: 0.7080 (tt) REVERT: A 147 LEU cc_start: 0.9368 (tt) cc_final: 0.9074 (tt) REVERT: A 176 LYS cc_start: 0.9231 (mtmp) cc_final: 0.9016 (pttp) REVERT: A 184 ILE cc_start: 0.9224 (mt) cc_final: 0.8802 (mt) REVERT: A 193 ILE cc_start: 0.8126 (mt) cc_final: 0.7808 (tt) REVERT: A 195 VAL cc_start: 0.8754 (t) cc_final: 0.8361 (t) REVERT: A 251 MET cc_start: 0.8958 (ttm) cc_final: 0.8740 (ttm) REVERT: A 274 MET cc_start: 0.8458 (ttm) cc_final: 0.8159 (tmm) REVERT: A 366 ARG cc_start: 0.8123 (tpt90) cc_final: 0.7589 (tpt90) REVERT: A 382 LYS cc_start: 0.8303 (mttt) cc_final: 0.7644 (mtmt) REVERT: A 428 PRO cc_start: 0.8273 (Cg_exo) cc_final: 0.8069 (Cg_endo) REVERT: B 40 MET cc_start: 0.7777 (mmm) cc_final: 0.6946 (mmt) REVERT: B 43 ILE cc_start: 0.9195 (mt) cc_final: 0.8987 (mm) REVERT: B 44 TYR cc_start: 0.7473 (m-10) cc_final: 0.6495 (m-10) REVERT: B 83 ASP cc_start: 0.8329 (m-30) cc_final: 0.7672 (m-30) REVERT: B 86 THR cc_start: 0.8787 (m) cc_final: 0.7599 (m) REVERT: B 183 MET cc_start: 0.7909 (mmt) cc_final: 0.7582 (mmp) REVERT: B 212 LEU cc_start: 0.9337 (tp) cc_final: 0.9071 (tt) REVERT: B 283 SER cc_start: 0.9475 (t) cc_final: 0.9196 (p) REVERT: B 328 TYR cc_start: 0.8930 (t80) cc_final: 0.8505 (t80) REVERT: B 329 VAL cc_start: 0.9552 (t) cc_final: 0.9137 (p) REVERT: B 333 ASP cc_start: 0.9152 (t0) cc_final: 0.8672 (t0) REVERT: B 396 GLN cc_start: 0.8902 (tp40) cc_final: 0.8670 (tp40) REVERT: B 476 LEU cc_start: 0.8747 (mt) cc_final: 0.8497 (mt) REVERT: C 67 LEU cc_start: 0.8715 (mt) cc_final: 0.8345 (mm) REVERT: C 194 CYS cc_start: 0.8016 (m) cc_final: 0.7551 (m) REVERT: C 264 LEU cc_start: 0.9456 (mt) cc_final: 0.8992 (mt) REVERT: C 415 GLN cc_start: 0.8531 (mt0) cc_final: 0.7899 (tp40) REVERT: C 421 LEU cc_start: 0.9278 (mt) cc_final: 0.8574 (tt) REVERT: D 50 LYS cc_start: 0.8075 (mmpt) cc_final: 0.7606 (tmmt) REVERT: D 65 VAL cc_start: 0.9057 (t) cc_final: 0.8830 (t) REVERT: D 77 VAL cc_start: 0.9142 (t) cc_final: 0.8569 (m) REVERT: D 79 MET cc_start: 0.8599 (mmm) cc_final: 0.8272 (mmm) REVERT: D 112 ASN cc_start: 0.7226 (m-40) cc_final: 0.6822 (m-40) REVERT: D 148 ILE cc_start: 0.8981 (tt) cc_final: 0.8354 (tp) REVERT: D 178 LYS cc_start: 0.8178 (mtmm) cc_final: 0.6874 (pttm) REVERT: D 184 GLU cc_start: 0.7775 (tp30) cc_final: 0.7419 (tm-30) REVERT: D 193 HIS cc_start: 0.7155 (t70) cc_final: 0.6292 (t-90) REVERT: D 199 PHE cc_start: 0.8386 (t80) cc_final: 0.7993 (t80) REVERT: D 231 LYS cc_start: 0.7428 (mmtm) cc_final: 0.7228 (mmtm) REVERT: D 239 MET cc_start: 0.8755 (mtt) cc_final: 0.8359 (mtt) REVERT: D 274 ASN cc_start: 0.8952 (t0) cc_final: 0.7323 (t0) REVERT: D 362 TYR cc_start: 0.8280 (m-80) cc_final: 0.7587 (m-10) REVERT: D 401 LEU cc_start: 0.8659 (mt) cc_final: 0.8443 (mt) REVERT: D 410 LEU cc_start: 0.8760 (mt) cc_final: 0.8167 (tt) REVERT: D 417 ASP cc_start: 0.8185 (m-30) cc_final: 0.7219 (m-30) REVERT: D 435 PHE cc_start: 0.7941 (m-10) cc_final: 0.7600 (m-80) REVERT: D 476 LEU cc_start: 0.8164 (mt) cc_final: 0.7353 (mt) outliers start: 6 outliers final: 2 residues processed: 1785 average time/residue: 0.2721 time to fit residues: 774.1065 Evaluate side-chains 838 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 836 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 432 optimal weight: 0.5980 chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 chunk 494 optimal weight: 0.8980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 29 GLN a 175 ASN ** a 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 33 ASN b 62 ASN d 124 ASN ** d 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 206 GLN e 4 ASN e 27 ASN e 102 ASN g 76 GLN ** g 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 28 GLN M 34 GLN T 28 GLN G 28 GLN G 42 GLN L 34 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 GLN E 148 GLN E 334 ASN ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN F 71 ASN F 112 ASN F 193 HIS F 264 ASN F 310 GLN A 66 ASN A 187 GLN A 214 GLN A 267 GLN A 409 ASN A 423 GLN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN B 238 GLN B 345 HIS C 187 GLN C 389 GLN C 410 GLN C 423 GLN D 57 GLN D 60 ASN D 72 ASN D 133 HIS D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.129815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.106254 restraints weight = 116176.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.106023 restraints weight = 91337.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.106511 restraints weight = 68516.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.106989 restraints weight = 54812.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.107072 restraints weight = 50137.028| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.359 39808 Z= 0.458 Angle : 1.095 42.331 53954 Z= 0.601 Chirality : 0.069 2.994 6456 Planarity : 0.007 0.134 6961 Dihedral : 6.665 128.232 5589 Min Nonbonded Distance : 1.459 Molprobity Statistics. All-atom Clashscore : 25.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.68 % Favored : 97.07 % Rotamer: Outliers : 0.71 % Allowed : 4.04 % Favored : 95.25 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.11), residues: 5149 helix: 0.83 (0.09), residues: 2881 sheet: -0.90 (0.21), residues: 564 loop : -0.90 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG A 5 TYR 0.038 0.002 TYR a 74 PHE 0.199 0.003 PHE b 95 TRP 0.023 0.003 TRP e 57 HIS 0.019 0.003 HIS a 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00815 / 0.45 (39778) covalent geometry : angle 1.07834 / 0.59 (53943) SS BOND : bond 0.00086 / 0.05 ( 1) SS BOND : angle 1.61712 / 0.94 ( 2) hydrogen bonds : bond 0.10411 / 7.46 ( 2442) hydrogen bonds : angle 6.07956 / 4.55 ( 7176) Misc. bond : bond 0.02873 / 1.83 ( 26) link_TRANS : bond 0.02473 / 0.98 ( 3) link_TRANS : angle 14.62309 / 7.96 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1161 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 1132 time to evaluate : 1.578 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: a 110 TRP cc_start: 0.5429 (m100) cc_final: 0.3880 (m-10) REVERT: a 127 LEU cc_start: 0.1957 (OUTLIER) cc_final: 0.1704 (mp) REVERT: a 150 TYR cc_start: 0.7079 (t80) cc_final: 0.5619 (m-80) REVERT: a 189 ARG cc_start: 0.7302 (tmm160) cc_final: 0.6340 (ttp80) REVERT: d 156 ASN cc_start: 0.9093 (p0) cc_final: 0.8470 (p0) REVERT: d 194 ILE cc_start: 0.8867 (mt) cc_final: 0.8651 (tt) REVERT: p 101 MET cc_start: 0.6028 (ppp) cc_final: 0.5526 (ppp) REVERT: p 148 MET cc_start: 0.6970 (tmm) cc_final: 0.6137 (ppp) REVERT: p 170 VAL cc_start: 0.4953 (t) cc_final: 0.4272 (t) REVERT: p 218 VAL cc_start: 0.8440 (m) cc_final: 0.7797 (m) REVERT: e 27 ASN cc_start: 0.8424 (t160) cc_final: 0.7965 (t0) REVERT: g 46 GLU cc_start: 0.8497 (pp20) cc_final: 0.7758 (tm-30) REVERT: g 76 GLN cc_start: 0.8668 (tt0) cc_final: 0.7847 (tm-30) REVERT: g 245 LYS cc_start: 0.8741 (mttt) cc_final: 0.8163 (tptt) REVERT: g 290 GLN cc_start: 0.8581 (tt0) cc_final: 0.8335 (mm110) REVERT: g 292 LEU cc_start: 0.8273 (tp) cc_final: 0.7938 (tt) REVERT: g 356 ILE cc_start: 0.8475 (mt) cc_final: 0.8250 (mt) REVERT: O 48 LYS cc_start: 0.6740 (mppt) cc_final: 0.6429 (mttt) REVERT: P 60 MET cc_start: 0.5497 (mtm) cc_final: 0.4518 (mmm) REVERT: M 59 PHE cc_start: 0.6568 (m-80) cc_final: 0.5996 (m-80) REVERT: T 36 VAL cc_start: 0.8547 (t) cc_final: 0.8304 (p) REVERT: H 59 PHE cc_start: 0.4606 (m-80) cc_final: 0.4371 (m-80) REVERT: L 28 GLN cc_start: 0.6226 (mt0) cc_final: 0.5078 (tt0) REVERT: K 60 MET cc_start: 0.3787 (mmm) cc_final: 0.2670 (mmm) REVERT: J 37 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7059 (mt-10) REVERT: J 60 MET cc_start: 0.6601 (ttm) cc_final: 0.6096 (ttm) REVERT: J 72 LEU cc_start: 0.7705 (mt) cc_final: 0.7266 (pp) REVERT: E 184 ILE cc_start: 0.9041 (mt) cc_final: 0.8642 (mt) REVERT: E 194 CYS cc_start: 0.8760 (m) cc_final: 0.7861 (m) REVERT: E 219 MET cc_start: 0.7893 (mmm) cc_final: 0.7185 (mmm) REVERT: E 287 TYR cc_start: 0.8759 (m-80) cc_final: 0.8558 (m-80) REVERT: E 354 ILE cc_start: 0.8930 (mp) cc_final: 0.8647 (tt) REVERT: E 376 MET cc_start: 0.7776 (tpt) cc_final: 0.7449 (tpp) REVERT: E 402 ASP cc_start: 0.8044 (m-30) cc_final: 0.7638 (t70) REVERT: E 420 LEU cc_start: 0.8812 (mp) cc_final: 0.8606 (tt) REVERT: E 434 GLN cc_start: 0.8695 (mt0) cc_final: 0.7988 (mt0) REVERT: E 461 LEU cc_start: 0.8941 (tp) cc_final: 0.8705 (tt) REVERT: F 49 VAL cc_start: 0.9505 (t) cc_final: 0.9211 (m) REVERT: F 79 MET cc_start: 0.8423 (mmm) cc_final: 0.8118 (mmt) REVERT: F 118 VAL cc_start: 0.8697 (m) cc_final: 0.8235 (p) REVERT: F 132 ILE cc_start: 0.9246 (pt) cc_final: 0.8956 (mt) REVERT: F 247 MET cc_start: 0.7822 (mtm) cc_final: 0.7559 (mtm) REVERT: F 313 ILE cc_start: 0.9546 (mt) cc_final: 0.9300 (tp) REVERT: F 322 THR cc_start: 0.8941 (m) cc_final: 0.8592 (m) REVERT: F 336 ASP cc_start: 0.9340 (t0) cc_final: 0.8985 (t0) REVERT: F 351 VAL cc_start: 0.9413 (t) cc_final: 0.9070 (m) REVERT: F 404 ILE cc_start: 0.9160 (mm) cc_final: 0.8848 (mm) REVERT: A 122 ILE cc_start: 0.8083 (mt) cc_final: 0.7865 (mt) REVERT: A 206 VAL cc_start: 0.9032 (p) cc_final: 0.8679 (p) REVERT: A 219 MET cc_start: 0.7477 (tpp) cc_final: 0.7083 (tpp) REVERT: A 301 ARG cc_start: 0.8044 (mtp180) cc_final: 0.7632 (mtp85) REVERT: A 305 LEU cc_start: 0.8896 (mt) cc_final: 0.8610 (mt) REVERT: A 321 GLU cc_start: 0.7476 (tt0) cc_final: 0.6832 (tt0) REVERT: A 415 GLN cc_start: 0.7443 (mt0) cc_final: 0.6901 (mp10) REVERT: B 82 THR cc_start: 0.8559 (m) cc_final: 0.8275 (m) REVERT: B 328 TYR cc_start: 0.9164 (t80) cc_final: 0.8405 (t80) REVERT: B 329 VAL cc_start: 0.9632 (t) cc_final: 0.9220 (p) REVERT: B 374 MET cc_start: 0.8464 (mmm) cc_final: 0.8263 (mmt) REVERT: C 67 LEU cc_start: 0.8683 (mt) cc_final: 0.8448 (mm) REVERT: C 230 ASP cc_start: 0.6963 (p0) cc_final: 0.6758 (p0) REVERT: C 275 SER cc_start: 0.8957 (p) cc_final: 0.8628 (t) REVERT: C 314 MET cc_start: 0.6935 (ttt) cc_final: 0.6168 (ttt) REVERT: C 376 MET cc_start: 0.8444 (tpp) cc_final: 0.8050 (tpp) REVERT: C 377 LYS cc_start: 0.8695 (ttpp) cc_final: 0.8061 (tptt) REVERT: C 383 LEU cc_start: 0.8713 (tp) cc_final: 0.8266 (tp) REVERT: C 421 LEU cc_start: 0.9266 (mt) cc_final: 0.8751 (tt) REVERT: D 50 LYS cc_start: 0.8508 (mmpt) cc_final: 0.8101 (tmmt) REVERT: D 90 GLU cc_start: 0.7300 (tt0) cc_final: 0.7032 (tt0) REVERT: D 148 ILE cc_start: 0.8148 (tt) cc_final: 0.7855 (pt) REVERT: D 184 GLU cc_start: 0.7387 (tp30) cc_final: 0.7139 (tp30) REVERT: D 193 HIS cc_start: 0.7105 (t70) cc_final: 0.6535 (t-90) REVERT: D 234 LEU cc_start: 0.8181 (mt) cc_final: 0.7900 (mm) REVERT: D 239 MET cc_start: 0.8563 (mtt) cc_final: 0.8247 (mtt) REVERT: D 247 MET cc_start: 0.7732 (ttm) cc_final: 0.7513 (ttp) REVERT: D 362 TYR cc_start: 0.8274 (m-80) cc_final: 0.7669 (m-80) REVERT: D 375 LEU cc_start: 0.9000 (tp) cc_final: 0.8782 (tt) REVERT: D 417 ASP cc_start: 0.7810 (m-30) cc_final: 0.6958 (m-30) REVERT: D 476 LEU cc_start: 0.8263 (mt) cc_final: 0.7451 (mt) outliers start: 29 outliers final: 11 residues processed: 1156 average time/residue: 0.2360 time to fit residues: 453.9547 Evaluate side-chains 731 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 719 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 316 optimal weight: 0.8980 chunk 247 optimal weight: 0.0470 chunk 201 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 143 optimal weight: 30.0000 chunk 79 optimal weight: 9.9990 chunk 413 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 502 optimal weight: 9.9990 chunk 444 optimal weight: 10.0000 overall best weight: 3.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 135 ASN ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 206 ASN d 227 ASN ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 186 GLN p 206 GLN e 27 ASN e 30 GLN e 102 ASN ** e 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 130 ASN ** g 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 342 ASN ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN Q 28 GLN ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 GLN ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN G 42 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 GLN ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 HIS A 273 GLN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN D 60 ASN D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.125479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.101825 restraints weight = 117739.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.101181 restraints weight = 95598.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.102115 restraints weight = 75097.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.102118 restraints weight = 59626.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.102325 restraints weight = 54819.727| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.306 39808 Z= 0.423 Angle : 0.973 35.307 53954 Z= 0.535 Chirality : 0.064 2.569 6456 Planarity : 0.007 0.195 6961 Dihedral : 6.404 107.820 5589 Min Nonbonded Distance : 1.443 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.30 % Favored : 96.52 % Rotamer: Outliers : 0.49 % Allowed : 4.65 % Favored : 94.86 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.11), residues: 5149 helix: 0.84 (0.09), residues: 2927 sheet: -0.81 (0.20), residues: 612 loop : -0.75 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.051 0.001 ARG A 16 TYR 0.029 0.002 TYR T 66 PHE 0.138 0.003 PHE b 95 TRP 0.016 0.002 TRP e 57 HIS 0.016 0.002 HIS a 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.42 (39778) covalent geometry : angle 0.95747 / 0.53 (53943) SS BOND : bond 0.00509 / 0.27 ( 1) SS BOND : angle 1.18908 / 0.67 ( 2) hydrogen bonds : bond 0.09552 / 6.86 ( 2442) hydrogen bonds : angle 5.74839 / 4.29 ( 7176) Misc. bond : bond 0.02920 / 1.86 ( 26) link_TRANS : bond 0.03161 / 1.27 ( 3) link_TRANS : angle 13.35943 / 7.29 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 988 time to evaluate : 1.717 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: a 36 HIS cc_start: 0.3980 (m170) cc_final: 0.3586 (m170) REVERT: a 126 GLU cc_start: 0.6936 (tt0) cc_final: 0.6345 (mp0) REVERT: a 150 TYR cc_start: 0.7125 (t80) cc_final: 0.5501 (m-80) REVERT: b 90 MET cc_start: 0.6786 (mmm) cc_final: 0.5940 (ptm) REVERT: b 104 GLU cc_start: 0.8078 (mp0) cc_final: 0.7243 (pp20) REVERT: d 170 ASN cc_start: 0.8938 (m-40) cc_final: 0.8540 (m-40) REVERT: p 85 ASP cc_start: 0.6124 (t0) cc_final: 0.5880 (t0) REVERT: p 101 MET cc_start: 0.6004 (ppp) cc_final: 0.5408 (ppp) REVERT: p 102 PHE cc_start: 0.3887 (m-10) cc_final: 0.3123 (m-80) REVERT: e 21 GLU cc_start: 0.5822 (tm-30) cc_final: 0.5426 (tm-30) REVERT: e 27 ASN cc_start: 0.8628 (t160) cc_final: 0.8207 (t0) REVERT: g 46 GLU cc_start: 0.8615 (pp20) cc_final: 0.7804 (tm-30) REVERT: g 76 GLN cc_start: 0.8659 (tt0) cc_final: 0.7837 (tm-30) REVERT: g 85 PHE cc_start: 0.7946 (t80) cc_final: 0.7672 (t80) REVERT: g 197 ASP cc_start: 0.7177 (t0) cc_final: 0.6936 (t0) REVERT: g 245 LYS cc_start: 0.8731 (mttt) cc_final: 0.8196 (tptt) REVERT: g 292 LEU cc_start: 0.8421 (tp) cc_final: 0.8174 (tt) REVERT: g 346 GLN cc_start: 0.8475 (pt0) cc_final: 0.8232 (pt0) REVERT: S 41 ARG cc_start: 0.5616 (ttt-90) cc_final: 0.5384 (ttt-90) REVERT: P 60 MET cc_start: 0.5437 (mtm) cc_final: 0.5189 (tpt) REVERT: P 63 LEU cc_start: 0.3239 (mt) cc_final: 0.2785 (mt) REVERT: R 59 PHE cc_start: 0.6212 (m-80) cc_final: 0.5648 (m-80) REVERT: T 49 ILE cc_start: 0.6095 (mm) cc_final: 0.5866 (mm) REVERT: T 60 MET cc_start: 0.5114 (mmm) cc_final: 0.4143 (mmm) REVERT: L 39 ILE cc_start: 0.7166 (mm) cc_final: 0.6896 (mt) REVERT: K 34 GLN cc_start: 0.6720 (mt0) cc_final: 0.6312 (mt0) REVERT: J 22 ILE cc_start: 0.8895 (mm) cc_final: 0.8615 (pt) REVERT: J 37 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7584 (mt-10) REVERT: J 49 ILE cc_start: 0.7164 (tt) cc_final: 0.6748 (tt) REVERT: J 60 MET cc_start: 0.6937 (ttm) cc_final: 0.6534 (ttt) REVERT: J 72 LEU cc_start: 0.7551 (mt) cc_final: 0.7048 (pp) REVERT: I 48 LYS cc_start: 0.6889 (mttp) cc_final: 0.6510 (mttp) REVERT: I 59 PHE cc_start: 0.7804 (m-80) cc_final: 0.7481 (m-10) REVERT: E 56 PHE cc_start: 0.7353 (m-80) cc_final: 0.7135 (m-80) REVERT: E 184 ILE cc_start: 0.9193 (mt) cc_final: 0.8850 (mt) REVERT: E 194 CYS cc_start: 0.8967 (m) cc_final: 0.8045 (m) REVERT: E 219 MET cc_start: 0.7722 (mmm) cc_final: 0.6886 (mmm) REVERT: E 234 THR cc_start: 0.8674 (t) cc_final: 0.8384 (t) REVERT: E 287 TYR cc_start: 0.8900 (m-80) cc_final: 0.8514 (m-80) REVERT: E 300 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8124 (tp30) REVERT: E 338 ILE cc_start: 0.9414 (mm) cc_final: 0.9191 (mm) REVERT: E 376 MET cc_start: 0.7766 (tpt) cc_final: 0.7242 (tpp) REVERT: E 402 ASP cc_start: 0.8203 (m-30) cc_final: 0.7747 (t0) REVERT: E 420 LEU cc_start: 0.8916 (mp) cc_final: 0.8697 (tt) REVERT: E 434 GLN cc_start: 0.8715 (mt0) cc_final: 0.8002 (mt0) REVERT: E 498 MET cc_start: 0.8389 (ttt) cc_final: 0.7965 (tpt) REVERT: F 25 GLN cc_start: 0.8141 (pt0) cc_final: 0.7794 (pt0) REVERT: F 32 ASP cc_start: 0.8174 (m-30) cc_final: 0.7770 (m-30) REVERT: F 40 MET cc_start: 0.7531 (tpp) cc_final: 0.7226 (tpp) REVERT: F 79 MET cc_start: 0.8647 (mmm) cc_final: 0.7882 (mmt) REVERT: F 118 VAL cc_start: 0.8762 (m) cc_final: 0.8487 (p) REVERT: F 132 ILE cc_start: 0.9217 (pt) cc_final: 0.8958 (mm) REVERT: F 247 MET cc_start: 0.7849 (mtm) cc_final: 0.7590 (mtm) REVERT: F 325 GLN cc_start: 0.8724 (pt0) cc_final: 0.8472 (pt0) REVERT: F 336 ASP cc_start: 0.9386 (t0) cc_final: 0.9080 (t0) REVERT: F 347 ASP cc_start: 0.8024 (m-30) cc_final: 0.7802 (m-30) REVERT: F 435 PHE cc_start: 0.6718 (m-80) cc_final: 0.6458 (m-80) REVERT: A 32 VAL cc_start: 0.9316 (t) cc_final: 0.8865 (m) REVERT: A 46 ASP cc_start: 0.8112 (t0) cc_final: 0.7761 (t0) REVERT: A 122 ILE cc_start: 0.8226 (mt) cc_final: 0.7903 (mt) REVERT: A 219 MET cc_start: 