Starting phenix.real_space_refine on Tue Mar 3 19:37:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tas_10426/03_2026/6tas_10426.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tas_10426/03_2026/6tas_10426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tas_10426/03_2026/6tas_10426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tas_10426/03_2026/6tas_10426.map" model { file = "/net/cci-nas-00/data/ceres_data/6tas_10426/03_2026/6tas_10426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tas_10426/03_2026/6tas_10426.cif" } resolution = 2.75 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= 0.001 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 24 5.16 5 C 5412 2.51 5 N 1508 2.21 5 O 1606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8552 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "B" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1347 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "C" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1356 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 4, 'TRANS': 161} Chain: "G" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 233 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "D" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "E" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1347 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "F" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1356 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 4, 'TRANS': 161} Chain: "H" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 233 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4073 SG CYS G 227 66.952 25.150 72.746 1.00119.70 S ATOM 4098 SG CYS G 230 67.250 28.326 70.975 1.00110.74 S ATOM 4180 SG CYS G 240 63.716 27.219 71.933 1.00141.84 S ATOM 8348 SG CYS H 227 68.651 25.134 58.063 1.00119.70 S ATOM 8373 SG CYS H 230 68.384 28.313 59.924 1.00110.74 S ATOM 8455 SG CYS H 240 71.913 27.194 58.968 1.00141.84 S Time building chain proxies: 2.04, per 1000 atoms: 0.24 Number of scatterers: 8552 At special positions: 0 Unit cell: (136.843, 65.394, 131.999, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 24 16.00 O 1606 8.00 N 1508 7.00 C 5412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 323.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" NE2 HIS G 235 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 227 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 230 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 240 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS H 235 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 230 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 240 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 227 " Number of angles added : 6 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 0 sheets defined 63.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 57 through 75 removed outlier: 3.673A pdb=" N VAL A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 75 " --> pdb=" O TYR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 removed outlier: 3.555A pdb=" N LYS A 84 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER A 87 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.737A pdb=" N THR A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 101 " --> pdb=" O TRP A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.764A pdb=" N ALA A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A 112 " --> pdb=" O TRP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 removed outlier: 3.740A pdb=" N ILE A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 153 Processing helix chain 'A' and resid 154 through 157 removed outlier: 3.971A pdb=" N LEU A 157 " --> pdb=" O LEU A 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 157' Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 176 through 181 removed outlier: 3.518A pdb=" N LYS A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 203 removed outlier: 3.685A pdb=" N GLU A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 76 removed outlier: 3.519A pdb=" N GLY B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 83 removed outlier: 3.536A pdb=" N LEU B 83 " --> pdb=" O ASP B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 89 removed outlier: 4.554A pdb=" N SER B 87 " --> pdb=" O LYS B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 101 removed outlier: 3.522A pdb=" N THR B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 124 through 133 removed outlier: 4.292A pdb=" N ILE B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 133 " --> pdb=" O TYR B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 153 removed outlier: 3.622A pdb=" N PHE B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 172 removed outlier: 3.530A pdb=" N PHE B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 181 removed outlier: 3.563A pdb=" N ARG B 180 " --> pdb=" O ASN B 176 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 181 " --> pdb=" O ILE B 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 176 through 181' Processing helix chain 'B' and resid 184 through 188 removed outlier: 3.927A pdb=" N VAL B 188 " --> pdb=" O ARG