Starting phenix.real_space_refine on Tue Aug 26 16:40:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6fki_4272/08_2025/6fki_4272.cif Found real_map, /net/cci-nas-00/data/ceres_data/6fki_4272/08_2025/6fki_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6fki_4272/08_2025/6fki_4272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6fki_4272/08_2025/6fki_4272.map" model { file = "/net/cci-nas-00/data/ceres_data/6fki_4272/08_2025/6fki_4272.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6fki_4272/08_2025/6fki_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): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 8.82, per 1000 atoms: 0.22 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: 3.21 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 1.2 microseconds 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: 0.91 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: 7.71 Time building geometry restraints manager: 4.28 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: 23528 26.84 - 53.68: 627 53.68 - 80.52: 61 80.52 - 107.36: 7 107.36 - 134.20: 4 Dihedral angle restraints: 24227 sinusoidal: 9469 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 24224 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: 4.070 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: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 33.750 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 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 : 12.068 134.196 14763 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 aren 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 covalent geometry : bond 0.01499 (39778) covalent geometry : angle 1.41894 (53943) SS BOND : bond 0.66586 ( 1) SS BOND : angle 39.84707 ( 2) hydrogen bonds : bond 0.24405 ( 2442) hydrogen bonds : angle 8.60654 ( 7176) Misc. bond : bond 0.49770 ( 26) link_TRANS : bond 0.83942 ( 3) link_TRANS : angle 41.05044 ( 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 : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.6138 (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: 0.7340 (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: 0.7600 (m) REVERT: B 183 MET cc_start: 0.7909 (mmt) cc_final: 0.7581 (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: 0.8358 (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: 0.2283 time to fit residues: 646.2023 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 : 1.269 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 p 206 GLN e 4 ASN e 27 ASN e 102 ASN ** 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 ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.129892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.106197 restraints weight = 116176.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.105662 restraints weight = 98086.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.106506 restraints weight = 71940.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.106572 restraints weight = 61925.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.106898 restraints weight = 53254.380| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.352 39808 Z= 0.458 Angle : 1.092 41.441 53954 Z= 0.599 Chirality : 0.069 2.982 6456 Planarity : 0.008 0.134 6961 Dihedral : 7.559 128.712 5682 Min Nonbonded Distance : 1.470 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.82 % Favored : 96.99 % Rotamer: Outliers : 0.73 % Allowed : 4.19 % Favored : 95.08 % Cbeta Deviations : 0.34 % 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 aren not related in a simple way. whole: -0.02 (0.11), residues: 5149 helix: 0.78 (0.09), residues: 2882 sheet: -0.91 (0.21), residues: 564 loop : -0.91 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG A 5 TYR 0.038 0.002 TYR a 74 PHE 0.205 0.003 PHE b 95 TRP 0.026 0.003 TRP a 117 HIS 0.021 0.003 HIS a 25 Details of bonding type rmsd covalent geometry : bond 0.00808 (39778) covalent geometry : angle 1.07653 (53943) SS BOND : bond 0.00250 ( 1) SS BOND : angle 1.77067 ( 2) hydrogen bonds : bond 0.10358 ( 2442) hydrogen bonds : angle 6.10051 ( 7176) Misc. bond : bond 0.02888 ( 26) link_TRANS : bond 0.02686 ( 3) link_TRANS : angle 14.17215 ( 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 1164 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 1134 time to evaluate : 1.624 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: a 110 TRP cc_start: 0.5367 (m100) cc_final: 0.3980 (m-10) REVERT: a 127 LEU cc_start: 0.1924 (OUTLIER) cc_final: 0.1674 (mp) REVERT: a 150 TYR cc_start: 0.7082 (t80) cc_final: 0.5620 (m-80) REVERT: a 189 ARG cc_start: 0.7330 (tmm160) cc_final: 0.6385 (ttp80) REVERT: d 156 ASN cc_start: 0.9092 (p0) cc_final: 0.8464 (p0) REVERT: p 101 MET cc_start: 0.5994 (ppp) cc_final: 0.5516 (ppp) REVERT: p 148 MET cc_start: 0.6971 (tmm) cc_final: 0.6082 (ppp) REVERT: p 170 VAL cc_start: 0.5014 (t) cc_final: 0.4321 (t) REVERT: p 218 VAL cc_start: 0.8445 (m) cc_final: 0.7794 (m) REVERT: e 27 ASN cc_start: 0.8456 (t160) cc_final: 0.8003 (t0) REVERT: g 46 GLU cc_start: 0.8532 (pp20) cc_final: 0.7771 (tm-30) REVERT: g 76 GLN cc_start: 0.8690 (tt0) cc_final: 0.7850 (tm-30) REVERT: g 245 LYS cc_start: 0.8745 (mttt) cc_final: 0.8181 (tptt) REVERT: g 290 GLN cc_start: 0.8553 (tt0) cc_final: 0.8318 (mm110) REVERT: g 292 LEU cc_start: 0.8267 (tp) cc_final: 0.7954 (tt) REVERT: g 356 ILE cc_start: 0.8480 (mt) cc_final: 0.8259 (mt) REVERT: O 48 LYS cc_start: 0.6612 (mppt) cc_final: 0.6304 (mttt) REVERT: P 60 MET cc_start: 0.5447 (mtm) cc_final: 0.4511 (mmm) REVERT: R 59 PHE cc_start: 0.6023 (m-80) cc_final: 0.5811 (m-80) REVERT: M 59 PHE cc_start: 0.6580 (m-80) cc_final: 0.5991 (m-80) REVERT: T 36 VAL cc_start: 0.8529 (t) cc_final: 0.8293 (p) REVERT: L 28 GLN cc_start: 0.6203 (mt0) cc_final: 0.5070 (tt0) REVERT: K 60 MET cc_start: 0.4003 (mmm) cc_final: 0.2860 (mmm) REVERT: J 37 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7070 (mt-10) REVERT: J 60 MET cc_start: 0.6647 (ttm) cc_final: 0.6178 (ttm) REVERT: J 72 LEU cc_start: 0.7703 (mt) cc_final: 0.7266 (pp) REVERT: E 184 ILE cc_start: 0.9040 (mt) cc_final: 0.8671 (mt) REVERT: E 194 CYS cc_start: 0.8769 (m) cc_final: 0.7864 (m) REVERT: E 219 MET cc_start: 0.7887 (mmm) cc_final: 0.7173 (mmm) REVERT: E 354 ILE cc_start: 0.8923 (mp) cc_final: 0.8634 (tt) REVERT: E 376 MET cc_start: 0.7784 (tpt) cc_final: 0.7469 (tpp) REVERT: E 402 ASP cc_start: 0.8034 (m-30) cc_final: 0.7635 (t70) REVERT: E 420 LEU cc_start: 0.8817 (mp) cc_final: 0.8608 (tt) REVERT: E 434 GLN cc_start: 0.8703 (mt0) cc_final: 0.7996 (mt0) REVERT: E 461 LEU cc_start: 0.8943 (tp) cc_final: 0.8725 (tt) REVERT: F 49 VAL cc_start: 0.9502 (t) cc_final: 0.9274 (m) REVERT: F 79 MET cc_start: 0.8427 (mmm) cc_final: 0.8099 (mmt) REVERT: F 118 VAL cc_start: 0.8691 (m) cc_final: 0.8238 (p) REVERT: F 132 ILE cc_start: 0.9242 (pt) cc_final: 0.8968 (mt) REVERT: F 247 MET cc_start: 0.7811 (mtm) cc_final: 0.7570 (mtm) REVERT: F 294 SER cc_start: 0.9668 (t) cc_final: 0.9452 (p) REVERT: F 313 ILE cc_start: 0.9540 (mt) cc_final: 0.9303 (tp) REVERT: F 336 ASP cc_start: 0.9342 (t0) cc_final: 0.8959 (t0) REVERT: F 351 VAL cc_start: 0.9402 (t) cc_final: 0.9052 (m) REVERT: F 404 ILE cc_start: 0.9162 (mm) cc_final: 0.8855 (mm) REVERT: A 122 ILE cc_start: 0.8062 (mt) cc_final: 0.7836 (mt) REVERT: A 206 VAL cc_start: 0.9039 (p) cc_final: 0.8787 (p) REVERT: A 219 MET cc_start: 0.7481 (tpp) cc_final: 0.6986 (tmm) REVERT: A 267 GLN cc_start: 0.8896 (tt0) cc_final: 0.8634 (tp40) REVERT: A 301 ARG cc_start: 0.8030 (mtp180) cc_final: 0.7627 (mtp85) REVERT: A 305 LEU cc_start: 0.8899 (mt) cc_final: 0.8623 (mt) REVERT: A 321 GLU cc_start: 0.7431 (tt0) cc_final: 0.6802 (tt0) REVERT: A 415 GLN cc_start: 0.7490 (mt0) cc_final: 0.6952 (mp10) REVERT: B 82 THR cc_start: 0.8550 (m) cc_final: 0.8257 (m) REVERT: B 328 TYR cc_start: 0.9150 (t80) cc_final: 0.8374 (t80) REVERT: B 329 VAL cc_start: 0.9628 (t) cc_final: 0.9224 (p) REVERT: B 374 MET cc_start: 0.8474 (mmm) cc_final: 0.8262 (mmt) REVERT: C 67 LEU cc_start: 0.8681 (mt) cc_final: 0.8444 (mm) REVERT: C 230 ASP cc_start: 0.6976 (p0) cc_final: 0.6769 (p0) REVERT: C 241 TYR cc_start: 0.8564 (m-80) cc_final: 0.8054 (m-10) REVERT: C 275 SER cc_start: 0.8947 (p) cc_final: 0.8605 (t) REVERT: C 314 MET cc_start: 0.6914 (ttt) cc_final: 0.6158 (ttt) REVERT: C 376 MET cc_start: 0.8420 (tpp) cc_final: 0.8019 (tpp) REVERT: C 377 LYS cc_start: 0.8698 (ttpp) cc_final: 0.8065 (tptt) REVERT: C 383 LEU cc_start: 0.8709 (tp) cc_final: 0.8257 (tp) REVERT: C 421 LEU cc_start: 0.9265 (mt) cc_final: 0.8755 (tt) REVERT: D 50 LYS cc_start: 0.8537 (mmpt) cc_final: 0.8114 (tmmt) REVERT: D 90 GLU cc_start: 0.7311 (tt0) cc_final: 0.7020 (tt0) REVERT: D 148 ILE cc_start: 0.8157 (tt) cc_final: 0.7869 (pt) REVERT: D 184 GLU cc_start: 0.7391 (tp30) cc_final: 0.7146 (tp30) REVERT: D 193 HIS cc_start: 0.7120 (t70) cc_final: 0.6542 (t-90) REVERT: D 234 LEU cc_start: 0.8239 (mt) cc_final: 0.7960 (mm) REVERT: D 239 MET cc_start: 0.8554 (mtt) cc_final: 0.8239 (mtt) REVERT: D 362 TYR cc_start: 0.8270 (m-80) cc_final: 0.7669 (m-80) REVERT: D 417 ASP cc_start: 0.7806 (m-30) cc_final: 0.6970 (m-30) REVERT: D 476 LEU cc_start: 0.8227 (mt) cc_final: 0.7391 (mt) outliers start: 30 outliers final: 12 residues processed: 1159 average time/residue: 0.2166 time to fit residues: 415.4926 Evaluate side-chains 743 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 730 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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: 8.9990 chunk 201 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 143 optimal weight: 30.0000 chunk 79 optimal weight: 10.0000 chunk 413 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 chunk 502 optimal weight: 10.0000 chunk 444 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 71 ASN e 102 ASN ** e 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 130 ASN ** 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** Q 28 GLN ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN G 42 GLN ** H 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 25 GLN F 264 ASN F 345 HIS ** A 273 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 C 410 GLN D 60 ASN D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.123132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.099656 restraints weight = 118362.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.099237 restraints weight = 100587.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.099850 restraints weight = 77604.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.099958 restraints weight = 66436.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.100232 restraints weight = 56381.801| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.310 39808 Z= 0.444 Angle : 1.010 34.656 53954 Z= 0.554 Chirality : 0.063 2.432 6456 Planarity : 0.007 0.156 6961 Dihedral : 7.347 104.280 5682 Min Nonbonded Distance : 1.460 Molprobity Statistics. All-atom Clashscore : 22.87 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.46 % Favored : 96.31 % Rotamer: Outliers : 0.46 % Allowed : 5.19 % Favored : 94.35 % Cbeta Deviations : 0.32 % 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 aren not related in a simple way. whole: 0.02 (0.11), residues: 5149 helix: 0.73 (0.09), residues: 2920 sheet: -0.79 (0.20), residues: 583 loop : -0.81 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG p 152 TYR 0.030 0.003 TYR T 66 PHE 0.124 0.003 PHE b 95 TRP 0.016 0.003 TRP e 57 HIS 0.018 0.002 HIS a 36 Details of bonding type rmsd covalent geometry : bond 0.00794 (39778) covalent geometry : angle 0.99509 (53943) SS BOND : bond 0.00775 ( 1) SS BOND : angle 1.30255 ( 2) hydrogen bonds : bond 0.09759 ( 2442) hydrogen bonds : angle 5.83782 ( 7176) Misc. bond : bond 0.02509 ( 26) link_TRANS : bond 0.03297 ( 3) link_TRANS : angle 13.29250 ( 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 969 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 950 time to evaluate : 1.079 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: a 36 HIS cc_start: 0.3817 (m170) cc_final: 0.3284 (m170) REVERT: a 126 GLU cc_start: 0.6364 (tt0) cc_final: 0.6063 (mp0) REVERT: a 150 TYR cc_start: 0.7103 (t80) cc_final: 0.5412 (m-80) REVERT: b 90 MET cc_start: 0.6289 (mmm) cc_final: 0.5286 (ptm) REVERT: d 166 GLU cc_start: 0.7648 (pp20) cc_final: 0.7247 (pp20) REVERT: d 170 ASN cc_start: 0.8982 (m-40) cc_final: 0.8643 (m-40) REVERT: p 85 ASP cc_start: 0.6245 (t0) cc_final: 0.5881 (t0) REVERT: p 101 MET cc_start: 0.5943 (ppp) cc_final: 0.5349 (ppp) REVERT: p 102 PHE cc_start: 0.3954 (m-10) cc_final: 0.3154 (m-80) REVERT: e 21 GLU cc_start: 0.6059 (tm-30) cc_final: 0.5613 (tm-30) REVERT: e 27 ASN cc_start: 0.8589 (t160) cc_final: 0.8144 (t0) REVERT: g 46 GLU cc_start: 0.8687 (pp20) cc_final: 0.7892 (tm-30) REVERT: g 76 GLN cc_start: 0.8754 (tt0) cc_final: 0.7986 (tm-30) REVERT: g 197 ASP cc_start: 0.7114 (t70) cc_final: 0.6601 (t0) REVERT: g 245 LYS cc_start: 0.8734 (mttt) cc_final: 0.8195 (tptt) REVERT: g 292 LEU cc_start: 0.8574 (tp) cc_final: 0.8295 (tt) REVERT: g 311 SER cc_start: 0.9121 (m) cc_final: 0.8683 (p) REVERT: g 346 GLN cc_start: 0.8425 (pt0) cc_final: 0.8187 (pt0) REVERT: S 24 PRO cc_start: 0.6978 (Cg_exo) cc_final: 0.6467 (Cg_endo) REVERT: S 28 GLN cc_start: 0.6961 (tt0) cc_final: 0.5782 (tt0) REVERT: S 41 ARG cc_start: 0.5733 (ttt-90) cc_final: 0.5481 (ttt-90) REVERT: S 60 MET cc_start: 0.7381 (tmm) cc_final: 0.6960 (tmm) REVERT: N 60 MET cc_start: 0.8022 (ptp) cc_final: 0.7688 (ptm) REVERT: O 55 LEU cc_start: 0.5566 (tt) cc_final: 0.5323 (tt) REVERT: P 28 GLN cc_start: 0.6575 (tm-30) cc_final: 0.6268 (tm-30) REVERT: P 63 LEU cc_start: 0.3677 (mt) cc_final: 0.3376 (mt) REVERT: R 56 SER cc_start: 0.7680 (m) cc_final: 0.7468 (t) REVERT: R 59 PHE cc_start: 0.6088 (m-80) cc_final: 0.5855 (m-80) REVERT: M 59 PHE cc_start: 0.7120 (m-80) cc_final: 0.6784 (m-80) REVERT: T 49 ILE cc_start: 0.6233 (mm) cc_final: 0.6011 (mm) REVERT: T 60 MET cc_start: 0.5288 (mmm) cc_final: 0.4589 (mmm) REVERT: T 61 GLU cc_start: 0.3212 (tp30) cc_final: 0.1869 (mt-10) REVERT: H 28 GLN cc_start: 0.8514 (mt0) cc_final: 0.8299 (mt0) REVERT: L 39 ILE cc_start: 0.7395 (mm) cc_final: 0.7119 (mt) REVERT: L 68 LEU cc_start: 0.5345 (OUTLIER) cc_final: 0.4906 (tt) REVERT: K 34 GLN cc_start: 0.6666 (mt0) cc_final: 0.6315 (mt0) REVERT: K 60 MET cc_start: 0.5020 (mmm) cc_final: 0.4641 (mmm) REVERT: J 22 ILE cc_start: 0.8852 (mm) cc_final: 0.8558 (pt) REVERT: J 37 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7542 (mt-10) REVERT: J 49 ILE cc_start: 0.7393 (tt) cc_final: 0.7049 (tt) REVERT: J 60 MET cc_start: 0.6795 (ttm) cc_final: 0.6344 (ttm) REVERT: J 72 LEU cc_start: 0.7431 (mt) cc_final: 0.6925 (pp) REVERT: I 48 LYS cc_start: 0.6996 (mttp) cc_final: 0.6617 (mttp) REVERT: E 184 ILE cc_start: 0.9089 (mt) cc_final: 0.8727 (mt) REVERT: E 194 CYS cc_start: 0.8868 (m) cc_final: 0.7944 (m) REVERT: E 219 MET cc_start: 0.7763 (mmm) cc_final: 0.6995 (mmm) REVERT: E 234 THR cc_start: 0.8549 (t) cc_final: 0.8224 (t) REVERT: E 334 ASN cc_start: 0.8873 (m-40) cc_final: 0.8650 (t0) REVERT: E 376 MET cc_start: 0.7666 (tpt) cc_final: 0.7187 (tpp) REVERT: E 402 ASP cc_start: 0.8245 (m-30) cc_final: 0.7792 (t0) REVERT: E 434 GLN cc_start: 0.8655 (mt0) cc_final: 0.8029 (mt0) REVERT: E 498 MET cc_start: 0.8217 (ttt) cc_final: 0.7870 (tpt) REVERT: F 32 ASP cc_start: 0.8170 (m-30) cc_final: 0.7939 (m-30) REVERT: F 118 VAL cc_start: 0.8586 (m) cc_final: 0.8232 (p) REVERT: F 325 GLN cc_start: 0.8650 (pt0) cc_final: 0.8381 (pt0) REVERT: F 336 ASP cc_start: 0.9326 (t0) cc_final: 0.9116 (t0) REVERT: F 347 ASP cc_start: 0.8110 (m-30) cc_final: 0.7861 (m-30) REVERT: A 46 ASP cc_start: 0.8021 (t0) cc_final: 0.7766 (t0) REVERT: A 122 ILE cc_start: 0.8256 (mt) cc_final: 0.7952 (mt) REVERT: A 219 MET cc_start: 0.7556 (tpp) cc_final: 0.7322 (tpt) REVERT: A 251 MET cc_start: 0.8795 (ttm) cc_final: 0.8532 (ttm) REVERT: A 290 ASP cc_start: 0.7718 (m-30) cc_final: 0.6915 (m-30) REVERT: A 301 ARG cc_start: 0.8289 (mtp180) cc_final: 0.8021 (mtp85) REVERT: A 436 MET cc_start: 0.8210 (ppp) cc_final: 0.7797 (ppp) REVERT: B 79 MET cc_start: 0.8511 (mmm) cc_final: 0.8033 (mmt) REVERT: B 328 TYR cc_start: 0.9172 (t80) cc_final: 0.8297 (t80) REVERT: B 374 MET cc_start: 0.8274 (mmm) cc_final: 0.8054 (mmm) REVERT: C 67 LEU cc_start: 0.8797 (mt) cc_final: 0.8547 (mm) REVERT: C 230 ASP cc_start: 0.6830 (p0) cc_final: 0.6592 (p0) REVERT: C 231 SER cc_start: 0.9124 (p) cc_final: 0.8808 (t) REVERT: C 234 THR cc_start: 0.8897 (t) cc_final: 0.8634 (t) REVERT: C 275 SER cc_start: 0.9102 (p) cc_final: 0.8540 (t) REVERT: C 344 PHE cc_start: 0.8063 (m-80) cc_final: 0.7739 (m-80) REVERT: C 383 LEU cc_start: 0.8357 (tp) cc_final: 0.7910 (tp) REVERT: C 421 LEU cc_start: 0.9375 (mt) cc_final: 0.8734 (tt) REVERT: C 451 LEU cc_start: 0.8505 (mm) cc_final: 0.8233 (tp) REVERT: D 49 VAL cc_start: 0.9383 (p) cc_final: 0.9134 (m) REVERT: D 193 HIS cc_start: 0.7201 (t70) cc_final: 0.6775 (t70) REVERT: D 241 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7895 (mm-30) REVERT: D 273 ASP cc_start: 0.8551 (t0) cc_final: 0.8221 (t0) REVERT: D 362 TYR cc_start: 0.8351 (m-80) cc_final: 0.7752 (m-80) outliers start: 19 outliers final: 8 residues processed: 967 average time/residue: 0.2143 time to fit residues: 345.6593 Evaluate side-chains 659 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 650 time to evaluate : 1.403 ------------------------------------------------------------------------------- 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: 2.9990 chunk 183 optimal weight: 9.9990 chunk 502 optimal weight: 10.0000 chunk 398 optimal weight: 8.9990 chunk 277 optimal weight: 6.9990 chunk 231 optimal weight: 0.8980 chunk 10 optimal weight: 30.0000 chunk 290 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 293 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 120 GLN b 180 ASN ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 116 ASN ** 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** ** Q 42 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** E 497 GLN F 345 HIS A 201 GLN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 GLN ** 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 173 GLN C 410 GLN D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS D 396 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 = 0.3894 r_free = 0.3894 target = 0.123104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.099820 restraints weight = 117944.