0.7546 (tpp) cc_final: 0.7215 (tpp) REVERT: A 251 MET cc_start: 0.8972 (ttm) cc_final: 0.8526 (ttm) REVERT: A 305 LEU cc_start: 0.9013 (mt) cc_final: 0.8805 (mt) REVERT: A 415 GLN cc_start: 0.7066 (mp10) cc_final: 0.6775 (mp-120) REVERT: A 436 MET cc_start: 0.8259 (ppp) cc_final: 0.7772 (ppp) REVERT: B 79 MET cc_start: 0.8577 (mmm) cc_final: 0.8084 (mmt) REVERT: B 89 MET cc_start: 0.7388 (ttm) cc_final: 0.7076 (ttm) REVERT: B 328 TYR cc_start: 0.9198 (t80) cc_final: 0.8300 (t80) REVERT: B 329 VAL cc_start: 0.9716 (t) cc_final: 0.9385 (p) REVERT: B 374 MET cc_start: 0.8427 (mmm) cc_final: 0.8184 (mmm) REVERT: B 490 LEU cc_start: 0.8967 (mt) cc_final: 0.8738 (mt) REVERT: C 67 LEU cc_start: 0.8780 (mt) cc_final: 0.8505 (mm) REVERT: C 230 ASP cc_start: 0.6844 (p0) cc_final: 0.6618 (p0) REVERT: C 231 SER cc_start: 0.9088 (p) cc_final: 0.8788 (t) REVERT: C 234 THR cc_start: 0.8829 (t) cc_final: 0.8598 (t) REVERT: C 275 SER cc_start: 0.9092 (p) cc_final: 0.8678 (t) REVERT: C 344 PHE cc_start: 0.8239 (m-80) cc_final: 0.7932 (m-80) REVERT: C 383 LEU cc_start: 0.8524 (tp) cc_final: 0.8089 (tp) REVERT: C 421 LEU cc_start: 0.9408 (mt) cc_final: 0.8785 (tt) REVERT: D 44 TYR cc_start: 0.7928 (m-80) cc_final: 0.7584 (m-80) REVERT: D 49 VAL cc_start: 0.9393 (p) cc_final: 0.9152 (m) REVERT: D 60 ASN cc_start: 0.7063 (m-40) cc_final: 0.6794 (t0) REVERT: D 162 TYR cc_start: 0.7525 (m-10) cc_final: 0.7243 (m-10) REVERT: D 193 HIS cc_start: 0.7215 (t70) cc_final: 0.6733 (t70) REVERT: D 239 MET cc_start: 0.8620 (mtt) cc_final: 0.8342 (mtt) REVERT: D 273 ASP cc_start: 0.8548 (t0) cc_final: 0.8120 (t0) REVERT: D 362 TYR cc_start: 0.8369 (m-80) cc_final: 0.7727 (m-80) REVERT: D 417 ASP cc_start: 0.7972 (m-30) cc_final: 0.7263 (m-30) outliers start: 20 outliers final: 8 residues processed: 1004 average time/residue: 0.2328 time to fit residues: 392.8919 Evaluate side-chains 671 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 663 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 395 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 502 optimal weight: 6.9990 chunk 398 optimal weight: 7.9990 chunk 277 optimal weight: 6.9990 chunk 231 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 290 optimal weight: 4.9990 chunk 30 optimal weight: 40.0000 chunk 47 optimal weight: 5.9990 chunk 293 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 180 ASN p 167 GLN e 116 ASN ** g 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 342 ASN ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 GLN F 19 ASN F 25 GLN F 264 ASN F 345 HIS ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 GLN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS D 396 GLN D 472 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.122954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.099964 restraints weight = 117742.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.099083 restraints weight = 95433.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.100039 restraints weight = 81226.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.100047 restraints weight = 65168.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.100295 restraints weight = 59534.113| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.6388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.273 39808 Z= 0.407 Angle : 0.967 43.030 53954 Z= 0.528 Chirality : 0.066 2.881 6456 Planarity : 0.008 0.332 6961 Dihedral : 6.319 94.845 5589 Min Nonbonded Distance : 1.422 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.28 % Favored : 96.47 % Rotamer: Outliers : 0.32 % Allowed : 4.07 % Favored : 95.62 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.12), residues: 5149 helix: 0.83 (0.09), residues: 2904 sheet: -0.78 (0.20), residues: 603 loop : -0.79 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.050 0.001 ARG A 16 TYR 0.025 0.002 TYR T 66 PHE 0.119 0.003 PHE b 95 TRP 0.025 0.002 TRP a 117 HIS 0.018 0.002 HIS a 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00694 / 0.40 (39778) covalent geometry : angle 0.95078 / 0.52 (53943) SS BOND : bond 0.00502 / 0.26 ( 1) SS BOND : angle 0.76268 / 0.44 ( 2) hydrogen bonds : bond 0.09451 / 6.79 ( 2442) hydrogen bonds : angle 5.62799 / 4.21 ( 7176) Misc. bond : bond 0.02829 / 1.88 ( 26) link_TRANS : bond 0.03166 / 1.22 ( 3) link_TRANS : angle 13.49146 / 7.30 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 904 time to evaluate : 1.516 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: a 126 GLU cc_start: 0.6814 (tt0) cc_final: 0.5846 (pm20) REVERT: b 90 MET cc_start: 0.6516 (mmm) cc_final: 0.5788 (ptm) REVERT: b 104 GLU cc_start: 0.7749 (mp0) cc_final: 0.7484 (pp20) REVERT: b 107 LYS cc_start: 0.4779 (tttt) cc_final: 0.4447 (tmmt) REVERT: d 163 ASN cc_start: 0.8299 (m-40) cc_final: 0.8050 (m110) REVERT: d 167 ASP cc_start: 0.8491 (m-30) cc_final: 0.8281 (m-30) REVERT: d 170 ASN cc_start: 0.9150 (m-40) cc_final: 0.8665 (m-40) REVERT: d 241 LEU cc_start: 0.8370 (tp) cc_final: 0.7788 (pp) REVERT: p 101 MET cc_start: 0.6074 (ppp) cc_final: 0.5564 (ppp) REVERT: p 102 PHE cc_start: 0.4163 (m-10) cc_final: 0.3685 (m-80) REVERT: e 27 ASN cc_start: 0.8482 (t0) cc_final: 0.7748 (t0) REVERT: g 46 GLU cc_start: 0.8775 (pp20) cc_final: 0.7986 (tm-30) REVERT: g 76 GLN cc_start: 0.8806 (tt0) cc_final: 0.7935 (tm-30) REVERT: g 197 ASP cc_start: 0.7390 (t0) cc_final: 0.7095 (t0) REVERT: g 214 TYR cc_start: 0.7919 (p90) cc_final: 0.7327 (p90) REVERT: g 245 LYS cc_start: 0.8830 (mttt) cc_final: 0.8183 (tptt) REVERT: g 290 GLN cc_start: 0.8678 (mt0) cc_final: 0.8364 (mm110) REVERT: g 311 SER cc_start: 0.9168 (m) cc_final: 0.8712 (p) REVERT: N 60 MET cc_start: 0.6931 (ptt) cc_final: 0.6625 (ptt) REVERT: O 34 GLN cc_start: 0.8047 (tt0) cc_final: 0.7700 (tt0) REVERT: O 60 MET cc_start: 0.5732 (mtm) cc_final: 0.5512 (mtm) REVERT: P 60 MET cc_start: 0.5504 (mtm) cc_final: 0.5239 (tpt) REVERT: P 63 LEU cc_start: 0.3645 (mt) cc_final: 0.3273 (mp) REVERT: T 15 LEU cc_start: 0.6691 (pp) cc_final: 0.6405 (tp) REVERT: T 49 ILE cc_start: 0.6221 (mm) cc_final: 0.5602 (mm) REVERT: T 60 MET cc_start: 0.5075 (mmm) cc_final: 0.4033 (mmm) REVERT: G 42 GLN cc_start: 0.8741 (tp-100) cc_final: 0.8536 (tp40) REVERT: H 28 GLN cc_start: 0.8577 (mt0) cc_final: 0.8083 (mt0) REVERT: L 39 ILE cc_start: 0.7401 (mm) cc_final: 0.7159 (mt) REVERT: K 34 GLN cc_start: 0.6798 (mt0) cc_final: 0.6361 (mt0) REVERT: K 60 MET cc_start: 0.4837 (mmm) cc_final: 0.3818 (mmm) REVERT: J 37 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7492 (mt-10) REVERT: J 44 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6973 (tm-30) REVERT: J 60 MET cc_start: 0.7143 (ttm) cc_final: 0.6857 (ttm) REVERT: J 63 LEU cc_start: 0.7001 (mt) cc_final: 0.6762 (mt) REVERT: J 72 LEU cc_start: 0.7435 (mt) cc_final: 0.6954 (pp) REVERT: I 48 LYS cc_start: 0.7140 (mttp) cc_final: 0.6672 (ttmt) REVERT: I 60 MET cc_start: 0.5298 (mmm) cc_final: 0.4475 (mmm) REVERT: E 147 LEU cc_start: 0.8930 (tp) cc_final: 0.8664 (tp) REVERT: E 219 MET cc_start: 0.7953 (mmm) cc_final: 0.7148 (mmm) REVERT: E 234 THR cc_start: 0.8614 (t) cc_final: 0.8368 (t) REVERT: E 251 MET cc_start: 0.8043 (ptt) cc_final: 0.7701 (ptt) REVERT: E 287 TYR cc_start: 0.8941 (m-80) cc_final: 0.8537 (m-80) REVERT: E 314 MET cc_start: 0.7269 (ttt) cc_final: 0.7048 (ttt) REVERT: E 342 GLN cc_start: 0.8522 (mp-120) cc_final: 0.8318 (mp-120) REVERT: E 376 MET cc_start: 0.7803 (tpt) cc_final: 0.7397 (tpp) REVERT: E 402 ASP cc_start: 0.8229 (m-30) cc_final: 0.7704 (t0) REVERT: E 434 GLN cc_start: 0.8800 (mt0) cc_final: 0.8197 (mt0) REVERT: E 498 MET cc_start: 0.8487 (ttt) cc_final: 0.8157 (tpt) REVERT: F 32 ASP cc_start: 0.8326 (m-30) cc_final: 0.8018 (m-30) REVERT: F 40 MET cc_start: 0.7507 (tpp) cc_final: 0.7268 (tpp) REVERT: F 118 VAL cc_start: 0.8745 (m) cc_final: 0.8369 (p) REVERT: F 211 ASP cc_start: 0.7639 (m-30) cc_final: 0.6902 (t70) REVERT: F 212 LEU cc_start: 0.9011 (tp) cc_final: 0.8622 (tp) REVERT: F 215 GLU cc_start: 0.7859 (mt-10) cc_final: 0.6934 (mt-10) REVERT: F 288 LEU cc_start: 0.9284 (mm) cc_final: 0.8841 (tp) REVERT: F 336 ASP cc_start: 0.9315 (t0) cc_final: 0.9094 (t0) REVERT: F 347 ASP cc_start: 0.8270 (m-30) cc_final: 0.7993 (m-30) REVERT: A 32 VAL cc_start: 0.9308 (t) cc_final: 0.8897 (m) REVERT: A 122 ILE cc_start: 0.8191 (mt) cc_final: 0.7879 (mt) REVERT: A 264 LEU cc_start: 0.9388 (mt) cc_final: 0.9104 (tp) REVERT: A 290 ASP cc_start: 0.7921 (m-30) cc_final: 0.7113 (m-30) REVERT: A 436 MET cc_start: 0.8522 (ppp) cc_final: 0.8065 (ppp) REVERT: B 168 ILE cc_start: 0.9348 (mm) cc_final: 0.9135 (mm) REVERT: B 490 LEU cc_start: 0.9070 (mt) cc_final: 0.8857 (mt) REVERT: B 492 MET cc_start: 0.9076 (ppp) cc_final: 0.8779 (ppp) REVERT: C 67 LEU cc_start: 0.8927 (mt) cc_final: 0.8646 (mm) REVERT: C 83 ILE cc_start: 0.9194 (mm) cc_final: 0.8964 (mm) REVERT: C 258 LEU cc_start: 0.9175 (tp) cc_final: 0.8912 (tp) REVERT: C 