B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 205 removed outlier: 4.104A pdb=" N LEU B 194 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 195 " --> pdb=" O PHE B 191 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU B 196 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 75 Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.885A pdb=" N ILE C 86 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER C 87 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 88 " --> pdb=" O GLY C 85 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 101 Processing helix chain 'C' and resid 107 through 120 Processing helix chain 'C' and resid 124 through 133 removed outlier: 3.809A pdb=" N ILE C 128 " --> pdb=" O PRO C 124 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE C 133 " --> pdb=" O TYR C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 155 removed outlier: 3.609A pdb=" N PHE C 146 " --> pdb=" O PRO C 142 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 176 through 181 removed outlier: 3.520A pdb=" N ARG C 180 " --> pdb=" O ASN C 176 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS C 181 " --> pdb=" O ILE C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 176 through 181' Processing helix chain 'C' and resid 190 through 204 removed outlier: 3.969A pdb=" N LEU C 194 " --> pdb=" O THR C 190 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU C 196 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN C 204 " --> pdb=" O ILE C 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 245 Processing helix chain 'D' and resid 57 through 75 removed outlier: 3.674A pdb=" N VAL D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU D 75 " --> pdb=" O TYR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 89 removed outlier: 3.554A pdb=" N LYS D 84 " --> pdb=" O ASN D 81 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER D 87 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 removed outlier: 3.738A pdb=" N THR D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D 101 " --> pdb=" O TRP D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 119 removed outlier: 3.764A pdb=" N ALA D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE D 112 " --> pdb=" O TRP D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 132 removed outlier: 3.738A pdb=" N ILE D 128 " --> pdb=" O PRO D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 153 Processing helix chain 'D' and resid 154 through 157 removed outlier: 3.971A pdb=" N LEU D 157 " --> pdb=" O LEU D 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 154 through 157' Processing helix chain 'D' and resid 163 through 172 Processing helix chain 'D' and resid 176 through 181 removed outlier: 3.518A pdb=" N LYS D 181 " --> pdb=" O ILE D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 203 removed outlier: 3.685A pdb=" N GLU D 196 " --> pdb=" O LYS D 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 76 removed outlier: 3.520A pdb=" N GLY E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.535A pdb=" N LEU E 83 " --> pdb=" O ASP E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 89 removed outlier: 4.554A pdb=" N SER E 87 " --> pdb=" O LYS E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 101 removed outlier: 3.523A pdb=" N THR E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 120 Processing helix chain 'E' and resid 124 through 133 removed outlier: 4.291A pdb=" N ILE E 128 " --> pdb=" O PRO E 124 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR E 129 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE E 133 " --> pdb=" O TYR E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 153 removed outlier: 3.621A pdb=" N PHE E 146 " --> pdb=" O PRO E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 172 removed outlier: 3.530A pdb=" N PHE E 172 " --> pdb=" O LEU E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 181 removed outlier: 3.563A pdb=" N ARG E 180 " --> pdb=" O ASN E 176 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS E 181 " --> pdb=" O ILE E 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 176 through 181' Processing helix chain 'E' and resid 184 through 188 removed outlier: 3.927A pdb=" N VAL E 188 " --> pdb=" O ARG E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 205 removed outlier: 4.104A pdb=" N LEU E 194 " --> pdb=" O THR E 190 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU E 195 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU E 196 " --> pdb=" O LYS E 192 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 80 through 90 removed outlier: 3.884A pdb=" N ILE F 86 " --> pdb=" O LEU F 83 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER F 87 " --> pdb=" O LYS F 84 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU F 88 " --> pdb=" O GLY F 85 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE F 90 " --> pdb=" O SER F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 101 Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 124 through 133 removed outlier: 3.809A pdb=" N ILE F 128 " --> pdb=" O PRO F 124 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE F 133 " --> pdb=" O TYR