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.099437 restraints weight = 99057.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.099725 restraints weight = 76168.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.100219 restraints weight = 63329.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.100375 restraints weight = 54842.321| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.6435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.272 39808 Z= 0.397 Angle : 0.942 42.505 53954 Z= 0.516 Chirality : 0.065 2.866 6456 Planarity : 0.007 0.228 6961 Dihedral : 7.011 90.125 5682 Min Nonbonded Distance : 1.433 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.32 % Favored : 96.50 % Rotamer: Outliers : 0.19 % Allowed : 3.77 % Favored : 96.03 % Cbeta Deviations : 0.30 % 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 aren not related in a simple way. whole: 0.08 (0.12), residues: 5149 helix: 0.77 (0.09), residues: 2922 sheet: -0.76 (0.20), residues: 588 loop : -0.76 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.051 0.001 ARG p 152 TYR 0.021 0.002 TYR L 66 PHE 0.139 0.003 PHE b 95 TRP 0.029 0.002 TRP a 117 HIS 0.017 0.002 HIS a 36 Details of bonding type rmsd covalent geometry : bond 0.00668 (39778) covalent geometry : angle 0.92556 (53943) SS BOND : bond 0.00409 ( 1) SS BOND : angle 0.92818 ( 2) hydrogen bonds : bond 0.09425 ( 2442) hydrogen bonds : angle 5.62271 ( 7176) Misc. bond : bond 0.02521 ( 26) link_TRANS : bond 0.03202 ( 3) link_TRANS : angle 13.47755 ( 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 898 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 890 time to evaluate : 1.242 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 36 HIS cc_start: 0.3391 (m170) cc_final: 0.2707 (m90) REVERT: a 126 GLU cc_start: 0.6478 (tt0) cc_final: 0.5922 (pm20) REVERT: b 90 MET cc_start: 0.6243 (mmm) cc_final: 0.5502 (ptm) REVERT: b 104 GLU cc_start: 0.7707 (mp0) cc_final: 0.7423 (pp20) REVERT: b 107 LYS cc_start: 0.4792 (tttt) cc_final: 0.4404 (tmmt) REVERT: d 241 LEU cc_start: 0.8386 (tp) cc_final: 0.7844 (pp) REVERT: p 85 ASP cc_start: 0.6092 (t0) cc_final: 0.5422 (t0) REVERT: p 101 MET cc_start: 0.6039 (ppp) cc_final: 0.5545 (ppp) REVERT: p 102 PHE cc_start: 0.4070 (m-10) cc_final: 0.3695 (m-80) REVERT: e 27 ASN cc_start: 0.8343 (t0) cc_final: 0.7765 (t0) REVERT: g 46 GLU cc_start: 0.8489 (pp20) cc_final: 0.7572 (tm-30) REVERT: g 76 GLN cc_start: 0.8697 (tt0) cc_final: 0.8122 (tm-30) REVERT: g 197 ASP cc_start: 0.7144 (t70) cc_final: 0.6600 (t0) REVERT: g 214 TYR cc_start: 0.7756 (p90) cc_final: 0.7247 (p90) REVERT: g 245 LYS cc_start: 0.8787 (mttt) cc_final: 0.8142 (tptt) REVERT: g 290 GLN cc_start: 0.8591 (mt0) cc_final: 0.8346 (mm110) REVERT: g 311 SER cc_start: 0.9101 (m) cc_final: 0.8653 (p) REVERT: S 24 PRO cc_start: 0.7215 (Cg_exo) cc_final: 0.6728 (Cg_endo) REVERT: S 60 MET cc_start: 0.7687 (tmm) cc_final: 0.7166 (tmm) REVERT: O 34 GLN cc_start: 0.8092 (tt0) cc_final: 0.7754 (tt0) REVERT: O 60 MET cc_start: 0.5862 (mtm) cc_final: 0.5653 (mtm) REVERT: P 60 MET cc_start: 0.5386 (tpt) cc_final: 0.3538 (tpp) REVERT: M 50 ARG cc_start: 0.7082 (tpt90) cc_final: 0.6675 (mmm-85) REVERT: M 59 PHE cc_start: 0.7058 (m-80) cc_final: 0.6711 (m-80) REVERT: T 15 LEU cc_start: 0.6703 (pp) cc_final: 0.6377 (tp) REVERT: T 49 ILE cc_start: 0.6431 (mm) cc_final: 0.5760 (mm) REVERT: T 60 MET cc_start: 0.4773 (mmm) cc_final: 0.3765 (mmm) REVERT: T 61 GLU cc_start: 0.3139 (tp30) cc_final: 0.1713 (mt-10) REVERT: H 28 GLN cc_start: 0.8609 (mt0) cc_final: 0.8142 (mt0) REVERT: K 34 GLN cc_start: 0.6636 (mt0) cc_final: 0.6291 (mt0) REVERT: J 37 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7553 (mt-10) REVERT: J 60 MET cc_start: 0.6990 (ttm) cc_final: 0.6668 (ttm) REVERT: J 63 LEU cc_start: 0.6895 (mt) cc_final: 0.6613 (mt) REVERT: J 72 LEU cc_start: 0.7340 (mt) cc_final: 0.6825 (pp) REVERT: I 48 LYS cc_start: 0.7123 (mttp) cc_final: 0.6572 (ttmt) REVERT: I 60 MET cc_start: 0.5217 (mmm) cc_final: 0.4530 (mmm) REVERT: E 219 MET cc_start: 0.7736 (mmm) cc_final: 0.7023 (mmm) REVERT: E 234 THR cc_start: 0.8466 (t) cc_final: 0.8191 (t) REVERT: E 259 ILE cc_start: 0.9343 (pt) cc_final: 0.9112 (pt) REVERT: E 376 MET cc_start: 0.7446 (tpt) cc_final: 0.7201 (tpp) REVERT: E 402 ASP cc_start: 0.8090 (m-30) cc_final: 0.7603 (t0) REVERT: E 434 GLN cc_start: 0.8651 (mt0) cc_final: 0.8049 (mt0) REVERT: F 32 ASP cc_start: 0.8217 (m-30) cc_final: 0.7943 (m-30) REVERT: F 79 MET cc_start: 0.8465 (mmt) cc_final: 0.8031 (mmt) REVERT: F 118 VAL cc_start: 0.8540 (m) cc_final: 0.8067 (p) REVERT: F 183 MET cc_start: 0.7957 (mtt) cc_final: 0.6749 (mmm) REVERT: F 212 LEU cc_start: 0.8895 (tp) cc_final: 0.8598 (tp) REVERT: F 288 LEU cc_start: 0.9190 (mm) cc_final: 0.8795 (tp) REVERT: F 347 ASP cc_start: 0.8088 (m-30) cc_final: 0.7865 (m-30) REVERT: F 481 ASP cc_start: 0.8436 (p0) cc_final: 0.8208 (p0) REVERT: A 70 ASN cc_start: 0.8741 (p0) cc_final: 0.8292 (p0) REVERT: A 122 ILE cc_start: 0.8175 (mt) cc_final: 0.7843 (mt) REVERT: A 231 SER cc_start: 0.9469 (p) cc_final: 0.9111 (t) REVERT: A 290 ASP cc_start: 0.7597 (m-30) cc_final: 0.6705 (m-30) REVERT: A 293 TYR cc_start: 0.8998 (t80) cc_final: 0.8516 (t80) REVERT: A 301 ARG cc_start: 0.8292 (mtp180) cc_final: 0.8082 (mtp85) REVERT: A 436 MET cc_start: 0.8339 (ppp) cc_final: 0.7934 (ppp) REVERT: C 231 SER cc_start: 0.9158 (p) cc_final: 0.8802 (t) REVERT: C 275 SER cc_start: 0.9064 (p) cc_final: 0.8500 (t) REVERT: C 344 PHE cc_start: 0.8168 (m-80) cc_final: 0.7854 (m-80) REVERT: C 383 LEU cc_start: 0.8306 (tp) cc_final: 0.8048 (tp) REVERT: C 451 LEU cc_start: 0.8577 (mm) cc_final: 0.8245 (tp) REVERT: D 27 ILE cc_start: 0.9055 (mm) cc_final: 0.8749 (mp) REVERT: D 241 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7755 (mm-30) REVERT: D 247 MET cc_start: 0.7774 (ttp) cc_final: 0.7523 (ttp) REVERT: D 273 ASP cc_start: 0.8591 (t0) cc_final: 0.8208 (t0) REVERT: D 362 TYR cc_start: 0.8236 (m-80) cc_final: 0.7557 (m-80) REVERT: D 417 ASP cc_start: 0.7963 (m-30) cc_final: 0.7334 (m-30) outliers start: 8 outliers final: 5 residues processed: 896 average time/residue: 0.1934 time to fit residues: 291.7243 Evaluate side-chains 625 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 620 time to evaluate : 1.525 ------------------------------------------------------------------------------- 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: 0.0870 chunk 363 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 274 optimal weight: 8.9990 chunk 44 optimal weight: 20.0000 chunk 282 optimal weight: 5.9990 chunk 256 optimal weight: 6.9990 chunk 334 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 392 optimal weight: 5.9990 chunk 275 optimal weight: 1.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 120 GLN b 123 ASN b 165 HIS d 188 ASN ** p 167 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** O 34 GLN Q 28 GLN ** Q 42 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 GLN F 188 ASN A 389 GLN ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 208 GLN D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** 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 = 0.3887 r_free = 0.3887 target = 0.122813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.099534 restraints weight = 118147.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.098866 restraints weight = 101081.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.099658 restraints weight = 80461.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.099837 restraints weight = 63930.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.100039 restraints weight = 54674.651| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.6790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.270 39808 Z= 0.389 Angle : 0.924 37.421 53954 Z= 0.507 Chirality : 0.063 2.789 6456 Planarity : 0.009 0.480 6961 Dihedral : 6.932 87.890 5682 Min Nonbonded Distance : 1.420 Molprobity Statistics. All-atom Clashscore : 22.