275 SER cc_start: 0.8994 (p) cc_final: 0.8637 (t) REVERT: C 344 PHE cc_start: 0.8320 (m-80) cc_final: 0.7990 (m-80) REVERT: C 383 LEU cc_start: 0.8509 (tp) cc_final: 0.8154 (tp) REVERT: D 27 ILE cc_start: 0.9156 (mm) cc_final: 0.8798 (mp) REVERT: D 185 LEU cc_start: 0.8896 (tp) cc_final: 0.8426 (tp) REVERT: D 193 HIS cc_start: 0.6974 (t70) cc_final: 0.6718 (t-90) REVERT: D 273 ASP cc_start: 0.8681 (t0) cc_final: 0.8249 (t0) REVERT: D 362 TYR cc_start: 0.8404 (m-80) cc_final: 0.7724 (m-80) REVERT: D 417 ASP cc_start: 0.8047 (m-30) cc_final: 0.7461 (m-30) REVERT: D 476 LEU cc_start: 0.8720 (mm) cc_final: 0.8329 (mm) outliers start: 13 outliers final: 5 residues processed: 911 average time/residue: 0.2324 time to fit residues: 355.8899 Evaluate side-chains 641 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 636 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 99 optimal weight: 1.9990 chunk 363 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 274 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 chunk 282 optimal weight: 6.9990 chunk 256 optimal weight: 9.9990 chunk 334 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 392 optimal weight: 5.9990 chunk 275 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 123 ASN d 188 ASN ** p 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 76 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 342 ASN ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN E 97 GLN E 164 GLN E 295 HIS F 19 ASN F 188 ASN F 238 GLN F 345 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.122040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.099792 restraints weight = 118798.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.098765 restraints weight = 103359.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.099130 restraints weight = 82948.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.099459 restraints weight = 67353.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.099592 restraints weight = 60348.890| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.6853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.271 39808 Z= 0.396 Angle : 0.921 36.675 53954 Z= 0.507 Chirality : 0.064 2.817 6456 Planarity : 0.007 0.142 6961 Dihedral : 6.641 174.960 5589 Min Nonbonded Distance : 1.406 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.28 % Favored : 96.48 % Rotamer: Outliers : 0.12 % Allowed : 3.87 % Favored : 96.01 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.12), residues: 5149 helix: 0.78 (0.09), residues: 2923 sheet: -0.72 (0.21), residues: 590 loop : -0.75 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG A 16 TYR 0.048 0.002 TYR D 162 PHE 0.143 0.003 PHE b 95 TRP 0.017 0.002 TRP a 94 HIS 0.022 0.002 HIS a 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.39 (39778) covalent geometry : angle 0.90504 / 0.50 (53943) SS BOND : bond 0.00431 / 0.23 ( 1) SS BOND : angle 0.68783 / 0.40 ( 2) hydrogen bonds : bond 0.09374 / 6.73 ( 2442) hydrogen bonds : angle 5.51727 / 4.13 ( 7176) Misc. bond : bond 0.02704 / 1.81 ( 26) link_TRANS : bond 0.02757 / 1.05 ( 3) link_TRANS : angle 13.37537 / 7.22 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 878 time to evaluate : 1.523 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: a 126 GLU cc_start: 0.7046 (tt0) cc_final: 0.5786 (pm20) REVERT: b 90 MET cc_start: 0.6760 (mmm) cc_final: 0.5930 (ppp) REVERT: b 104 GLU cc_start: 0.7627 (mp0) cc_final: 0.7278 (pp20) REVERT: b 107 LYS cc_start: 0.4912 (tttt) cc_final: 0.4538 (tmmt) REVERT: b 175 MET cc_start: 0.6954 (mtm) cc_final: 0.5937 (ttt) REVERT: d 72 ASP cc_start: 0.7531 (t0) cc_final: 0.6818 (t0) REVERT: d 241 LEU cc_start: 0.8514 (tp) cc_final: 0.8004 (pp) REVERT: p 101 MET cc_start: 0.6029 (ppp) cc_final: 0.5378 (ppp) REVERT: p 102 PHE cc_start: 0.3971 (m-10) cc_final: 0.3525 (m-80) REVERT: e 27 ASN cc_start: 0.8410 (t0) cc_final: 0.7707 (t0) REVERT: e 73 GLU cc_start: 0.7018 (tp30) cc_final: 0.6465 (tp30) REVERT: g 46 GLU cc_start: 0.8559 (pp20) cc_final: 0.7677 (tm-30) REVERT: g 76 GLN cc_start: 0.8757 (tt0) cc_final: 0.8190 (tm-30) REVERT: g 214 TYR cc_start: 0.7761 (p90) cc_final: 0.7266 (p90) REVERT: g 245 LYS cc_start: 0.8768 (mttt) cc_final: 0.8108 (tptt) REVERT: g 290 GLN cc_start: 0.8586 (mt0) cc_final: 0.8283 (mm110) REVERT: g 299 TYR cc_start: 0.6418 (t80) cc_final: 0.5710 (t80) REVERT: g 311 SER cc_start: 0.9077 (m) cc_final: 0.8633 (p) REVERT: g 323 MET cc_start: 0.8813 (mmp) cc_final: 0.8570 (mmp) REVERT: S 28 GLN cc_start: 0.6537 (tt0) cc_final: 0.6077 (tt0) REVERT: N 60 MET cc_start: 0.6719 (ptt) cc_final: 0.6042 (ptt) REVERT: O 34 GLN cc_start: 0.8363 (tt0) cc_final: 0.8144 (tt0) REVERT: O 55 LEU cc_start: 0.5915 (tt) cc_final: 0.5647 (tt) REVERT: O 56 SER cc_start: 0.7648 (p) cc_final: 0.7286 (m) REVERT: P 60 MET cc_start: 0.5599 (mtm) cc_final: 0.4636 (tpp) REVERT: P 63 LEU cc_start: 0.3882 (mt) cc_final: 0.3513 (mp) REVERT: M 59 PHE cc_start: 0.7306 (m-80) cc_final: 0.6848 (m-80) REVERT: T 60 MET cc_start: 0.4724 (mmm) cc_final: 0.3909 (mmm) REVERT: K 34 GLN cc_start: 0.6678 (mt0) cc_final: 0.6322 (mt0) REVERT: K 60 MET cc_start: 0.4379 (mmm) cc_final: 0.3927 (mmm) REVERT: J 37 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7418 (mt-10) REVERT: J 55 LEU cc_start: 0.6803 (mm) cc_final: 0.6506 (tp) REVERT: J 60 MET cc_start: 0.7385 (ttm) cc_final: 0.7160 (ttm) REVERT: J 72 LEU cc_start: 0.7308 (mt) cc_final: 0.6841 (pp) REVERT: I 48 LYS cc_start: 0.7111 (mttp) cc_final: 0.6610 (ttmt) REVERT: E 219 MET cc_start: 0.7766 (mmm) cc_final: 0.7101 (mmm) REVERT: E 234 THR cc_start: 0.8306 (t) cc_final: 0.8101 (t) REVERT: E 259 ILE cc_start: 0.9373 (pt) cc_final: 0.9124 (pt) REVERT: E 287 TYR cc_start: 0.8847 (m-80) cc_final: 0.8583 (m-80) REVERT: E 402 ASP cc_start: 0.8112 (m-30) cc_final: 0.7590 (t0) REVERT: E 434 GLN cc_start: 0.8627 (mt0) cc_final: 0.8049 (mt0) REVERT: E 497 GLN cc_start: 0.7030 (tp-100) cc_final: 0.6803 (tp-100) REVERT: F 32 ASP cc_start: 0.8219 (m-30) cc_final: 0.8011 (m-30) REVERT: F 40 MET cc_start: 0.7424 (tpp) cc_final: 0.7068 (tpt) REVERT: F 79 MET cc_start: 0.8476 (mmt) cc_final: 0.8136 (mmt) REVERT: F 118 VAL cc_start: 0.8605 (m) cc_final: 0.8141 (p) REVERT: F 212 LEU cc_start: 0.8987 (tp) cc_final: 0.8757 (tt) REVERT: F 322 THR cc_start: 0.9070 (m) cc_final: 0.8864 (m) REVERT: F 347 ASP cc_start: 0.8267 (m-30) cc_final: 0.7929 (m-30) REVERT: A 32 VAL cc_start: 0.9249 (t) cc_final: 0.8822 (m) REVERT: A 85 GLU cc_start: 0.8385 (pt0) cc_final: 0.8167 (pt0) REVERT: A 251 MET cc_start: 0.8674 (ttm) cc_final: 0.8353 (ttp) REVERT: A 293 TYR cc_start: 0.8876 (t80) cc_final: 0.8391 (t80) REVERT: A 301 ARG cc_start: 0.8480 (mtp180) cc_final: 0.8047 (mtp85) REVERT: A 394 GLU cc_start: 0.6097 (tm-30) cc_final: 0.5476 (mm-30) REVERT: A 436 MET cc_start: 0.8437 (ppp) cc_final: 0.7885 (ppp) REVERT: B 90 GLU cc_start: 0.7491 (tt0) cc_final: 0.7190 (tm-30) REVERT: B 490 LEU cc_start: 0.9121 (mt) cc_final: 0.8880 (mt) REVERT: C 67 LEU cc_start: 0.8907 (mt) cc_final: 0.8669 (mm) REVERT: C 157 MET cc_start: 0.8341 (mmt) cc_final: 0.7585 (mmp) REVERT: C 230 ASP cc_start: 0.7060 (p0) cc_final: 0.6789 (p0) REVERT: C 234 THR cc_start: 0.9002 (t) cc_final: 0.8793 (t) REVERT: C 258 LEU cc_start: 0.9035 (tp) cc_final: 0.8776 (tp) REVERT: C 344 PHE cc_start: 0.8233 (m-80) cc_final: 0.7848 (m-80) REVERT: C 383 LEU cc_start: 0.8187 (tp) cc_final: 0.7974 (tp) REVERT: D 27 ILE cc_start: 0.9060 (mm) cc_final: 0.8766 (mp) REVERT: D 79 MET cc_start: 0.8196 (mmm) cc_final: 0.7954 (mmm) REVERT: D 241 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7710 (mm-30) REVERT: D 273 ASP cc_start: 0.8592 (t0) cc_final: 0.8273 (t0) REVERT: D 417 ASP cc_start: 0.8035 (m-30) cc_final: 0.7301 (m-30) REVERT: D 435 PHE cc_start: 0.8134 (m-80) cc_final: 0.7785 (m-80) REVERT: D 476 LEU cc_start: 0.8609 (mm) cc_final: 0.8089 (mm) outliers start: 5 outliers final: 3 residues processed: 883 average time/residue: 0.2320 time to fit residues: 345.8536 Evaluate side-chains 610 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 607 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 256 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 442 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 497 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 chunk 478 optimal weight: 0.9980 chunk 303 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 176 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 98 ASN b 165 HIS b 170 ASN b 180 ASN ** p 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 342 ASN ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN G 42 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 GLN E 351 ASN F 310 GLN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 GLN C 236 GLN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.121770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.098878 restraints weight = 119798.