F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 155 removed outlier: 3.609A pdb=" N PHE F 146 " --> pdb=" O PRO F 142 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA F 155 " --> pdb=" O ARG F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 172 Processing helix chain 'F' and resid 176 through 181 removed outlier: 3.521A pdb=" N ARG F 180 " --> pdb=" O ASN F 176 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS F 181 " --> pdb=" O ILE F 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 176 through 181' Processing helix chain 'F' and resid 190 through 204 removed outlier: 3.814A pdb=" N LEU F 194 " --> pdb=" O THR F 190 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU F 196 " --> pdb=" O LYS F 192 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN F 204 " --> pdb=" O ILE F 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 245 343 hydrogen bonds defined for protein. 957 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: 1.00 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1450 1.31 - 1.43: 2492 1.43 - 1.56: 4776 1.56 - 1.69: 0 1.69 - 1.82: 36 Bond restraints: 8754 Sorted by residual: bond pdb=" C HIS F 189 " pdb=" O HIS F 189 " ideal model delta sigma weight residual 1.235 1.180 0.055 1.26e-02 6.30e+03 1.89e+01 bond pdb=" C PRO D 121 " pdb=" O PRO D 121 " ideal model delta sigma weight residual 1.232 1.190 0.043 1.20e-02 6.94e+03 1.26e+01 bond pdb=" N HIS H 235 " pdb=" CA HIS H 235 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.19e-02 7.06e+03 1.24e+01 bond pdb=" N PHE A 133 " pdb=" CA PHE A 133 " ideal model delta sigma weight residual 1.456 1.498 -0.041 1.23e-02 6.61e+03 1.13e+01 bond pdb=" N CYS B 48 " pdb=" CA CYS B 48 " ideal model delta sigma weight residual 1.454 1.498 -0.044 1.34e-02 5.57e+03 1.09e+01 ... (remaining 8749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 11513 2.55 - 5.09: 249 5.09 - 7.64: 32 7.64 - 10.19: 3 10.19 - 12.73: 1 Bond angle restraints: 11798 Sorted by residual: angle pdb=" O HIS F 186 " pdb=" C HIS F 186 " pdb=" N SER F 187 " ideal model delta sigma weight residual 122.03 130.38 -8.35 1.04e+00 9.25e-01 6.45e+01 angle pdb=" CA HIS D 118 " pdb=" CB HIS D 118 " pdb=" CG HIS D 118 " ideal model delta sigma weight residual 113.80 120.42 -6.62 1.00e+00 1.00e+00 4.39e+01 angle pdb=" N HIS H 235 " pdb=" CA HIS H 235 " pdb=" C HIS H 235 " ideal model delta sigma weight residual 107.88 116.05 -8.17 1.41e+00 5.03e-01 3.36e+01 angle pdb=" CB ARG G 233 " pdb=" CG ARG G 233 " pdb=" CD ARG G 233 " ideal model delta sigma weight residual 111.30 124.03 -12.73 2.30e+00 1.89e-01 3.06e+01 angle pdb=" CA HIS F 186 " pdb=" C HIS F 186 " pdb=" N SER F 187 " ideal model delta sigma weight residual 116.92 110.62 6.30 1.16e+00 7.43e-01 2.95e+01 ... (remaining 11793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.88: 4318 14.88 - 29.76: 615 29.76 - 44.64: 188 44.64 - 59.52: 27 59.52 - 74.40: 6 Dihedral angle restraints: 5154 sinusoidal: 2146 harmonic: 3008 Sorted by residual: dihedral pdb=" C THR C 190 " pdb=" N THR C 190 " pdb=" CA THR C 190 " pdb=" CB THR C 190 " ideal model delta harmonic sigma weight residual -122.00 -134.93 12.93 0 2.50e+00 1.60e-01 2.67e+01 dihedral pdb=" C PHE A 133 " pdb=" N PHE A 133 " pdb=" CA PHE A 133 " pdb=" CB PHE A 133 " ideal model delta harmonic sigma weight residual -122.60 -134.25 11.65 0 2.50e+00 1.60e-01 2.17e+01 dihedral pdb=" N THR C 190 " pdb=" C THR C 190 " pdb=" CA THR C 190 " pdb=" CB THR C 190 " ideal model delta harmonic sigma weight residual 123.40 134.19 -10.79 0 2.50e+00 1.60e-01 1.86e+01 ... (remaining 5151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1129 0.083 - 0.165: 92 0.165 - 0.248: 8 0.248 - 0.330: 4 0.330 - 0.413: 3 Chirality restraints: 1236 Sorted by residual: chirality pdb=" CA THR C 190 " pdb=" N THR C 190 " pdb=" C THR C 190 " pdb=" CB THR C 190 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA HIS F 189 " pdb=" N HIS F 189 " pdb=" C HIS F 189 " pdb=" CB HIS F 189 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CA PHE A 133 " pdb=" N PHE A 133 " pdb=" C PHE A 133 " pdb=" CB PHE A 133 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 1233 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS F 186 " -0.019 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C HIS F 186 " 0.073 2.00e-02 2.50e+03 pdb=" O HIS F 186 " -0.029 2.00e-02 2.50e+03 pdb=" N SER F 187 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 232 " 0.018 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C PHE G 232 " -0.068 2.00e-02 2.50e+03 pdb=" O PHE G 232 " 0.027 2.00e-02 2.50e+03 pdb=" N ARG G 233 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS G 230 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C CYS G 230 " 0.067 2.00e-02 2.50e+03 pdb=" O CYS G 230 " -0.025 2.00e-02 2.50e+03 pdb=" N SER G 231 " -0.023 2.00e-02 2.50e+03 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 71 2.66 - 3.22: 7804 3.22 - 3.78: 10856 3.78 - 4.34: 13552 4.34 - 4.90: 22148 Nonbonded interactions: 54431 Sorted by model distance: nonbonded pdb=" OD1 ASP D 163 " pdb=" N GLU D 164 " model vdw 2.094 3.120 nonbonded pdb=" OD1 ASP A 163 " pdb=" N GLU A 164 " model vdw 2.095 3.120 nonbonded