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.53 % Favored : 96.27 % Rotamer: Outliers : 0.15 % Allowed : 3.14 % Favored : 96.71 % 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 aren not related in a simple way. whole: 0.14 (0.12), residues: 5149 helix: 0.82 (0.09), residues: 2923 sheet: -0.76 (0.20), residues: 610 loop : -0.71 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.054 0.001 ARG A 16 TYR 0.041 0.002 TYR L 66 PHE 0.119 0.002 PHE b 95 TRP 0.013 0.002 TRP a 117 HIS 0.019 0.002 HIS a 36 Details of bonding type rmsd covalent geometry : bond 0.00656 (39778) covalent geometry : angle 0.90788 (53943) SS BOND : bond 0.00337 ( 1) SS BOND : angle 0.80024 ( 2) hydrogen bonds : bond 0.09435 ( 2442) hydrogen bonds : angle 5.57856 ( 7176) Misc. bond : bond 0.02566 ( 26) link_TRANS : bond 0.02974 ( 3) link_TRANS : angle 13.40727 ( 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 863 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 857 time to evaluate : 1.437 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: a 122 LEU cc_start: 0.5341 (OUTLIER) cc_final: 0.4495 (mt) REVERT: a 126 GLU cc_start: 0.6929 (tt0) cc_final: 0.5893 (pm20) REVERT: a 189 ARG cc_start: 0.7636 (ptm160) cc_final: 0.7434 (ptt90) REVERT: b 90 MET cc_start: 0.6269 (mmm) cc_final: 0.5631 (ptm) REVERT: b 104 GLU cc_start: 0.7750 (mp0) cc_final: 0.7482 (pp20) REVERT: b 107 LYS cc_start: 0.4841 (tttt) cc_final: 0.4345 (tmmt) REVERT: b 127 GLU cc_start: 0.7984 (pm20) cc_final: 0.7164 (tm-30) REVERT: b 175 MET cc_start: 0.6668 (mtm) cc_final: 0.6234 (mtm) REVERT: d 167 ASP cc_start: 0.8021 (m-30) cc_final: 0.7808 (m-30) REVERT: d 241 LEU cc_start: 0.8412 (tp) cc_final: 0.7879 (pp) REVERT: p 101 MET cc_start: 0.5890 (ppp) cc_final: 0.5391 (ppp) REVERT: p 102 PHE cc_start: 0.4142 (m-10) cc_final: 0.3651 (m-80) REVERT: e 27 ASN cc_start: 0.8465 (t0) cc_final: 0.7835 (t0) REVERT: e 73 GLU cc_start: 0.7141 (tp30) cc_final: 0.6560 (tp30) REVERT: g 46 GLU cc_start: 0.8614 (pp20) cc_final: 0.7737 (tm-30) REVERT: g 76 GLN cc_start: 0.8683 (tt0) cc_final: 0.8152 (tm-30) REVERT: g 197 ASP cc_start: 0.7311 (t70) cc_final: 0.6816 (t0) REVERT: g 214 TYR cc_start: 0.7670 (p90) cc_final: 0.7249 (p90) REVERT: g 245 LYS cc_start: 0.8811 (mttt) cc_final: 0.8132 (tptt) REVERT: g 290 GLN cc_start: 0.8714 (mt0) cc_final: 0.8439 (mm110) REVERT: g 299 TYR cc_start: 0.6545 (t80) cc_final: 0.5942 (t80) REVERT: g 311 SER cc_start: 0.9103 (m) cc_final: 0.8709 (p) REVERT: S 24 PRO cc_start: 0.7308 (Cg_exo) cc_final: 0.6779 (Cg_endo) REVERT: S 60 MET cc_start: 0.7605 (tmm) cc_final: 0.6932 (tmm) REVERT: N 60 MET cc_start: 0.6836 (ptt) cc_final: 0.6397 (ptt) REVERT: P 60 MET cc_start: 0.5184 (tpt) cc_final: 0.3337 (tpp) REVERT: P 63 LEU cc_start: 0.3761 (mp) cc_final: 0.3427 (mp) REVERT: M 57 LEU cc_start: 0.6954 (mm) cc_final: 0.6750 (mm) REVERT: M 59 PHE cc_start: 0.7275 (m-80) cc_final: 0.6810 (m-80) REVERT: T 60 MET cc_start: 0.4757 (mmm) cc_final: 0.3901 (mmm) REVERT: T 61 GLU cc_start: 0.3281 (tp30) cc_final: 0.1888 (mt-10) REVERT: K 34 GLN cc_start: 0.6723 (mt0) cc_final: 0.6390 (mt0) REVERT: K 60 MET cc_start: 0.4353 (mmm) cc_final: 0.3898 (mmm) REVERT: J 37 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7547 (mt-10) REVERT: J 55 LEU cc_start: 0.6696 (mm) cc_final: 0.6333 (tp) REVERT: J 60 MET cc_start: 0.7303 (ttm) cc_final: 0.7077 (ttm) REVERT: J 72 LEU cc_start: 0.7337 (mt) cc_final: 0.6863 (pp) REVERT: I 48 LYS cc_start: 0.7101 (mttp) cc_final: 0.6572 (ttmt) REVERT: I 60 MET cc_start: 0.5022 (mmm) cc_final: 0.4822 (mmm) REVERT: E 147 LEU cc_start: 0.8990 (tp) cc_final: 0.8761 (tp) REVERT: E 219 MET cc_start: 0.7884 (mmm) cc_final: 0.7177 (mmm) REVERT: E 251 MET cc_start: 0.8196 (ptt) cc_final: 0.7994 (ptt) REVERT: E 314 MET cc_start: 0.7836 (tpt) cc_final: 0.7580 (tpt) REVERT: E 376 MET cc_start: 0.7606 (tpt) cc_final: 0.7371 (tpp) REVERT: E 402 ASP cc_start: 0.8197 (m-30) cc_final: 0.7669 (t0) REVERT: E 434 GLN cc_start: 0.8754 (mt0) cc_final: 0.8123 (mt0) REVERT: F 72 ASN cc_start: 0.9099 (p0) cc_final: 0.8767 (p0) REVERT: F 118 VAL cc_start: 0.8765 (m) cc_final: 0.8321 (p) REVERT: F 347 ASP cc_start: 0.8275 (m-30) cc_final: 0.7996 (m-30) REVERT: A 70 ASN cc_start: 0.8766 (p0) cc_final: 0.8300 (p0) REVERT: A 122 ILE cc_start: 0.8158 (mt) cc_final: 0.7865 (mt) REVERT: A 164 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8318 (tm-30) REVERT: A 219 MET cc_start: 0.7888 (mmm) cc_final: 0.7487 (mmm) REVERT: A 231 SER cc_start: 0.9524 (p) cc_final: 0.9188 (t) REVERT: A 251 MET cc_start: 0.8881 (ttm) cc_final: 0.8553 (ttm) REVERT: A 290 ASP cc_start: 0.7831 (m-30) cc_final: 0.6929 (m-30) REVERT: A 293 TYR cc_start: 0.9012 (t80) cc_final: 0.8644 (t80) REVERT: A 436 MET cc_start: 0.8489 (ppp) cc_final: 0.7906 (ppp) REVERT: B 168 ILE cc_start: 0.9335 (mm) cc_final: 0.9133 (mm) REVERT: B 183 MET cc_start: 0.7930 (mmp) cc_final: 0.7693 (mmp) REVERT: B 492 MET cc_start: 0.9096 (ppp) cc_final: 0.8816 (ppp) REVERT: C 194 CYS cc_start: 0.8075 (m) cc_final: 0.7713 (m) REVERT: C 234 THR cc_start: 0.8929 (t) cc_final: 0.8716 (t) REVERT: C 344 PHE cc_start: 0.8346 (m-80) cc_final: 0.7991 (m-80) REVERT: C 383 LEU cc_start: 0.8529 (tp) cc_final: 0.8272 (tp) REVERT: C 451 LEU cc_start: 0.8481 (mm) cc_final: 0.8188 (tp) REVERT: D 27 ILE cc_start: 0.9122 (mm) cc_final: 0.8861 (tt) REVERT: D 156 VAL cc_start: 0.8573 (m) cc_final: 0.8269 (m) REVERT: D 241 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7825 (mm-30) REVERT: D 273 ASP cc_start: 0.8578 (t0) cc_final: 0.8185 (t0) REVERT: D 362 TYR cc_start: 0.8382 (m-80) cc_final: 0.7672 (m-80) REVERT: D 417 ASP cc_start: 0.8129 (m-30) cc_final: 0.7436 (m-30) REVERT: D 476 LEU cc_start: 0.8714 (mm) cc_final: 0.8411 (mm) outliers start: 6 outliers final: 2 residues processed: 863 average time/residue: 0.1964 time to fit residues: 284.9584 Evaluate side-chains 609 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 606 time to evaluate : 1.468 ------------------------------------------------------------------------------- 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: 2.9990 chunk 66 optimal weight: 9.9990 chunk 442 optimal weight: 8.9990 chunk 223 optimal weight: 20.0000 chunk 497 optimal weight: 10.0000 chunk 175 optimal weight: 20.0000 chunk 478 optimal weight: 0.9990 chunk 303 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 240 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 g 361 ASN ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 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** ** I 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN E 351 ASN E 497 GLN F 325 GLN ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN ** C 84 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.119987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.096420 restraints weight = 119193.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.096266 restraints weight = 99847.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.097407 restraints weight = 69394.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.097695 restraints weight = 52348.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097930 restraints weight = 47759.305| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.7297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.268 39808 Z= 0.403 Angle : 0.930 35.484 53954 Z= 0.512 Chirality : 0.066 3.157 6456 Planarity : 0.008 0.328 6961 Dihedral : 7.150 140.031 5682 Min Nonbonded Distance : 1.417 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.81 % Favored : 95.96 % Rotamer: Outliers : 0.05 % Allowed : 2.73 % Favored : 97.22 % Cbeta Deviations : 0.28 % 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 aren not related in a simple way. whole: -0.01 (0.12), residues: 5149 helix: 0.69 (0.09), residues: 2922 sheet: -0.85 (0.20), residues: 615 loop : -0.75 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 418 TYR 0.038 0.002 TYR L 66 PHE 0.104 0.003 PHE b 95 TRP 0.014 0.002 TRP a 117 HIS 0.023 0.002 HIS a 36 Details of bonding type rmsd covalent geometry : bond 0.00687 (39778) covalent geometry : angle 0.91423 (53943) SS BOND : bond 0.00471 ( 1) SS BOND : angle 0.65537 ( 2) hydrogen bonds : bond 0.09442 ( 2442) hydrogen bonds : angle 5.62286 ( 7176) Misc. bond : bond 0.02453 ( 26) link_TRANS : bond 0.02960 ( 3) link_TRANS : angle 13.33009 ( 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 821 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 819 time to evaluate : 1.177 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: 0.6957 (tt0) cc_final: 0.5433 (pm20) REVERT: b 52 LEU cc_start: 0.6299 (mt) cc_final: 0.6032 (pp) REVERT: b 90 MET cc_start: 0.6466 (mmm) cc_final: 0.5759 (ptm) REVERT: b 104 GLU cc_start: 0.7677 (mp0) cc_final: 0.7334 (pp20) REVERT: b 107 LYS cc_start: 0.4711 (tttt) cc_final: 0.4456 (tmtt) REVERT: b 162 ASN cc_start: 0.7140 (m-40) cc_final: 0.6827 (t0) REVERT: p 101 MET cc_start: 0.5932 (ppp) cc_final: 0.5317 (ppp) REVERT: p 102 PHE cc_start: 0.3925 (m-10) cc_final: 0.3487 (m-80) REVERT: e 27 ASN cc_start: 0.8379 (t0) cc_final: 0.7756 (t0) REVERT: e 73 GLU cc_start: 0.6979 (tp30) cc_final: 0.6463 (tp30) REVERT: g 46 GLU cc_start: 0.8429 (pp20) cc_final: 0.7505 (tm-30) REVERT: g 76 GLN cc_start: 0.8727 (tt0) cc_final: 0.8071 (tm-30) REVERT: g 197 ASP cc_start: 0.7180 (t70) cc_final: 0.6690 (t0) REVERT: g 214 TYR cc_start: 0.7895 (p90) cc_final: 0.7349 (p90) REVERT: g 245 LYS cc_start: 0.8781 (mttt) cc_final: 0.8123 (tptt) REVERT: g 290 GLN cc_start: 0.8599 (mt0) cc_final: 0.8333 (mm110) REVERT: g 299 TYR cc_start: 0.6657 (t80) cc_final: 0.6115 (t80) REVERT: g 311 SER cc_start: 0.9220 (m) cc_final: 0.8715 (p) REVERT: S 28 GLN cc_start: 0.6779 (tt0) cc_final: 0.5899 (tt0) REVERT: S 60 MET cc_start: 0.7671 (tmm) cc_final: 0.6985 (tmm) REVERT: N 15 LEU cc_start: 0.6819 (mt) cc_final: 0.6460 (tt) REVERT: N 60 MET cc_start: 0.7189 (ptt) cc_final: 0.6395 (ptt) REVERT: O 34 GLN cc_start: 0.8608 (tt0) cc_final: 0.8373 (tt0) REVERT: O 48 LYS cc_start: 0.4134 (tttp) cc_final: 0.3911 (tptm) REVERT: O 59 PHE cc_start: 0.8137 (m-80) cc_final: 0.7891 (m-80) REVERT: P 60 MET cc_start: 0.5565 (tpt) cc_final: 0.4904 (mmm) REVERT: M 59 PHE cc_start: 0.7393 (m-80) cc_final: 0.6915 (m-80) REVERT: T 60 MET cc_start: 0.4890 (mmm) cc_final: 0.4406 (mmm) REVERT: G 34 GLN cc_start: 0.8035 (mt0) cc_final: 0.7485 (mt0) REVERT: H 54 LEU cc_start: 0.6711 (mm) cc_final: 0.5873 (tp) REVERT: K 34 GLN cc_start: 0.6755 (mt0) cc_final: 0.5967 (mt0) REVERT: K 59 PHE cc_start: 0.7136 (m-80) cc_final: 0.6560 (m-80) REVERT: J 37 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7594 (mt-10) REVERT: J 55 LEU cc_start: 0.6731 (mm) cc_final: 0.6471 (tp) REVERT: J 72 LEU cc_start: 0.7329 (mt) cc_final: 0.6852 (pp) REVERT: I 48 LYS cc_start: 0.7244 (mttp) cc_final: 0.6759 (ttmt) REVERT: I 50 ARG cc_start: 0.8129 (mmm-85) cc_final: 0.7578 (mmm160) REVERT: E 138 MET cc_start: 0.8460 (pmm) cc_final: 0.8201 (pmm) REVERT: E 147 LEU cc_start: 0.9038 (tp) cc_final: 0.8774 (tp) REVERT: E 219 MET cc_start: 0.7838 (mmm) cc_final: 0.7181 (mmm) REVERT: E 314 MET cc_start: 0.7923 (tpt) cc_final: 0.7654 (tpt) REVERT: E 402 ASP cc_start: 0.8226 (m-30) cc_final: 0.7557 (t0) REVERT: F 32 ASP cc_start: 0.8302 (m-30) cc_final: 0.8099 (m-30) REVERT: F 118 VAL cc_start: 0.8911 (m) cc_final: 0.8378 (p) REVERT: F 183 MET cc_start: 0.7740 (mtp) cc_final: 0.7495 (mtt) REVERT: F 215 GLU cc_start: 0.8264 (pp20) cc_final: 0.7931 (tm-30) REVERT: F 347 ASP cc_start: 0.8229 (m-30) cc_final: 0.7939 (m-30) REVERT: F 481 ASP cc_start: 0.8616 (p0) cc_final: 0.8403 (p0) REVERT: A 46 ASP cc_start: 0.8395 (t0) cc_final: 0.7813 (t0) REVERT: A 70 ASN cc_start: 0.8719 (p0) cc_final: 0.8294 (p0) REVERT: A 85 GLU cc_start: 0.7993 (pp20) cc_final: 0.7682 (pp20) REVERT: A 164 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8506 (tm-30) REVERT: A 231 SER cc_start: 0.9499 (p) cc_final: 0.9032 (t) REVERT: A 251 MET cc_start: 0.8773 (ttm) cc_final: 0.8541 (ttm) REVERT: A 436 MET cc_start: 0.8699 (ppp) cc_final: 0.8177 (ppp) REVERT: B 153 ILE cc_start: 0.9159 (mp) cc_final: 0.8854 (tp) REVERT: C 157 MET cc_start: 0.8385 (mmt) cc_final: 0.7597 (mmp) REVERT: C 194 CYS cc_start: 0.8004 (m) cc_final: 0.7351 (m) REVERT: C 258 LEU cc_start: 0.9112 (tp) cc_final: 0.8894 (tp) REVERT: C 451 LEU cc_start: 0.8336 (mm) cc_final: 0.8117 (tt) REVERT: D 162 TYR cc_start: 0.7512 (m-80) cc_final: 0.7207 (m-80) REVERT: D 193 HIS cc_start: 0.7081 (t-90) cc_final: 0.6835 (t70) REVERT: D 204 GLU cc_start: 0.7170 (pt0) cc_final: 0.6583 (pt0) REVERT: D 417 ASP cc_start: 0.8100 (m-30) cc_final: 0.7322 (m-30) REVERT: D 476 LEU cc_start: 0.8730 (mm) cc_final: 0.8169 (mm) outliers start: 2 outliers final: 1 residues processed: 821 average time/residue: 0.1969 time to fit residues: 274.6596 Evaluate side-chains 588 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 587 time to evaluate : 1.360 ------------------------------------------------------------------------------- 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: 6.9990 chunk 453 optimal weight: 1.9990 chunk 203 optimal weight: 6.9990 chunk 166 optimal weight: 20.0000 chunk 475 optimal weight: 3.9990 chunk 152 optimal weight: 20.0000 chunk 88 optimal weight: 0.0050 chunk 228 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 252 optimal weight: 8.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 180 ASN p 143 GLN ** p 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 102 ASN ** g 165 ASN ** 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** ** Q 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** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 GLN ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN D 389 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.122753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.099976 restraints weight = 116788.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.099699 restraints weight = 93755.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.100100 restraints weight = 78468.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.100240 restraints weight = 61457.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.100862 restraints weight = 53962.709| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.7480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.270 39808 Z= 0.375 Angle : 0.908 37.105 53954 Z= 0.497 Chirality : 0.064 2.957 6456 Planarity : 0.006 0.158 6961 Dihedral : 6.700 84.468 5682 Min Nonbonded Distance : 1.392 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.24 % Favored : 96.52 % Rotamer: Outliers : 0.05 % Allowed : 1.51 % Favored : 98.44 % Cbeta Deviations : 0.28 % 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 aren not related in a simple way. whole: 0.19 (0.12), residues: 5149 helix: 0.85 (0.10), residues: 2926 sheet: -0.79 (0.20), residues: 617 loop : -0.66 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.114 0.001 ARG A 16 TYR 0.042 0.002 TYR L 66 PHE 0.107 0.002 PHE b 95 TRP 0.012 0.001 TRP a 117 HIS 0.018 0.001 HIS a 36 Details of bonding type rmsd covalent geometry : bond 0.00604 (39778) covalent geometry : angle 0.89170 (53943) SS BOND : bond 0.00150 ( 1) SS BOND : angle 0.87629 ( 2) hydrogen bonds : bond 0.09311 ( 2442) hydrogen bonds : angle 5.48800 ( 7176) Misc. bond : bond 0.02696 ( 26) link_TRANS : bond 0.02958 ( 3) link_TRANS : angle 13.20435 ( 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 840 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 838 time to evaluate : 1.444 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: a 126 GLU cc_start: 0.7037 (tt0) cc_final: 0.5365 (pm20) REVERT: a 172 LEU cc_start: 0.7242 (tt) cc_final: 0.6981 (pp) REVERT: b 52 LEU cc_start: 0.6121 (mt) cc_final: 0.5768 (pp) REVERT: b 90 MET cc_start: 0.6509 (mmm) cc_final: 0.5863 (ptm) REVERT: b 107 LYS cc_start: 0.5005 (tttt) cc_final: 0.4738 (tmtt) REVERT: b 127 GLU cc_start: 0.8329 (pm20) cc_final: 0.7354 (tt0) REVERT: b 162 ASN cc_start: 0.7105 (m-40) cc_final: 0.6800 (t0) REVERT: d 167 ASP cc_start: 0.7887 (m-30) cc_final: 0.7650 (m-30) REVERT: p 101 MET cc_start: 0.5846 (ppp) cc_final: 0.5459 (ppp) REVERT: p 102 PHE cc_start: 0.3712 (m-10) cc_final: 0.3283 (m-80) REVERT: e 27 ASN cc_start: 0.8372 (t0) cc_final: 0.7737 (t0) REVERT: e 73 GLU cc_start: 0.7155 (tp30) cc_final: 0.6584 (tp30) REVERT: e 79 ASN cc_start: 0.7749 (p0) cc_final: 0.6899 (m110) REVERT: e 80 ASP cc_start: 0.7596 (t70) cc_final: 0.6876 (t0) REVERT: g 46 GLU cc_start: 0.8536 (pp20) cc_final: 0.7741 (tm-30) REVERT: g 76 GLN cc_start: 0.8673 (tt0) cc_final: 0.8191 (tm-30) REVERT: g 150 LYS cc_start: 0.8492 (mmmt) cc_final: 0.7404 (mtmt) REVERT: g 197 ASP cc_start: 0.7265 (t70) cc_final: 0.6787 (t0) REVERT: g 214 TYR cc_start: 0.7683 (p90) cc_final: 0.7247 (p90) REVERT: g 245 LYS cc_start: 0.8735 (mttt) cc_final: 0.8090 (tptt) REVERT: g 311 SER cc_start: 0.9224 (m) cc_final: 0.8713 (p) REVERT: S 28 GLN cc_start: 0.6855 (tt0) cc_final: 0.6057 (tt0) REVERT: S 60 MET cc_start: 0.7583 (tmm) cc_final: 0.6959 (tmm) REVERT: N 60 MET cc_start: 0.7192 (ptt) cc_final: 0.6826 (ptt) REVERT: O 60 MET cc_start: 0.4449 (mtm) cc_final: 0.4207 (mtm) REVERT: P 60 MET cc_start: 0.5590 (tpt) cc_final: 0.4083 (tpp) REVERT: Q 28 GLN cc_start: 0.6593 (tp40) cc_final: 0.6225 (mm-40) REVERT: R 60 MET cc_start: 0.5205 (mmm) cc_final: 0.4880 (mmm) REVERT: M 59 PHE cc_start: 0.7422 (m-80) cc_final: 0.6984 (m-80) REVERT: T 60 MET cc_start: 0.4734 (mmm) cc_final: 0.4321 (mmm) REVERT: H 37 GLU cc_start: 0.8219 (tt0) cc_final: 0.7369 (tm-30) REVERT: H 52 THR cc_start: 0.5572 (p) cc_final: 0.5224 (p) REVERT: K 34 