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097904 restraints weight = 102909.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.098661 restraints weight = 78489.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.098991 restraints weight = 60553.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.099150 restraints weight = 54084.815| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.7156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.268 39808 Z= 0.386 Angle : 0.938 47.100 53954 Z= 0.510 Chirality : 0.065 3.147 6456 Planarity : 0.009 0.524 6961 Dihedral : 6.225 87.970 5589 Min Nonbonded Distance : 1.400 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.48 % Favored : 96.29 % Rotamer: Outliers : 0.10 % Allowed : 2.51 % Favored : 97.39 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.12), residues: 5149 helix: 0.82 (0.09), residues: 2928 sheet: -0.90 (0.20), residues: 614 loop : -0.75 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG A 16 TYR 0.029 0.002 TYR J 66 PHE 0.157 0.003 PHE b 95 TRP 0.009 0.001 TRP e 15 HIS 0.021 0.002 HIS a 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.38 (39778) covalent geometry : angle 0.92167 / 0.50 (53943) SS BOND : bond 0.00292 / 0.15 ( 1) SS BOND : angle 0.73680 / 0.43 ( 2) hydrogen bonds : bond 0.09263 / 6.65 ( 2442) hydrogen bonds : angle 5.45910 / 4.09 ( 7176) Misc. bond : bond 0.02707 / 1.81 ( 26) link_TRANS : bond 0.02961 / 1.17 ( 3) link_TRANS : angle 13.49961 / 7.28 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 834 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 126 GLU cc_start: 0.6978 (tt0) cc_final: 0.5558 (pm20) REVERT: b 90 MET cc_start: 0.6709 (mmm) cc_final: 0.5826 (ptm) REVERT: b 107 LYS cc_start: 0.5015 (tttt) cc_final: 0.4720 (tmmt) REVERT: b 175 MET cc_start: 0.6954 (mtm) cc_final: 0.5928 (ttt) REVERT: d 72 ASP cc_start: 0.7477 (t0) cc_final: 0.6729 (t0) REVERT: d 109 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8231 (tp30) REVERT: p 101 MET cc_start: 0.5896 (ppp) cc_final: 0.5296 (ppp) REVERT: p 102 PHE cc_start: 0.3810 (m-10) cc_final: 0.3371 (m-80) REVERT: e 27 ASN cc_start: 0.8470 (t0) cc_final: 0.7734 (t0) REVERT: e 51 ILE cc_start: 0.7683 (mm) cc_final: 0.7470 (mp) REVERT: e 73 GLU cc_start: 0.7014 (tp30) cc_final: 0.6484 (tp30) REVERT: e 125 ARG cc_start: 0.7688 (ttt-90) cc_final: 0.7455 (tpt-90) REVERT: g 46 GLU cc_start: 0.8514 (pp20) cc_final: 0.7668 (tm-30) REVERT: g 76 GLN cc_start: 0.8697 (tt0) cc_final: 0.8270 (tm-30) REVERT: g 197 ASP cc_start: 0.7367 (t0) cc_final: 0.7049 (t0) REVERT: g 214 TYR cc_start: 0.7826 (p90) cc_final: 0.7262 (p90) REVERT: g 245 LYS cc_start: 0.8765 (mttt) cc_final: 0.8131 (tptt) REVERT: g 290 GLN cc_start: 0.8658 (mt0) cc_final: 0.8379 (mm110) REVERT: g 311 SER cc_start: 0.9089 (m) cc_final: 0.8618 (p) REVERT: g 323 MET cc_start: 0.8767 (mmp) cc_final: 0.8565 (mmp) REVERT: S 28 GLN cc_start: 0.6635 (tt0) cc_final: 0.6372 (tt0) REVERT: N 15 LEU cc_start: 0.6843 (mt) cc_final: 0.6486 (tt) REVERT: N 53 LEU cc_start: 0.6581 (mp) cc_final: 0.5959 (tt) REVERT: N 60 MET cc_start: 0.7006 (ptt) cc_final: 0.6468 (ptt) REVERT: O 34 GLN cc_start: 0.8001 (tt0) cc_final: 0.7782 (tt0) REVERT: M 59 PHE cc_start: 0.7298 (m-80) cc_final: 0.6827 (m-80) REVERT: T 60 MET cc_start: 0.4824 (mmm) cc_final: 0.4000 (mmm) REVERT: H 49 ILE cc_start: 0.7161 (mm) cc_final: 0.6446 (mm) REVERT: H 52 THR cc_start: 0.5374 (p) cc_final: 0.5039 (p) REVERT: H 60 MET cc_start: 0.5076 (ppp) cc_final: 0.4708 (ppp) REVERT: K 34 GLN cc_start: 0.6604 (mt0) cc_final: 0.6394 (mt0) REVERT: J 55 LEU cc_start: 0.6698 (mm) cc_final: 0.6373 (tp) REVERT: J 72 LEU cc_start: 0.7233 (mt) cc_final: 0.6805 (pp) REVERT: I 48 LYS cc_start: 0.7114 (mttp) cc_final: 0.6693 (ttmt) REVERT: E 56 PHE cc_start: 0.7192 (m-80) cc_final: 0.6988 (m-80) REVERT: E 147 LEU cc_start: 0.9050 (tp) cc_final: 0.8791 (tp) REVERT: E 219 MET cc_start: 0.7816 (mmm) cc_final: 0.7171 (mmm) REVERT: E 234 THR cc_start: 0.8251 (t) cc_final: 0.8048 (t) REVERT: E 287 TYR cc_start: 0.8803 (m-80) cc_final: 0.8573 (m-80) REVERT: E 402 ASP cc_start: 0.8161 (m-30) cc_final: 0.7589 (t0) REVERT: F 118 VAL cc_start: 0.8871 (m) cc_final: 0.8354 (p) REVERT: F 183 MET cc_start: 0.8434 (mmm) cc_final: 0.8185 (mmm) REVERT: F 336 ASP cc_start: 0.9048 (t0) cc_final: 0.8847 (t0) REVERT: F 346 LEU cc_start: 0.9062 (tt) cc_final: 0.8681 (mt) REVERT: F 347 ASP cc_start: 0.8263 (m-30) cc_final: 0.7963 (m-30) REVERT: F 481 ASP cc_start: 0.8657 (p0) cc_final: 0.8409 (p0) REVERT: A 32 VAL cc_start: 0.9306 (t) cc_final: 0.8847 (m) REVERT: A 46 ASP cc_start: 0.8260 (t0) cc_final: 0.7663 (t0) REVERT: A 66 ASN cc_start: 0.8346 (m-40) cc_final: 0.8042 (m-40) REVERT: A 164 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8409 (tm-30) REVERT: A 167 LEU cc_start: 0.9047 (tp) cc_final: 0.8449 (tp) REVERT: A 251 MET cc_start: 0.8799 (ttm) cc_final: 0.8530 (ttp) REVERT: A 301 ARG cc_start: 0.8361 (mtp180) cc_final: 0.7847 (mtp85) REVERT: A 394 GLU cc_start: 0.6156 (tm-30) cc_final: 0.5539 (mm-30) REVERT: A 436 MET cc_start: 0.8641 (ppp) cc_final: 0.8135 (ppp) REVERT: B 168 ILE cc_start: 0.9461 (mm) cc_final: 0.9169 (mm) REVERT: B 401 LEU cc_start: 0.9118 (mm) cc_final: 0.8692 (mm) REVERT: B 490 LEU cc_start: 0.9182 (mt) cc_final: 0.8958 (mt) REVERT: C 157 MET cc_start: 0.8353 (mmt) cc_final: 0.8126 (mmp) REVERT: C 258 LEU cc_start: 0.9132 (tp) cc_final: 0.8604 (tp) REVERT: C 344 PHE cc_start: 0.8312 (m-80) cc_final: 0.7833 (m-80) REVERT: D 31 LEU cc_start: 0.8444 (mt) cc_final: 0.7981 (mp) REVERT: D 164 ARG cc_start: 0.5882 (mpp80) cc_final: 0.5586 (mtt-85) REVERT: D 171 PHE cc_start: 0.8887 (m-80) cc_final: 0.8582 (m-80) REVERT: D 184 GLU cc_start: 0.7444 (tp30) cc_final: 0.6945 (mm-30) REVERT: D 193 HIS cc_start: 0.7016 (t70) cc_final: 0.6656 (t-90) REVERT: D 241 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7653 (mm-30) REVERT: D 343 PHE cc_start: 0.8609 (m-80) cc_final: 0.8146 (m-80) REVERT: D 417 ASP cc_start: 0.8103 (m-30) cc_final: 0.7319 (m-30) REVERT: D 476 LEU cc_start: 0.8649 (mm) cc_final: 0.8013 (mm) outliers start: 4 outliers final: 3 residues processed: 837 average time/residue: 0.2298 time to fit residues: 325.1082 Evaluate side-chains 600 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 597 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 229 optimal weight: 1.9990 chunk 270 optimal weight: 0.9990 chunk 453 optimal weight: 6.9990 chunk 203 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 475 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 88 optimal weight: 0.0270 chunk 228 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 252 optimal weight: 1.9990 overall best weight: 1.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 98 ASN b 165 HIS b 180 ASN p 167 GLN ** g 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 301 ASN ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 28 GLN ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN E 351 ASN E 497 GLN ** F 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 HIS D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN D 325 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.123818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.101982 restraints weight = 117586.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.101650 restraints weight = 100776.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.101920 restraints weight = 75880.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.102038 restraints weight = 66180.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.102211 restraints weight = 59506.043| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.7402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.275 39808 Z= 0.373 Angle : 0.932 49.130 53954 Z= 0.504 Chirality : 0.064 2.843 6456 Planarity : 0.009 0.477 6961 Dihedral : 6.071 89.126 5589 Min Nonbonded Distance : 1.377 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.28 % Favored : 96.50 % Rotamer: Outliers : 0.07 % Allowed : 1.56 % Favored : 98.37 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.12), residues: 5149 helix: 1.01 (0.10), residues: 2910 sheet: -0.81 (0.20), residues: 608 loop : -0.65 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG A 16 TYR 0.025 0.002 TYR T 66 PHE 0.170 0.002 PHE b 95 TRP 0.015 0.001 TRP a 117 HIS 0.018 0.001 HIS a 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.37 (39778) covalent geometry : angle 0.91630 / 0.49 (53943) SS BOND : bond 0.00070 / 0.04 ( 1) SS BOND : angle 1.05844 / 0.62 ( 2) hydrogen bonds : bond 0.09165 / 6.61 ( 2442) hydrogen bonds : angle 5.34347 / 4.00 ( 7176) Misc. bond : bond 0.02684 / 1.79 ( 26) link_TRANS : bond 0.02585 / 1.05 ( 3) link_TRANS : angle 13.33689 / 7.15 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 853 time to evaluate : 1.648 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: a 126 GLU cc_start: 0.6876 (tt0) cc_final: 0.5262 (pm20) REVERT: a 172 LEU cc_start: 0.7254 (tt) cc_final: 0.6956 (pp) REVERT: b 90 MET cc_start: 0.6646 (mmm) cc_final: 0.5977 (ptm) REVERT: b 175 MET cc_start: 0.6480 (mtm) cc_final: 0.5884 (ttt) REVERT: d 72 ASP cc_start: 0.7604 (t0) cc_final: 0.6827 (t0) REVERT: d 109 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8212 (tp30) REVERT: d 222 THR cc_start: 0.7912 (p) cc_final: 0.6923 (p) REVERT: p 101 MET cc_start: 0.5818 (ppp) cc_final: 0.5305 (ppp) REVERT: p 102 PHE cc_start: 0.3870 (m-10) cc_final: 0.3476 (m-80) REVERT: e 27 ASN cc_start: 0.8361 (t0) cc_final: 0.7639 (t0) REVERT: e 73 GLU cc_start: 0.7028 (tp30) cc_final: 0.6515 (tp30) REVERT: e 79 ASN cc_start: 0.7866 (p0) cc_final: 0.7122 (m110) REVERT: e 80 ASP cc_start: 0.7490 (t70) cc_final: 0.6689 (t0) REVERT: g 46 GLU cc_start: 0.8473 (pp20) cc_final: 0.7602 (tm-30) REVERT: g 76 GLN cc_start: 0.8706 (tt0) cc_final: 0.8167 (tm-30) REVERT: g 150 LYS cc_start: 0.8497 (mmmt) cc_final: 0.7397 (mtmt) REVERT: g 214 TYR cc_start: 0.7641 (p90) cc_final: 0.7213 (p90) REVERT: g 245 LYS cc_start: 0.8755 (mttt) cc_final: 0.8064 (tptt) REVERT: g 311 SER cc_start: 0.9136 (m) cc_final: 0.8671 (p) REVERT: g 355 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7364 (tm-30) REVERT: g 356 ILE cc_start: 0.9122 (mt) cc_final: 0.8535 (mt) REVERT: S 28 GLN cc_start: 0.6462 (tt0) cc_final: 0.6031 (tt0) REVERT: N 53 LEU cc_start: 0.6454 (mp) cc_final: 0.5812 (tt) REVERT: N 60 MET cc_start: 0.7173 (ptt) cc_final: 0.6703 (ptt) REVERT: O 34 GLN cc_start: 0.8166 (tt0) cc_final: 0.7959 (tt0) REVERT: P 60 MET cc_start: 0.5916 (mtm) cc_final: 0.5116 (tpt) REVERT: P 63 LEU cc_start: 0.3392 (mp) cc_final: 0.2922 (mp) REVERT: Q 60 MET cc_start: 0.7939 (mtt) cc_final: 0.7568 (mtp) REVERT: M 59 PHE cc_start: 0.7311 (m-80) cc_final: 0.6889 (m-80) REVERT: T 60 MET cc_start: 0.4635 (mmm) cc_final: 0.3943 (mmm) REVERT: H 37 GLU cc_start: 0.8197 (tt0) cc_final: 0.7352 (tm-30) REVERT: H 54 LEU cc_start: 0.6932 (mm) cc_final: 0.6109 (tp) REVERT: L 74 LEU cc_start: 0.5731 (mp) cc_final: 0.5510 (mp) REVERT: K 28 GLN cc_start: 0.7600 (mm-40) cc_final: 0.7264 (mm-40) REVERT: J 37 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7625 (mt-10) REVERT: J 44 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7124 (tm-30) REVERT: J 72 LEU cc_start: 0.7142 (mt) cc_final: 0.6747 (pp) REVERT: I 48 LYS cc_start: 0.7040 (mttp) cc_final: 0.6641 (ttmt) REVERT: E 56 PHE cc_start: 0.7115 (m-80) cc_final: 0.6914 (m-80) REVERT: E 138 MET cc_start: 0.8220 (pmm) cc_final: 0.7615 (mtm) REVERT: E 147 LEU cc_start: 0.9045 (tp) cc_final: 0.8689 (tp) REVERT: E 219 MET cc_start: 0.7721 (mmm) cc_final: 0.7057 (mmm) REVERT: E 227 GLU cc_start: 0.8346 (tp30) cc_final: 0.8073 (tp30) REVERT: E 402 ASP cc_start: 0.8158 (m-30) cc_final: 0.7584 (t0) REVERT: F 40 MET cc_start: 0.7749 (tpt) cc_final: 0.7450 (tpp) REVERT: F 79 MET cc_start: 0.8428 (mmt) cc_final: 0.7955 (mmt) REVERT: F 118 VAL cc_start: 0.8917 (m) cc_final: 0.8522 (p) REVERT: F 212 LEU cc_start: 0.8945 (tt) cc_final: 0.8442 (tt) REVERT: F 236 TYR cc_start: 0.8303 (m-10) cc_final: 0.8023 (m-10) REVERT: F 306 MET cc_start: 0.9616 (tpp) cc_final: 0.9395 (tpp) REVERT: F 336 ASP cc_start: 0.8992 (t0) cc_final: 0.8786 (t0) REVERT: F 347 ASP cc_start: 0.8252 (m-30) cc_final: 0.7929 (m-30) REVERT: A 46 ASP cc_start: 0.8303 (t0) cc_final: 0.7716 (t0) REVERT: A 66 ASN cc_start: 0.8314 (m-40) cc_final: 0.8002 (m-40) REVERT: A 77 MET cc_start: 0.7411 (mmt) cc_final: 0.7136 (mmt) REVERT: A 164 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8434 (tm-30) REVERT: A 166 GLU cc_start: 0.9157 (tp30) cc_final: 0.8806 (tp30) REVERT: A 219 MET cc_start: 0.7974 (mmm) cc_final: 0.7682 (mmm) REVERT: A 236 GLN cc_start: 0.9111 (mt0) cc_final: 0.8727 (mt0) REVERT: A 293 TYR cc_start: 0.9017 (t80) cc_final: 0.8799 (t80) REVERT: A 301 ARG cc_start: 0.8386 (mtp180) cc_final: 0.7779 (mtp85) REVERT: A 394 GLU cc_start: 0.6087 (tm-30) cc_final: 0.5548 (mm-30) REVERT: A 436 MET cc_start: 0.8171 (ppp) cc_final: 0.7627 (ppp) REVERT: B 168 ILE cc_start: 0.9346 (mm) cc_final: 0.9060 (mm) REVERT: B 490 LEU cc_start: 0.9188 (mt) cc_final: 0.8935 (mt) REVERT: C 110 ASN cc_start: 0.8110 (t0) cc_final: 0.7783 (t0) REVERT: C 157 MET cc_start: 0.8294 (mmt) cc_final: 0.8062 (mmp) REVERT: C 230 ASP cc_start: 0.7081 (p0) cc_final: 0.6860 (p0) REVERT: C 258 LEU cc_start: 0.9260 (tp) cc_final: 0.8960 (tp) REVERT: C 344 PHE cc_start: 0.8330 (m-80) cc_final: 0.7948 (m-80) REVERT: C 436 MET cc_start: 0.8895 (ppp) cc_final: 0.8553 (ptt) REVERT: D 31 LEU cc_start: 0.8447 (mt) cc_final: 0.7948 (mp) REVERT: D 171 PHE cc_start: 0.8928 (m-80) cc_final: 0.8603 (m-80) REVERT: D 241 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7509 (mm-30) REVERT: D 254 LEU cc_start: 0.9097 (tp) cc_final: 0.8897 (tp) REVERT: D 273 ASP cc_start: 0.8672 (t0) cc_final: 0.8456 (t0) REVERT: D 328 TYR cc_start: 0.8244 (t80) cc_final: 0.8004 (t80) REVERT: D 343 PHE cc_start: 0.8642 (m-80) cc_final: 0.8210 (m-80) REVERT: D 476 LEU cc_start: 0.8764 (mm) cc_final: 0.8062 (mm) outliers start: 3 outliers final: 1 residues processed: 854 average time/residue: 0.2272 time to fit residues: 329.9659 Evaluate side-chains 627 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 626 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 107 optimal weight: 8.9990 chunk 287 optimal weight: 10.0000 chunk 371 optimal weight: 5.9990 chunk 186 optimal weight: 7.9990 chunk 478 optimal weight: 6.9990 chunk 344 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 423 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 320 optimal weight: 9.9990 chunk 303 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 180 ASN g 290 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 342 ASN g 361 ASN ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 28 GLN ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN E 351 ASN ** E 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 GLN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN B 389 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 GLN D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN D 472 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.119382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.096297 restraints weight = 126501.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.095647 restraints weight = 114000.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.096548 restraints weight = 88641.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.096708 restraints weight = 69922.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.096897 restraints weight = 59660.947| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.7766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.279 39808 Z= 0.409 Angle : 0.987 50.533 53954 Z= 0.532 Chirality : 0.068 3.298 6456 Planarity : 0.009 0.469 6961 Dihedral : 6.199 86.893 5589 Min Nonbonded Distance : 1.383 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.06 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.12), residues: 5149 helix: 0.84 (0.10), residues: 2921 sheet: -0.91 (0.20), residues: 615 loop : -0.70 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG A 16 TYR 0.037 0.002 TYR L 66 PHE 0.205 0.003 PHE b 95 TRP 0.015 0.002 TRP a 44 HIS 0.018 0.002 HIS a 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.40 (39778) covalent geometry : angle 0.97323 / 0.52 (53943) SS BOND : bond 0.00365 / 0.19 ( 1) SS BOND : angle 0.92740 / 0.53 ( 2) hydrogen bonds : bond 0.09327 / 6.72 ( 2442) hydrogen bonds : angle 5.50581 / 4.12 ( 7176) Misc. bond : bond 0.02704 / 1.82 ( 26) link_TRANS : bond 0.02787 / 1.12 ( 3) link_TRANS : angle 12.85686 / 6.86 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 794 time to evaluate : 1.580 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: a 126 GLU cc_start: 0.6864 (tt0) cc_final: 0.5213 (pm20) REVERT: a 238 TYR cc_start: 0.7982 (m-80) cc_final: 0.7254 (m-80) REVERT: b 90 MET cc_start: 0.6796 (mmm) cc_final: 0.6016 (ptm) REVERT: d 72 ASP cc_start: 0.7660 (t0) cc_final: 0.6815 (t0) REVERT: p 101 MET cc_start: 0.5762 (ppp) cc_final: 0.5201 (ppp) REVERT: p 102 PHE cc_start: 0.4176 (m-10) cc_final: 0.3682 (m-80) REVERT: e 21 GLU cc_start: 0.6756 (tm-30) cc_final: 0.6545 (tm-30) REVERT: e 27 ASN cc_start: 0.7961 (t0) cc_final: 0.7547 (t0) REVERT: e 73 GLU cc_start: 0.7027 (tp30) cc_final: 0.6521 (tp30) REVERT: e 127 GLU cc_start: 0.8454 (tp30) cc_final: 0.8211 (tp30) REVERT: g 46 GLU cc_start: 0.8433 (pp20) cc_final: 0.7519 (tm-30) REVERT: g 76 GLN cc_start: 0.8669 (tt0) cc_final: 0.8175 (tm-30) REVERT: g 214 TYR cc_start: 0.7867 (p90) cc_final: 0.7636 (p90) REVERT: g 245 LYS cc_start: 0.8731 (mttt) cc_final: 0.8087 (tptt) REVERT: g 299 TYR cc_start: 0.6502 (t80) cc_final: 0.6064 (t80) REVERT: g 311 SER cc_start: 0.9207 (m) cc_final: 0.8780 (p) REVERT: S 28 GLN cc_start: 0.6733 (tt0) cc_final: 0.6397 (tt0) REVERT: S 49 ILE cc_start: 0.7446 (mt) cc_final: 0.7112 (mt) REVERT: N 15 LEU cc_start: 0.6832 (mt) cc_final: 0.6458 (tt) REVERT: N 60 MET cc_start: 0.7346 (ptt) cc_final: 0.6810 (ptt) REVERT: M 59 PHE cc_start: 0.7290 (m-80) cc_final: 0.6824 (m-80) REVERT: T 60 MET cc_start: 0.4530 (mmm) cc_final: 0.3976 (mmm) REVERT: H 37 GLU cc_start: 0.8198 (tt0) cc_final: 0.7346 (tm-30) REVERT: H 54 LEU cc_start: 0.7052 (mm) cc_final: 0.6298 (tp) REVERT: J 55 LEU cc_start: 0.6763 (mm) cc_final: 0.6370 (tp) REVERT: J 72 LEU cc_start: 0.7163 (mt) cc_final: 0.6671 (pp) REVERT: I 48 LYS cc_start: 0.7170 (mttp) cc_final: 0.6715 (ttmt) REVERT: E 138 MET cc_start: 0.8485 (pmm) cc_final: 0.7929 (mtm) REVERT: E 147 LEU cc_start: 0.9005 (tp) cc_final: 0.8740 (tp) REVERT: E 219 MET cc_start: 0.7740 (mmm) cc_final: 0.7232 (mmm) REVERT: E 227 GLU cc_start: 0.8371 (tp30) cc_final: 0.8082 (tp30) REVERT: F 40 MET cc_start: 0.7526 (tpt) cc_final: 0.7053 (tpt) REVERT: F 118 VAL cc_start: 0.8805 (m) cc_final: 0.8335 (p) REVERT: F 132 ILE cc_start: 0.9313 (pt) cc_final: 0.8972 (mm) REVERT: F 347 ASP cc_start: 0.8196 (m-30) cc_final: 0.7829 (m-30) REVERT: A 46 ASP cc_start: 0.8408 (t0) cc_final: 0.7919 (t70) REVERT: A 66 ASN cc_start: 0.8305 (m-40) cc_final: 0.8064 (m-40) REVERT: A 122 ILE cc_start: 0.8359 (mt) cc_final: 0.8032 (mt) REVERT: A 166 GLU cc_start: 0.9118 (tp30) cc_final: 0.8877 (tp30) REVERT: A 208 GLN cc_start: 0.7149 (tm-30) cc_final: 0.6701 (tm-30) REVERT: A 236 GLN cc_start: 0.9030 (mt0) cc_final: 0.8749 (mt0) REVERT: A 301 ARG cc_start: 0.8418 (mtp180) cc_final: 0.7967 (mtp85) REVERT: A 394 GLU cc_start: 0.6030 (tm-30) cc_final: 0.5526 (mm-30) REVERT: A 399 PHE cc_start: 0.5794 (m-10) cc_final: 0.5500 (t80) REVERT: A 436 MET cc_start: 0.8004 (ppp) cc_final: 0.7547 (ppp) REVERT: B 168 ILE cc_start: 0.9347 (mm) cc_final: 0.9134 (mm) REVERT: B 179 THR cc_start: 0.7946 (m) cc_final: 0.7660 (m) REVERT: C 258 LEU cc_start: 0.8902 (tp) cc_final: 0.8368 (tp) REVERT: C 344 PHE cc_start: 0.8402 (m-80) cc_final: 0.7892 (m-80) REVERT: D 171 PHE cc_start: 0.8884 (m-80) cc_final: 0.8683 (m-80) REVERT: D 435 PHE cc_start: 0.8613 (m-80) cc_final: 0.8219 (m-80) outliers start: 0 outliers final: 0 residues processed: 794 average time/residue: 0.2268 time to fit residues: 306.8593 Evaluate side-chains 582 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 582 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 423 optimal weight: 6.9990 chunk 303 optimal weight: 6.9990 chunk 240 optimal weight: 0.7980 chunk 421 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 410 optimal weight: 8.9990 chunk 401 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 390 optimal weight: 4.9990 chunk 225 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 342 ASN ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN E 351 ASN F 210 ASN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN D 210 ASN D 238 GLN D 472 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.121054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.097857 restraints weight = 118657.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.097042 restraints weight = 108737.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.097833 restraints weight = 82792.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.098019 restraints weight = 66442.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.098333 restraints weight = 58643.339| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.7968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.272 39808 Z= 0.380 Angle : 0.956 51.196 53954 Z= 0.514 Chirality : 0.066 3.098 6456 Planarity : 0.009 0.471 6961 Dihedral : 6.039 86.336 5589 Min Nonbonded Distance : 1.386 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.69 % Favored : 96.08 % Rotamer: Outliers : 0.02 % Allowed : 0.88 % Favored : 99.10 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.12), residues: 5149 helix: 0.90 (0.10), residues: 2914 sheet: -0.87 (0.20), residues: 593 loop : -0.66 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG A 16 TYR 0.039 0.002 TYR L 66 PHE 0.209 0.003 PHE b 95 TRP 0.011 0.001 TRP a 117 HIS 0.017 0.001 HIS a 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.37 (39778) covalent geometry : angle 0.94198 / 0.51 (53943) SS BOND : bond 0.00165 / 0.09 ( 1) SS BOND : angle 0.85057 / 0.50 ( 2) hydrogen bonds : bond 0.09198 / 6.64 ( 2442) hydrogen bonds : angle 5.44724 / 4.08 ( 7176) Misc. bond : bond 0.02724 / 1.79 ( 26) link_TRANS : bond 0.02804 / 1.12 ( 3) link_TRANS : angle 12.75779 / 6.78 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 811 time to evaluate : 1.521 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: a 116 PRO cc_start: 0.4897 (Cg_endo) cc_final: 0.4619 (Cg_exo) REVERT: b 90 MET cc_start: 0.6781 (mmm) cc_final: 0.6133 (ptm) REVERT: d 72 ASP cc_start: 0.7539 (t0) cc_final: 0.6794 (t0) REVERT: p 101 MET cc_start: 0.5715 (ppp) cc_final: 0.5407 (ppp) REVERT: p 102 PHE cc_start: 0.3875 (m-10) cc_final: 0.3507 (m-80) REVERT: e 21 GLU cc_start: 0.6709 (tm-30) cc_final: 0.6430 (tm-30) REVERT: e 27 ASN cc_start: 0.7679 (t0) cc_final: 0.7408 (t0) REVERT: e 73 GLU cc_start: 0.7075 (tp30) cc_final: 0.6657 (tp30) REVERT: e 79 ASN cc_start: 0.7914 (p0) cc_final: 0.7182 (m110) REVERT: e 80 ASP cc_start: 0.7686 (t70) cc_final: 0.6790 (t0) REVERT: g 46 GLU cc_start: 0.8392 (pp20) cc_final: 0.7512 (tm-30) REVERT: g 76 GLN cc_start: 0.8654 (tt0) cc_final: 0.8174 (tm-30) REVERT: g 245 LYS cc_start: 0.8724 (mttt) cc_final: 0.8068 (tptt) REVERT: g 299 TYR cc_start: 0.6456 (t80) cc_final: 0.6047 (t80) REVERT: g 311 SER cc_start: 0.9243 (m) cc_final: 0.8848 (p) REVERT: N 60 MET cc_start: 0.7386 (ptt) cc_final: 0.5654 (ppp) REVERT: P 60 MET cc_start: 0.6083 (mtm) cc_final: 0.5305 (tpt) REVERT: P 63 LEU cc_start: 0.3600 (mp) cc_final: 0.3145 (mp) REVERT: M 59 PHE cc_start: 0.7170 (m-80) cc_final: 0.6738 (m-80) REVERT: G 60 MET cc_start: 0.2544 (ttt) cc_final: 0.2194 (tmm) REVERT: H 37 GLU cc_start: 0.8116 (tt0) cc_final: 0.7350 (tm-30) REVERT: H 54 LEU cc_start: 0.7091 (mm) cc_final: 0.6319 (tp) REVERT: K 55 LEU cc_start: 0.7062 (tt) cc_final: 0.6564 (tp) REVERT: J 55 LEU cc_start: 0.6612 (mm) cc_final: 0.6294 (tp) REVERT: J 72 LEU cc_start: 0.7055 (mt) cc_final: 0.6641 (pp) REVERT: I 48 LYS cc_start: 0.7169 (mttp) cc_final: 0.6764 (ttmt) REVERT: E 147 LEU cc_start: 0.8990 (tp) cc_final: 0.8728 (tp) REVERT: E 219 MET cc_start: 0.7658 (mmm) cc_final: 0.7168 (mmm) REVERT: E 227 GLU cc_start: 0.8304 (tp30) cc_final: 0.8053 (tp30) REVERT: E 402 ASP cc_start: 0.7944 (m-30) cc_final: 0.7506 (t0) REVERT: F 79 MET cc_start: 0.8344 (mmt) cc_final: 0.7929 (mmt) REVERT: F 118 VAL cc_start: 0.8801 (m) cc_final: 0.8334 (p) REVERT: F 347 ASP cc_start: 0.8270 (m-30) cc_final: 0.7871 (m-30) REVERT: A 32 VAL cc_start: 0.9181 (t) cc_final: 0.8693 (m) REVERT: A 46 ASP cc_start: 0.8351 (t0) cc_final: 0.7990 (t70) REVERT: A 66 ASN cc_start: 0.8393 (m-40) cc_final: 0.8177 (m-40) REVERT: A 77 MET cc_start: 0.7554 (mmt) cc_final: 0.7321 (mmt) REVERT: A 122 ILE cc_start: 0.8314 (mt) cc_final: 0.7982 (mt) REVERT: A 166 GLU cc_start: 0.9100 (tp30) cc_final: 0.8659 (tp30) REVERT: A 167 LEU cc_start: 0.8918 (tp) cc_final: 0.8636 (tp) REVERT: A 236 GLN cc_start: 0.8996 (mt0) cc_final: 0.8701 (mt0) REVERT: A 251 MET cc_start: 0.8705 (ttm) cc_final: 0.8498 (ttm) REVERT: A 301 ARG cc_start: 0.8337 (mtp180) cc_final: 0.7866 (mtp85) REVERT: A 394 GLU cc_start: 0.6198 (tm-30) cc_final: 0.5649 (mm-30) REVERT: A 399 PHE cc_start: 0.5862 (m-10) cc_final: 0.5574 (t80) REVERT: A 436 MET cc_start: 0.8111 (ppp) cc_final: 0.7613 (ppp) REVERT: B 168 ILE cc_start: 0.9390 (mm) cc_final: 0.9140 (mm) REVERT: B 184 GLU cc_start: 0.6747 (tp30) cc_final: 0.6176 (tp30) REVERT: C 70 ASN cc_start: 0.7280 (m-40) cc_final: 0.7053 (m-40) REVERT: C 182 ASP cc_start: 0.8369 (t70) cc_final: 0.7818 (t0) REVERT: C 230 ASP cc_start: 0.7151 (p0) cc_final: 0.6948 (p0) REVERT: C 251 MET cc_start: 0.7795 (ptp) cc_final: 0.7523 (mtm) REVERT: C 258 LEU cc_start: 0.9104 (tp) cc_final: 0.8751 (tp) REVERT: C 275 SER cc_start: 0.9132 (p) cc_final: 0.8773 (t) REVERT: C 344 PHE cc_start: 0.8409 (m-80) cc_final: 0.7920 (m-80) REVERT: D 31 LEU cc_start: 0.8390 (mt) cc_final: 0.7887 (mp) REVERT: D 171 PHE cc_start: 0.8879 (m-80) cc_final: 0.8469 (m-80) REVERT: D 343 PHE cc_start: 0.8634 (m-80) cc_final: 0.8362 (m-80) REVERT: D 417 ASP cc_start: 0.8056 (m-30) cc_final: 0.7599 (m-30) outliers start: 1 outliers final: 1 residues processed: 812 average time/residue: 0.2268 time to fit residues: 313.0191 Evaluate side-chains 603 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 602 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 3 optimal weight: 4.9990 chunk 329 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 chunk 422 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 181 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 chunk 279 optimal weight: 10.0000 chunk 335 optimal weight: 1.