GLN cc_start: 0.6714 (mt0) cc_final: 0.6394 (mt0) REVERT: K 60 MET cc_start: 0.6301 (mtm) cc_final: 0.5795 (ptp) REVERT: J 37 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7415 (mt-10) REVERT: J 55 LEU cc_start: 0.6809 (mm) cc_final: 0.6410 (tp) REVERT: J 72 LEU cc_start: 0.7188 (mt) cc_final: 0.6759 (pp) REVERT: I 48 LYS cc_start: 0.7215 (mttp) cc_final: 0.6739 (ttmt) REVERT: I 50 ARG cc_start: 0.8087 (mmm-85) cc_final: 0.7582 (mmm160) REVERT: E 56 PHE cc_start: 0.7194 (m-80) cc_final: 0.6963 (m-80) REVERT: E 147 LEU cc_start: 0.9039 (tp) cc_final: 0.8774 (tp) REVERT: E 166 GLU cc_start: 0.8917 (tp30) cc_final: 0.8688 (tp30) REVERT: E 219 MET cc_start: 0.7760 (mmm) cc_final: 0.7123 (mmm) REVERT: E 227 GLU cc_start: 0.8488 (tp30) cc_final: 0.8207 (tp30) REVERT: E 314 MET cc_start: 0.8054 (tpt) cc_final: 0.7621 (tpt) REVERT: E 402 ASP cc_start: 0.8177 (m-30) cc_final: 0.7542 (t0) REVERT: F 79 MET cc_start: 0.8458 (mmt) cc_final: 0.8015 (mmt) REVERT: F 118 VAL cc_start: 0.8859 (m) cc_final: 0.8435 (p) REVERT: F 183 MET cc_start: 0.7730 (mtp) cc_final: 0.7508 (mtp) REVERT: F 212 LEU cc_start: 0.8932 (tp) cc_final: 0.8682 (tp) REVERT: F 247 MET cc_start: 0.7929 (mtp) cc_final: 0.7725 (mtm) REVERT: F 302 LEU cc_start: 0.9634 (tt) cc_final: 0.9184 (tt) REVERT: F 305 GLU cc_start: 0.7765 (mt-10) cc_final: 0.6956 (mt-10) REVERT: F 347 ASP cc_start: 0.8291 (m-30) cc_final: 0.7993 (m-30) REVERT: A 46 ASP cc_start: 0.8429 (t0) cc_final: 0.7803 (t0) REVERT: A 66 ASN cc_start: 0.8406 (m-40) cc_final: 0.8014 (m-40) REVERT: A 85 GLU cc_start: 0.8097 (pp20) cc_final: 0.7686 (pp20) REVERT: A 122 ILE cc_start: 0.8243 (mt) cc_final: 0.7905 (mt) REVERT: A 164 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8438 (tm-30) REVERT: A 231 SER cc_start: 0.9463 (p) cc_final: 0.9145 (t) REVERT: A 251 MET cc_start: 0.8857 (ttm) cc_final: 0.8621 (ttm) REVERT: A 436 MET cc_start: 0.8357 (ppp) cc_final: 0.7758 (ppp) REVERT: B 171 PHE cc_start: 0.9054 (m-80) cc_final: 0.8524 (m-10) REVERT: C 84 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8252 (pp30) REVERT: C 157 MET cc_start: 0.8323 (mmt) cc_final: 0.8111 (mmp) REVERT: C 194 CYS cc_start: 0.7849 (m) cc_final: 0.7512 (m) REVERT: C 230 ASP cc_start: 0.7122 (p0) cc_final: 0.6821 (p0) REVERT: C 451 LEU cc_start: 0.8365 (mm) cc_final: 0.8010 (tp) REVERT: D 31 LEU cc_start: 0.8332 (mt) cc_final: 0.7971 (mp) REVERT: D 193 HIS cc_start: 0.7036 (t-90) cc_final: 0.6776 (t70) REVERT: D 204 GLU cc_start: 0.7085 (pt0) cc_final: 0.6526 (pt0) REVERT: D 247 MET cc_start: 0.8035 (ttp) cc_final: 0.7578 (ttp) REVERT: D 273 ASP cc_start: 0.8653 (t0) cc_final: 0.8392 (t0) REVERT: D 417 ASP cc_start: 0.8118 (m-30) cc_final: 0.7341 (m-30) REVERT: D 476 LEU cc_start: 0.8776 (mm) cc_final: 0.8180 (mm) outliers start: 2 outliers final: 1 residues processed: 839 average time/residue: 0.1971 time to fit residues: 279.4759 Evaluate side-chains 617 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 615 time to evaluate : 1.399 ------------------------------------------------------------------------------- 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: 5.9990 chunk 287 optimal weight: 6.9990 chunk 371 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 478 optimal weight: 3.9990 chunk 344 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 423 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 320 optimal weight: 9.9990 chunk 303 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 186 GLN g 290 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 342 ASN ** 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** ** K 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 GLN E 351 ASN ** E 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 GLN ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 72 ASN ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 GLN D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.117368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.095431 restraints weight = 121711.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.093954 restraints weight = 91634.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.094610 restraints weight = 81953.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.094886 restraints weight = 70408.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.095134 restraints weight = 57739.576| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.7929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.264 39808 Z= 0.426 Angle : 0.977 35.949 53954 Z= 0.531 Chirality : 0.066 2.944 6456 Planarity : 0.007 0.144 6961 Dihedral : 6.917 76.125 5682 Min Nonbonded Distance : 1.407 Molprobity Statistics. All-atom Clashscore : 23.33 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.33 % Favored : 95.44 % Rotamer: Outliers : 0.02 % Allowed : 1.41 % Favored : 98.56 % Cbeta Deviations : 0.28 % 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 aren not related in a simple way. whole: -0.15 (0.12), residues: 5149 helix: 0.57 (0.09), residues: 2936 sheet: -0.93 (0.20), residues: 613 loop : -0.80 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 16 TYR 0.040 0.003 TYR L 66 PHE 0.104 0.003 PHE b 95 TRP 0.018 0.002 TRP a 44 HIS 0.019 0.002 HIS a 36 Details of bonding type rmsd covalent geometry : bond 0.00768 (39778) covalent geometry : angle 0.96329 (53943) SS BOND : bond 0.00340 ( 1) SS BOND : angle 1.00571 ( 2) hydrogen bonds : bond 0.09552 ( 2442) hydrogen bonds : angle 5.73256 ( 7176) Misc. bond : bond 0.02557 ( 26) link_TRANS : bond 0.02612 ( 3) link_TRANS : angle 12.73903 ( 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 770 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 769 time to evaluate : 1.728 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: 0.5360 (ptp-110) cc_final: 0.4524 (mmm160) REVERT: a 116 PRO cc_start: 0.4527 (Cg_endo) cc_final: 0.4201 (Cg_exo) REVERT: a 126 GLU cc_start: 0.6911 (tt0) cc_final: 0.5082 (pm20) REVERT: a 238 TYR cc_start: 0.8414 (m-10) cc_final: 0.7832 (m-80) REVERT: b 90 MET cc_start: 0.6548 (mmm) cc_final: 0.5805 (ptm) REVERT: b 107 LYS cc_start: 0.4792 (tttt) cc_final: 0.4569 (tmtt) REVERT: p 101 MET cc_start: 0.5974 (ppp) cc_final: 0.5341 (ppp) REVERT: p 102 PHE cc_start: 0.3744 (m-10) cc_final: 0.3305 (m-80) REVERT: e 21 GLU cc_start: 0.6960 (tm-30) cc_final: 0.6679 (tm-30) REVERT: e 27 ASN cc_start: 0.7982 (t0) cc_final: 0.7476 (t0) REVERT: e 33 VAL cc_start: 0.7915 (m) cc_final: 0.7705 (m) REVERT: e 73 GLU cc_start: 0.6974 (tp30) cc_final: 0.6464 (tp30) REVERT: e 79 ASN cc_start: 0.7926 (p0) cc_final: 0.7272 (m-40) REVERT: e 80 ASP cc_start: 0.7669 (t70) cc_final: 0.6946 (t70) REVERT: g 46 GLU cc_start: 0.8462 (pp20) cc_final: 0.7594 (tm-30) REVERT: g 76 GLN cc_start: 0.8644 (tt0) cc_final: 0.8133 (tm-30) REVERT: g 212 MET cc_start: 0.7388 (tpp) cc_final: 0.7069 (tpp) REVERT: g 214 TYR cc_start: 0.8043 (p90) cc_final: 0.7827 (p90) REVERT: g 245 LYS cc_start: 0.8699 (mttt) cc_final: 0.8046 (tptt) REVERT: g 299 TYR cc_start: 0.6687 (t80) cc_final: 0.6291 (t80) REVERT: g 311 SER cc_start: 0.9205 (m) cc_final: 0.8847 (p) REVERT: g 346 GLN cc_start: 0.8256 (pt0) cc_final: 0.8055 (pt0) REVERT: S 60 MET cc_start: 0.7561 (tmm) cc_final: 0.7111 (tmm) REVERT: N 15 LEU cc_start: 0.6885 (mt) cc_final: 0.6666 (tt) REVERT: N 60 MET cc_start: 0.7441 (ptt) cc_final: 0.6798 (ptt) REVERT: O 76 PHE cc_start: 0.1857 (m-10) cc_final: 0.0832 (t80) REVERT: P 60 MET cc_start: 0.5924 (tpt) cc_final: 0.4163 (tpp) REVERT: R 60 MET cc_start: 0.5463 (mmm) cc_final: 0.5177 (mmm) REVERT: M 59 PHE cc_start: 0.7316 (m-80) cc_final: 0.6817 (m-80) REVERT: G 61 GLU cc_start: 0.5728 (mm-30) cc_final: 0.4729 (tp30) REVERT: J 72 LEU cc_start: 0.7304 (mt) cc_final: 0.6732 (pp) REVERT: I 48 LYS cc_start: 0.7350 (mttp) cc_final: 0.6981 (ttmt) REVERT: I 50 ARG cc_start: 0.8237 (mmm-85) cc_final: 0.7825 (mmm-85) REVERT: E 147 LEU cc_start: 0.8996 (tp) cc_final: 0.8754 (tp) REVERT: E 219 MET cc_start: 0.7854 (mmm) cc_final: 0.7350 (mmm) REVERT: E 227 GLU cc_start: 0.8416 (tp30) cc_final: 0.8127 (tp30) REVERT: E 314 MET cc_start: 0.7930 (tpt) cc_final: 0.7669 (tpt) REVERT: E 401 SER cc_start: 0.7550 (p) cc_final: 0.7238 (t) REVERT: E 402 ASP cc_start: 0.8225 (m-30) cc_final: 0.7151 (t0) REVERT: F 32 ASP cc_start: 0.8421 (m-30) cc_final: 0.8219 (m-30) REVERT: F 118 VAL cc_start: 0.8846 (m) cc_final: 0.8397 (p) REVERT: F 183 MET cc_start: 0.7651 (mtp) cc_final: 0.7404 (mtp) REVERT: F 212 LEU cc_start: 0.8983 (tp) cc_final: 0.8727 (tp) REVERT: F 215 GLU cc_start: 0.8226 (pp20) cc_final: 0.7991 (tm-30) REVERT: F 305 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7330 (mt-10) REVERT: F 347 ASP cc_start: 0.8316 (m-30) cc_final: 0.7974 (m-30) REVERT: A 46 ASP cc_start: 0.8472 (t0) cc_final: 0.7858 (t0) REVERT: A 66 ASN cc_start: 0.8496 (m-40) cc_final: 0.8137 (m-40) REVERT: A 122 ILE cc_start: 0.8348 (mt) cc_final: 0.8051 (mt) REVERT: A 195 VAL cc_start: 0.8795 (t) cc_final: 0.8561 (t) REVERT: A 251 MET cc_start: 0.8762 (ttm) cc_final: 0.8440 (ttp) REVERT: A 436 MET cc_start: 0.8147 (ppp) cc_final: 0.7826 (ppp) REVERT: C 70 ASN cc_start: 0.7308 (m-40) cc_final: 0.7093 (m-40) REVERT: C 194 CYS cc_start: 0.7708 (m) cc_final: 0.7271 (m) REVERT: C 451 LEU cc_start: 0.8311 (mm) cc_final: 0.8101 (tt) REVERT: D 162 TYR cc_start: 0.7452 (m-80) cc_final: 0.7232 (m-80) REVERT: D 176 VAL cc_start: 0.8856 (m) cc_final: 0.8352 (t) REVERT: D 204 GLU cc_start: 0.7242 (pt0) cc_final: 0.6568 (pt0) REVERT: D 205 ARG cc_start: 0.7298 (mtt90) cc_final: 0.7055 (mtm-85) REVERT: D 247 MET cc_start: 0.8206 (ttp) cc_final: 0.7939 (ttp) REVERT: D 417 ASP cc_start: 0.8027 (m-30) cc_final: 0.7166 (m-30) outliers start: 1 outliers final: 0 residues processed: 769 average time/residue: 0.1983 time to fit residues: 256.4922 Evaluate side-chains 568 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 568 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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: 9.9990 chunk 240 optimal weight: 0.9980 chunk 421 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 410 optimal weight: 6.9990 chunk 401 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 390 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 120 GLN p 143 GLN e 94 GLN e 102 ASN ** g 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 342 ASN ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 28 GLN ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** H 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 GLN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 ASN F 60 ASN F 325 GLN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN ** B 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN C 334 ASN D 112 ASN D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.119665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.097202 restraints weight = 118161.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.096518 restraints weight = 104770.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.097152 restraints weight = 74612.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.097596 restraints weight = 58280.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097711 restraints weight = 52814.853| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.8126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.266 39808 Z= 0.381 Angle : 0.947 34.951 53954 Z= 0.516 Chirality : 0.069 3.487 6456 Planarity : 0.006 0.141 6961 Dihedral : 6.768 77.082 5682 Min Nonbonded Distance : 1.409 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.55 % Favored : 96.17 % Rotamer: Outliers : 0.05 % Allowed : 1.00 % Favored : 98.95 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.12), residues: 5149 helix: 0.69 (0.09), residues: 2926 sheet: -0.84 (0.21), residues: 590 loop : -0.78 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG A 16 TYR 0.042 0.002 TYR B 162 PHE 0.102 0.002 PHE b 95 TRP 0.012 0.001 TRP a 44 HIS 0.017 0.002 HIS a 36 Details of bonding type rmsd covalent geometry : bond 0.00634 (39778) covalent geometry : angle 0.93295 (53943) SS BOND : bond 0.00222 ( 1) SS BOND : angle 0.87045 ( 2) hydrogen bonds : bond 0.09414 ( 2442) hydrogen bonds : angle 5.61363 ( 7176) Misc. bond : bond 0.02529 ( 26) link_TRANS : bond 0.02739 ( 3) link_TRANS : angle 12.74602 ( 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 792 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 790 time to evaluate : 1.166 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: 0.6602 (tt0) cc_final: 0.4906 (pm20) REVERT: a 238 TYR cc_start: 0.8457 (m-10) cc_final: 0.8106 (m-80) REVERT: a 244 GLU cc_start: 0.2409 (tp30) cc_final: 0.1944 (tp30) REVERT: b 90 MET cc_start: 0.6628 (mmm) cc_final: 0.5960 (ptm) REVERT: b 107 LYS cc_start: 0.4690 (tttt) cc_final: 0.4480 (tmtt) REVERT: b 127 GLU cc_start: 0.8323 (pm20) cc_final: 0.6371 (tt0) REVERT: d 222 THR cc_start: 0.7752 (p) cc_final: 0.6002 (p) REVERT: p 101 MET cc_start: 0.6023 (ppp) cc_final: 0.5435 (ppp) REVERT: p 102 PHE cc_start: 0.3518 (m-10) cc_final: 0.3135 (m-80) REVERT: e 19 VAL cc_start: 0.7333 (p) cc_final: 0.6957 (t) REVERT: e 21 GLU cc_start: 0.6796 (tm-30) cc_final: 0.6500 (tm-30) REVERT: e 73 GLU cc_start: 0.7101 (tp30) cc_final: 0.6637 (tp30) REVERT: e 79 ASN cc_start: 0.7808 (p0) cc_final: 0.7357 (m-40) REVERT: e 80 ASP cc_start: 0.7731 (t70) cc_final: 0.7051 (t70) REVERT: g 46 GLU cc_start: 0.8374 (pp20) cc_final: 0.7474 (tm-30) REVERT: g 76 GLN cc_start: 0.8606 (tt0) cc_final: 0.8235 (tm-30) REVERT: g 245 LYS cc_start: 0.8692 (mttt) cc_final: 0.8052 (tptt) REVERT: g 299 TYR cc_start: 0.6590 (t80) cc_final: 0.6245 (t80) REVERT: g 311 SER cc_start: 0.9165 (m) cc_final: 0.8815 (p) REVERT: S 60 MET cc_start: 0.7706 (tmm) cc_final: 0.7131 (tmm) REVERT: N 15 LEU cc_start: 0.6851 (mt) cc_final: 0.6533 (tt) REVERT: N 60 MET cc_start: 0.7487 (ptt) cc_final: 0.6949 (ptt) REVERT: P 60 MET cc_start: 0.5931 (tpt) cc_final: 0.4200 (tpp) REVERT: G 60 MET cc_start: 0.2736 (ttt) cc_final: 0.2276 (tmm) REVERT: H 37 GLU cc_start: 0.8203 (tt0) cc_final: 0.7419 (tm-30) REVERT: H 54 LEU cc_start: 0.7082 (mm) cc_final: 0.6418 (tp) REVERT: K 50 ARG cc_start: 0.8062 (ttt180) cc_final: 0.7656 (tpm170) REVERT: J 60 MET cc_start: 0.7375 (ttm) cc_final: 0.7082 (ttm) REVERT: J 72 LEU cc_start: 0.7148 (mt) cc_final: 0.6687 (pp) REVERT: I 48 LYS cc_start: 0.7250 (mttp) cc_final: 0.6843 (ttmt) REVERT: E 219 MET cc_start: 0.7688 (mmm) cc_final: 0.7244 (mmm) REVERT: E 227 GLU cc_start: 0.8343 (tp30) cc_final: 0.8094 (tp30) REVERT: E 234 THR cc_start: 0.8285 (t) cc_final: 0.7986 (m) REVERT: E 274 MET cc_start: 0.8248 (mtm) cc_final: 0.7960 (mtm) REVERT: E 314 MET cc_start: 0.7923 (tpt) cc_final: 0.7502 (tpt) REVERT: E 351 ASN cc_start: 0.8754 (m-40) cc_final: 0.8551 (m110) REVERT: E 402 ASP cc_start: 0.8214 (m-30) cc_final: 0.7446 (t0) REVERT: F 79 MET cc_start: 0.8391 (mmt) cc_final: 0.8045 (mmt) REVERT: F 118 VAL cc_start: 0.8824 (m) cc_final: 0.8325 (p) REVERT: F 212 LEU cc_start: 0.8863 (tp) cc_final: 0.8628 (tp) REVERT: F 215 GLU cc_start: 0.8149 (pp20) cc_final: 0.7894 (tm-30) REVERT: F 305 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7342 (mt-10) REVERT: F 347 ASP cc_start: 0.8297 (m-30) cc_final: 0.7914 (m-30) REVERT: A 12 ILE cc_start: 0.8128 (mt) cc_final: 0.7257 (tp) REVERT: A 46 ASP cc_start: 0.8433 (t0) cc_final: 0.7844 (t0) REVERT: A 66 ASN cc_start: 0.8308 (m-40) cc_final: 0.7995 (m-40) REVERT: A 85 GLU cc_start: 0.8151 (pp20) cc_final: 0.7940 (pp20) REVERT: A 122 ILE cc_start: 0.8258 (mt) cc_final: 0.7966 (mt) REVERT: A 251 MET cc_start: 0.8752 (ttm) cc_final: 0.8419 (ttp) REVERT: A 436 MET cc_start: 0.8280 (ppp) cc_final: 0.7728 (ppp) REVERT: C 70 ASN cc_start: 0.7335 (m-40) cc_final: 0.7114 (m-40) REVERT: C 154 ILE cc_start: 0.8716 (mp) cc_final: 0.8361 (tp) REVERT: C 194 CYS cc_start: 0.7759 (m) cc_final: 0.7268 (m) REVERT: C 230 ASP cc_start: 0.7047 (p0) cc_final: 0.6600 (p0) REVERT: C 258 LEU cc_start: 0.9019 (tp) cc_final: 0.8801 (tp) REVERT: C 344 PHE cc_start: 0.8451 (m-80) cc_final: 0.8130 (m-80) REVERT: C 451 LEU cc_start: 0.8269 (mm) cc_final: 0.7968 (tp) REVERT: D 171 PHE cc_start: 0.8874 (m-80) cc_final: 0.8477 (m-10) REVERT: D 204 GLU cc_start: 0.7146 (pt0) cc_final: 0.6463 (pt0) REVERT: D 205 ARG cc_start: 0.7173 (mtt90) cc_final: 0.6875 (mtm180) REVERT: D 247 MET cc_start: 0.7965 (ttp) cc_final: 0.7639 (ttp) REVERT: D 273 ASP cc_start: 0.8701 (t0) cc_final: 0.8457 (t0) REVERT: D 417 ASP cc_start: 0.8111 (m-30) cc_final: 0.7298 (m-30) outliers start: 2 outliers final: 0 residues processed: 792 average time/residue: 0.2043 time to fit residues: 272.9627 Evaluate side-chains 579 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 579 time to evaluate : 1.501 ------------------------------------------------------------------------------- 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: 3.9990 chunk 329 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 422 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 chunk 181 optimal weight: 7.9990 chunk 101 optimal weight: 0.0030 chunk 237 optimal weight: 0.8980 chunk 151 optimal weight: 8.9990 chunk 279 optimal weight: 9.9990 chunk 335 optimal weight: 0.9990 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 227 GLN b 120 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 34 GLN ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** H 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 GLN ** I 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN F 60 ASN F 325 GLN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 HIS ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 193 HIS ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.120590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.097712 restraints weight = 118606.