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 132 ASN p 143 GLN ** e 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 28 GLN ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN E 351 ASN ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN A 212 ASN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN D 210 ASN D 310 GLN D 325 GLN D 472 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.116367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.095101 restraints weight = 123389.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.093978 restraints weight = 88584.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.093882 restraints weight = 90519.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.094185 restraints weight = 77339.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.094421 restraints weight = 65260.985| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.8367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.298 39808 Z= 0.444 Angle : 1.067 52.310 53954 Z= 0.573 Chirality : 0.069 3.040 6456 Planarity : 0.009 0.478 6961 Dihedral : 6.415 79.671 5589 Min Nonbonded Distance : 1.392 Molprobity Statistics. All-atom Clashscore : 24.38 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.84 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.11), residues: 5149 helix: 0.44 (0.09), residues: 2946 sheet: -0.99 (0.20), residues: 605 loop : -0.79 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG A 16 TYR 0.038 0.003 TYR F 162 PHE 0.306 0.003 PHE b 95 TRP 0.023 0.003 TRP a 44 HIS 0.019 0.002 HIS a 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00803 / 0.44 (39778) covalent geometry : angle 1.05524 / 0.57 (53943) SS BOND : bond 0.00428 / 0.23 ( 1) SS BOND : angle 1.27883 / 0.72 ( 2) hydrogen bonds : bond 0.09467 / 6.82 ( 2442) hydrogen bonds : angle 5.76800 / 4.31 ( 7176) Misc. bond : bond 0.02900 / 1.85 ( 26) link_TRANS : bond 0.02788 / 1.12 ( 3) link_TRANS : angle 12.43509 / 6.57 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 748 time to evaluate : 1.925 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: a 92 ARG cc_start: 0.5683 (ptp-110) cc_final: 0.4769 (mmm160) REVERT: a 189 ARG cc_start: 0.7471 (ptm160) cc_final: 0.7222 (ptt90) REVERT: a 201 VAL cc_start: 0.7074 (t) cc_final: 0.6873 (t) REVERT: a 217 MET cc_start: 0.4176 (mmp) cc_final: 0.3909 (mmt) REVERT: a 244 GLU cc_start: 0.2488 (tp30) cc_final: 0.2118 (tp30) REVERT: b 90 MET cc_start: 0.6891 (mmm) cc_final: 0.6089 (ptm) REVERT: d 222 THR cc_start: 0.7911 (p) cc_final: 0.6934 (p) REVERT: p 101 MET cc_start: 0.5836 (ppp) cc_final: 0.5220 (ppp) REVERT: p 102 PHE cc_start: 0.4065 (m-10) cc_final: 0.3570 (m-80) REVERT: p 143 GLN cc_start: 0.4979 (mp10) cc_final: 0.4411 (tp-100) REVERT: e 63 MET cc_start: 0.8147 (mmp) cc_final: 0.6992 (mmp) REVERT: e 73 GLU cc_start: 0.7158 (tp30) cc_final: 0.6692 (tp30) REVERT: g 46 GLU cc_start: 0.8587 (pp20) cc_final: 0.7735 (tm-30) REVERT: g 76 GLN cc_start: 0.8769 (tt0) cc_final: 0.8274 (tm-30) REVERT: g 98 GLU cc_start: 0.6876 (pp20) cc_final: 0.6402 (pp20) REVERT: g 214 TYR cc_start: 0.8068 (p90) cc_final: 0.7782 (p90) REVERT: g 245 LYS cc_start: 0.8727 (mttt) cc_final: 0.8016 (tptt) REVERT: g 299 TYR cc_start: 0.6658 (t80) cc_final: 0.6241 (t80) REVERT: g 311 SER cc_start: 0.9279 (m) cc_final: 0.8893 (p) REVERT: g 346 GLN cc_start: 0.8351 (pt0) cc_final: 0.8136 (pt0) REVERT: N 60 MET cc_start: 0.7478 (ptt) cc_final: 0.7026 (ptt) REVERT: O 76 PHE cc_start: 0.1971 (m-10) cc_final: 0.1072 (t80) REVERT: P 60 MET cc_start: 0.6017 (mtm) cc_final: 0.5207 (tpt) REVERT: P 63 LEU cc_start: 0.3591 (mp) cc_final: 0.3260 (mp) REVERT: Q 28 GLN cc_start: 0.6945 (mt0) cc_final: 0.6568 (mm110) REVERT: M 59 PHE cc_start: 0.7320 (m-80) cc_final: 0.6892 (m-80) REVERT: M 74 LEU cc_start: 0.8023 (mt) cc_final: 0.7520 (tt) REVERT: G 60 MET cc_start: 0.3104 (ttt) cc_final: 0.2746 (tmm) REVERT: H 37 GLU cc_start: 0.8225 (tt0) cc_final: 0.7359 (tm-30) REVERT: H 54 LEU cc_start: 0.7124 (mm) cc_final: 0.6533 (tp) REVERT: J 72 LEU cc_start: 0.7143 (mt) cc_final: 0.6671 (pp) REVERT: I 48 LYS cc_start: 0.7172 (mttp) cc_final: 0.6894 (ttmt) REVERT: E 219 MET cc_start: 0.7773 (mmm) cc_final: 0.7035 (mmm) REVERT: E 227 GLU cc_start: 0.8360 (tp30) cc_final: 0.8154 (tp30) REVERT: E 402 ASP cc_start: 0.8056 (m-30) cc_final: 0.7401 (t0) REVERT: F 79 MET cc_start: 0.8238 (mmt) cc_final: 0.7768 (mmt) REVERT: F 118 VAL cc_start: 0.8932 (m) cc_final: 0.8451 (p) REVERT: F 183 MET cc_start: 0.8274 (mtp) cc_final: 0.7809 (mmm) REVERT: F 213 TYR cc_start: 0.8836 (t80) cc_final: 0.8622 (t80) REVERT: F 347 ASP cc_start: 0.8262 (m-30) cc_final: 0.7918 (m-30) REVERT: F 462 LEU cc_start: 0.8521 (mt) cc_final: 0.8297 (mt) REVERT: A 122 ILE cc_start: 0.8406 (mt) cc_final: 0.8103 (mt) REVERT: A 166 GLU cc_start: 0.9095 (tp30) cc_final: 0.8698 (tp30) REVERT: A 167 LEU cc_start: 0.9041 (tp) cc_final: 0.8812 (tp) REVERT: A 231 SER cc_start: 0.9457 (p) cc_final: 0.9197 (p) REVERT: A 236 GLN cc_start: 0.9138 (mt0) cc_final: 0.8806 (mt0) REVERT: A 293 TYR cc_start: 0.9047 (t80) cc_final: 0.8710 (t80) REVERT: A 301 ARG cc_start: 0.8394 (mtp180) cc_final: 0.7901 (mtp85) REVERT: A 366 ARG cc_start: 0.8099 (tpt90) cc_final: 0.7728 (tpt90) REVERT: A 394 GLU cc_start: 0.5910 (tm-30) cc_final: 0.5499 (mm-30) REVERT: A 399 PHE cc_start: 0.5855 (m-10) cc_final: 0.5408 (t80) REVERT: A 436 MET cc_start: 0.8248 (ppp) cc_final: 0.7787 (ppp) REVERT: B 168 ILE cc_start: 0.9421 (mm) cc_final: 0.9216 (mm) REVERT: B 208 GLU cc_start: 0.8373 (pt0) cc_final: 0.8013 (pt0) REVERT: B 247 MET cc_start: 0.7782 (tmm) cc_final: 0.7580 (tmm) REVERT: C 157 MET cc_start: 0.8063 (mmt) cc_final: 0.7834 (mmm) REVERT: C 182 ASP cc_start: 0.8347 (t70) cc_final: 0.7877 (t0) REVERT: C 258 LEU cc_start: 0.8880 (tp) cc_final: 0.8288 (tp) REVERT: C 275 SER cc_start: 0.9139 (p) cc_final: 0.8835 (t) REVERT: C 344 PHE cc_start: 0.8559 (m-80) cc_final: 0.7887 (m-80) REVERT: D 205 ARG cc_start: 0.7400 (mtt90) cc_final: 0.7013 (mtt90) REVERT: D 254 LEU cc_start: 0.9057 (tp) cc_final: 0.8853 (tp) REVERT: D 417 ASP cc_start: 0.8075 (m-30) cc_final: 0.7129 (m-30) outliers start: 0 outliers final: 0 residues processed: 748 average time/residue: 0.2278 time to fit residues: 289.6531 Evaluate side-chains 570 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 570 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 65 optimal weight: 10.0000 chunk 459 optimal weight: 3.9990 chunk 501 optimal weight: 8.9990 chunk 219 optimal weight: 10.0000 chunk 170 optimal weight: 20.0000 chunk 402 optimal weight: 5.9990 chunk 321 optimal weight: 10.0000 chunk 141 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 293 optimal weight: 0.8980 chunk 135 optimal weight: 9.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 38 GLN ** p 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN E 214 GLN ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 GLN F 325 GLN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN D 210 ASN D 310 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.115666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.095012 restraints weight = 125368.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.093641 restraints weight = 127657.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.094853 restraints weight = 103907.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.094606 restraints weight = 81541.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.094662 restraints weight = 78192.534| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.8666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.276 39808 Z= 0.433 Angle : 1.036 52.014 53954 Z= 0.558 Chirality : 0.069 3.007 6456 Planarity : 0.009 0.471 6961 Dihedral : 6.445 79.933 5589 Min Nonbonded Distance : 1.390 Molprobity Statistics. All-atom Clashscore : 24.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.56 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.11), residues: 5149 helix: 0.34 (0.09), residues: 2936 sheet: -1.15 (0.20), residues: 615 loop : -0.89 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG A 16 TYR 0.043 0.003 TYR F 162 PHE 0.300 0.004 PHE b 95 TRP 0.022 0.002 TRP a 44 HIS 0.018 0.002 HIS a 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00774 / 0.43 (39778) covalent geometry : angle 1.02435 / 0.55 (53943) SS BOND : bond 0.02216 / 1.17 ( 1) SS BOND : angle 1.76658 / 0.99 ( 2) hydrogen bonds : bond 0.09436 / 6.79 ( 2442) hydrogen bonds : angle 5.78149 / 4.32 ( 7176) Misc. bond : bond 0.02807 / 1.83 ( 26) link_TRANS : bond 0.02962 / 1.18 ( 3) link_TRANS : angle 12.23474 / 6.44 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8076.35 seconds wall clock time: 140 minutes 24.82 seconds (8424.82 seconds total)