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.097397 restraints weight = 95619.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.097911 restraints weight = 71135.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.098078 restraints weight = 61965.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.098214 restraints weight = 58229.799| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.8309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.269 39808 Z= 0.376 Angle : 0.943 35.546 53954 Z= 0.513 Chirality : 0.067 3.324 6456 Planarity : 0.006 0.140 6961 Dihedral : 6.628 75.886 5682 Min Nonbonded Distance : 1.414 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.85 % Favored : 95.88 % Rotamer: Outliers : 0.02 % Allowed : 0.39 % Favored : 99.59 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.12), residues: 5149 helix: 0.76 (0.09), residues: 2929 sheet: -0.87 (0.20), residues: 606 loop : -0.68 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.043 0.001 ARG A 16 TYR 0.030 0.002 TYR b 124 PHE 0.101 0.002 PHE b 95 TRP 0.024 0.002 TRP a 28 HIS 0.018 0.002 HIS a 36 Details of bonding type rmsd covalent geometry : bond 0.00619 (39778) covalent geometry : angle 0.92868 (53943) SS BOND : bond 0.00119 ( 1) SS BOND : angle 0.92015 ( 2) hydrogen bonds : bond 0.09328 ( 2442) hydrogen bonds : angle 5.56830 ( 7176) Misc. bond : bond 0.02570 ( 26) link_TRANS : bond 0.02765 ( 3) link_TRANS : angle 12.69431 ( 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 788 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 787 time to evaluate : 1.129 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: a 241 GLU cc_start: 0.5991 (tp30) cc_final: 0.5682 (tp30) REVERT: b 22 PHE cc_start: 0.5287 (m-80) cc_final: 0.4871 (m-10) REVERT: b 90 MET cc_start: 0.6605 (mmm) cc_final: 0.5994 (ptm) REVERT: b 107 LYS cc_start: 0.4787 (tttt) cc_final: 0.4516 (tmtt) REVERT: b 127 GLU cc_start: 0.8338 (pm20) cc_final: 0.6468 (tt0) REVERT: p 101 MET cc_start: 0.6140 (ppp) cc_final: 0.5502 (ppp) REVERT: p 102 PHE cc_start: 0.3544 (m-10) cc_final: 0.3188 (m-80) REVERT: p 143 GLN cc_start: 0.4852 (mp-120) cc_final: 0.4260 (tp-100) REVERT: e 19 VAL cc_start: 0.7272 (p) cc_final: 0.6873 (t) REVERT: e 21 GLU cc_start: 0.6712 (tm-30) cc_final: 0.6437 (tm-30) REVERT: e 33 VAL cc_start: 0.7926 (m) cc_final: 0.7670 (m) REVERT: e 73 GLU cc_start: 0.7107 (tp30) cc_final: 0.6735 (tp30) REVERT: e 79 ASN cc_start: 0.7904 (p0) cc_final: 0.7573 (m-40) REVERT: e 80 ASP cc_start: 0.7949 (t70) cc_final: 0.7035 (t70) REVERT: g 46 GLU cc_start: 0.8433 (pp20) cc_final: 0.7481 (tm-30) REVERT: g 76 GLN cc_start: 0.8603 (tt0) cc_final: 0.8262 (tm-30) REVERT: g 98 GLU cc_start: 0.7174 (pp20) cc_final: 0.6964 (tm-30) REVERT: g 158 ILE cc_start: 0.7982 (mp) cc_final: 0.7747 (mp) REVERT: g 212 MET cc_start: 0.7400 (tpp) cc_final: 0.7179 (tpp) REVERT: g 214 TYR cc_start: 0.7870 (p90) cc_final: 0.7620 (p90) REVERT: g 245 LYS cc_start: 0.8650 (mttt) cc_final: 0.8051 (tptt) REVERT: g 270 MET cc_start: 0.7412 (mmm) cc_final: 0.7167 (mmm) REVERT: g 299 TYR cc_start: 0.6581 (t80) cc_final: 0.6194 (t80) REVERT: g 311 SER cc_start: 0.9139 (m) cc_final: 0.8797 (p) REVERT: S 60 MET cc_start: 0.7558 (tmm) cc_final: 0.6899 (tmm) REVERT: N 60 MET cc_start: 0.7427 (ptt) cc_final: 0.6935 (ptt) REVERT: P 60 MET cc_start: 0.5857 (tpt) cc_final: 0.4051 (tpp) REVERT: R 60 MET cc_start: 0.5340 (mmm) cc_final: 0.5078 (mmm) REVERT: M 74 LEU cc_start: 0.8092 (mt) cc_final: 0.7630 (tt) REVERT: G 60 MET cc_start: 0.2561 (ttt) cc_final: 0.2238 (tmm) REVERT: H 37 GLU cc_start: 0.8207 (tt0) cc_final: 0.7696 (tm-30) REVERT: H 54 LEU cc_start: 0.6937 (mm) cc_final: 0.6326 (tp) REVERT: J 60 MET cc_start: 0.7497 (ttm) cc_final: 0.7256 (ttm) REVERT: J 72 LEU cc_start: 0.7011 (mt) cc_final: 0.6584 (pp) REVERT: I 48 LYS cc_start: 0.7321 (mttp) cc_final: 0.6929 (ttmt) REVERT: I 60 MET cc_start: 0.6162 (mmm) cc_final: 0.5935 (mmm) REVERT: E 219 MET cc_start: 0.7708 (mmm) cc_final: 0.7144 (mmm) REVERT: E 234 THR cc_start: 0.8304 (t) cc_final: 0.7971 (m) REVERT: E 274 MET cc_start: 0.8266 (mtm) cc_final: 0.8010 (mtp) REVERT: E 314 MET cc_start: 0.7956 (tpt) cc_final: 0.7502 (tpt) REVERT: E 402 ASP cc_start: 0.8196 (m-30) cc_final: 0.7436 (t70) REVERT: F 79 MET cc_start: 0.8368 (mmt) cc_final: 0.8000 (mmt) REVERT: F 118 VAL cc_start: 0.8792 (m) cc_final: 0.8270 (p) REVERT: F 305 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7291 (mt-10) REVERT: F 347 ASP cc_start: 0.8179 (m-30) cc_final: 0.7899 (m-30) REVERT: A 46 ASP cc_start: 0.8253 (t0) cc_final: 0.7822 (t0) REVERT: A 66 ASN cc_start: 0.8416 (m-40) cc_final: 0.8180 (m-40) REVERT: A 122 ILE cc_start: 0.8130 (mt) cc_final: 0.7825 (mt) REVERT: A 166 GLU cc_start: 0.8980 (tp30) cc_final: 0.8604 (tp30) REVERT: A 167 LEU cc_start: 0.9057 (tt) cc_final: 0.8264 (tp) REVERT: A 251 MET cc_start: 0.8749 (ttm) cc_final: 0.8522 (ttm) REVERT: A 436 MET cc_start: 0.8261 (ppp) cc_final: 0.7802 (ppp) REVERT: B 168 ILE cc_start: 0.9243 (mm) cc_final: 0.9024 (mm) REVERT: B 490 LEU cc_start: 0.9226 (mt) cc_final: 0.9025 (mt) REVERT: C 48 VAL cc_start: 0.8833 (t) cc_final: 0.8606 (p) REVERT: C 70 ASN cc_start: 0.7255 (m-40) cc_final: 0.6917 (m-40) REVERT: C 154 ILE cc_start: 0.8725 (mp) cc_final: 0.8392 (tp) REVERT: C 172 ARG cc_start: 0.8566 (ppt170) cc_final: 0.8158 (ppt170) REVERT: C 176 LYS cc_start: 0.8854 (mtmt) cc_final: 0.8493 (mtmm) REVERT: C 194 CYS cc_start: 0.7763 (m) cc_final: 0.7281 (m) REVERT: C 230 ASP cc_start: 0.6831 (p0) cc_final: 0.6468 (p0) REVERT: C 231 SER cc_start: 0.9098 (p) cc_final: 0.8825 (t) REVERT: C 258 LEU cc_start: 0.8961 (tp) cc_final: 0.8731 (tp) REVERT: C 275 SER cc_start: 0.9121 (p) cc_final: 0.8629 (t) REVERT: C 344 PHE cc_start: 0.8533 (m-80) cc_final: 0.8197 (m-80) REVERT: C 451 LEU cc_start: 0.8158 (mm) cc_final: 0.7948 (tt) REVERT: C 455 ARG cc_start: 0.6943 (tpp-160) cc_final: 0.6709 (tpp-160) REVERT: D 171 PHE cc_start: 0.8877 (m-80) cc_final: 0.8503 (m-10) REVERT: D 204 GLU cc_start: 0.7113 (pt0) cc_final: 0.6662 (pt0) REVERT: D 247 MET cc_start: 0.8024 (ttp) cc_final: 0.7809 (ttp) outliers start: 1 outliers final: 0 residues processed: 787 average time/residue: 0.1970 time to fit residues: 262.4469 Evaluate side-chains 580 residues out of total 4106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 580 time to evaluate : 1.626 ------------------------------------------------------------------------------- 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: 7.9990 chunk 459 optimal weight: 0.9980 chunk 501 optimal weight: 0.9990 chunk 219 optimal weight: 9.9990 chunk 170 optimal weight: 4.9990 chunk 402 optimal weight: 5.9990 chunk 321 optimal weight: 0.0000 chunk 141 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 chunk 293 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 180 ASN g 301 ASN g 303 GLN ** 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** J 42 GLN ** I 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 GLN F 60 ASN F 325 GLN ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.121504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.098519 restraints weight = 118886.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.098164 restraints weight = 102807.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.098868 restraints weight = 70978.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.099009 restraints weight = 61747.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.099222 restraints weight = 55436.438| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.8448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.270 39808 Z= 0.374 Angle : 0.925 35.545 53954 Z= 0.504 Chirality : 0.066 3.119 6456 Planarity : 0.006 0.139 6961 Dihedral : 6.505 76.921 5682 Min Nonbonded Distance : 1.419 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.65 % Favored : 96.08 % Rotamer: Outliers : 0.02 % Allowed : 0.54 % Favored : 99.44 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.12), residues: 5149 helix: 0.83 (0.10), residues: 2920 sheet: -0.87 (0.20), residues: 616 loop : -0.70 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG A 16 TYR 0.035 0.002 TYR b 124 PHE 0.098 0.002 PHE b 95 TRP 0.019 0.002 TRP a 117 HIS 0.017 0.001 HIS a 36 Details of bonding type rmsd covalent geometry : bond 0.00600 (39778) covalent geometry : angle 0.91096 (53943) SS BOND : bond 0.00098 ( 1) SS BOND : angle 0.93759 ( 2) hydrogen bonds : bond 0.09242 ( 2442) hydrogen bonds : angle 5.50091 ( 7176) Misc. bond : bond 0.02533 ( 26) link_TRANS : bond 0.02564 ( 3) link_TRANS : angle 12.48333 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6893.55 seconds wall clock time: 119 minutes 48.63 seconds (7188.63 seconds total)