pdb=" OE2 GLU F 164 " pdb=" CD2 PHE F 191 " model vdw 2.232 3.340 nonbonded pdb=" NH1 ARG B 56 " pdb=" OD2 ASP C 144 " model vdw 2.263 3.120 nonbonded pdb=" NH1 ARG E 56 " pdb=" OD2 ASP F 144 " model vdw 2.264 3.120 ... (remaining 54426 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 41 through 204) selection = (chain 'C' and resid 41 through 204) selection = chain 'D' selection = (chain 'E' and resid 41 through 204) selection = (chain 'F' and resid 41 through 204) } ncs_group { reference = chain 'G' selection = chain 'H' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.230 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.810 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 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 : 0.006 0.055 8762 Z= 0.404 Angle : 0.874 12.733 11804 Z= 0.594 Chirality : 0.055 0.413 1236 Planarity : 0.005 0.044 1536 Dihedral : 14.836 74.403 3214 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 0.11 % Allowed : 6.55 % Favored : 93.34 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.24), residues: 1028 helix: -1.54 (0.17), residues: 498 sheet: None (None), residues: 0 loop : 0.08 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 233 TYR 0.016 0.002 TYR A 126 PHE 0.017 0.001 PHE B 191 TRP 0.017 0.002 TRP B 108 HIS 0.018 0.001 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00621 ( 8754) covalent geometry : angle 0.86576 (11798) hydrogen bonds : bond 0.21047 ( 343) hydrogen bonds : angle 5.56358 ( 957) metal coordination : bond 0.03255 ( 8) metal coordination : angle 5.50583 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.318 Fit side-chains REVERT: B 44 ASN cc_start: 0.9079 (p0) cc_final: 0.8767 (p0) REVERT: B 71 TYR cc_start: 0.7119 (t80) cc_final: 0.6669 (t80) REVERT: B 102 ARG cc_start: 0.7937 (ttm-80) cc_final: 0.7460 (tmm-80) REVERT: B 134 GLN cc_start: 0.7733 (tp40) cc_final: 0.7175 (tm130) REVERT: C 77 ILE cc_start: 0.9147 (pt) cc_final: 0.8944 (pp) REVERT: C 137 GLN cc_start: 0.8352 (tt0) cc_final: 0.8149 (tt0) REVERT: C 141 ASP cc_start: 0.8107 (m-30) cc_final: 0.7781 (m-30) REVERT: C 188 VAL cc_start: 0.6506 (OUTLIER) cc_final: 0.6304 (p) REVERT: C 196 GLU cc_start: 0.7474 (tt0) cc_final: 0.6961 (tt0) REVERT: C 202 GLU cc_start: 0.8285 (tt0) cc_final: 0.7408 (tp30) REVERT: D 80 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8039 (tm-30) REVERT: D 86 ILE cc_start: 0.8198 (tp) cc_final: 0.7995 (tp) REVERT: D 141 ASP cc_start: 0.7822 (m-30) cc_final: 0.7365 (m-30) REVERT: E 134 GLN cc_start: 0.7578 (tp40) cc_final: 0.7079 (tt0) REVERT: F 79 ASP cc_start: 0.8332 (t0) cc_final: 0.8043 (t0) REVERT: F 80 GLU cc_start: 0.8443 (pp20) cc_final: 0.8035 (tm-30) REVERT: F 102 ARG cc_start: 0.8587 (ttp-110) cc_final: 0.8316 (ttm170) REVERT: F 202 GLU cc_start: 0.8394 (tt0) cc_final: 0.7865 (tp30) outliers start: 1 outliers final: 1 residues processed: 144 average time/residue: 0.5025 time to fit residues: 77.3229 Evaluate side-chains 102 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 188 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.0270 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.0040 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 4.9990 overall best weight: 0.3052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS B 99 GLN B 137 GLN B 162 HIS B 186 HIS B 204 ASN C 197 GLN D 127 GLN D 135 ASN D 162 HIS E 99 GLN E 135 ASN E 137 GLN E 204 ASN F 197 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.139863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.126051 restraints weight = 14292.939| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.54 r_work: 0.3732 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8762 Z= 0.110 Angle : 0.523 8.844 11804 Z= 0.283 Chirality : 0.036 0.172 1236 Planarity : 0.003 0.026 1536 Dihedral : 4.280 35.675 1129 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.62 % Allowed : 12.99 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.26), residues: 1028 helix: 0.45 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -0.06 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 56 TYR 0.007 0.001 TYR C 91 PHE 0.022 0.001 PHE H 237 TRP 0.012 0.001 TRP E 108 HIS 0.009 0.001 HIS E 203 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 8754) covalent geometry : angle 0.50962 (11798) hydrogen bonds : bond 0.04197 ( 343) hydrogen bonds : angle 3.69304 ( 957) metal coordination : bond 0.02173 ( 8) metal coordination : angle 5.19025 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.270 Fit side-chains REVERT: B 102 ARG cc_start: 0.7587 (ttm-80) cc_final: 0.7299 (tmm-80) REVERT: B 134 GLN cc_start: 0.7782 (tp40) cc_final: 0.7578 (tm-30) REVERT: C 135 ASN cc_start: 0.8887 (p0) cc_final: 0.8686 (p0) REVERT: C 137 GLN cc_start: 0.8297 (tt0) cc_final: 0.8087 (tt0) REVERT: C 141 ASP cc_start: 0.8215 (m-30) cc_final: 0.7944 (m-30) REVERT: C 196 GLU cc_start: 0.7433 (tt0) cc_final: 0.7077 (tt0) REVERT: C 201 ILE cc_start: 0.7885 (tp) cc_final: 0.7588 (tp) REVERT: C 202 GLU cc_start: 0.8380 (tt0) cc_final: 0.7795 (tp30) REVERT: D 141 ASP cc_start: 0.7786 (m-30) cc_final: 0.7478 (m-30) REVERT: F 181 LYS cc_start: 0.8602 (tmmt) cc_final: 0.8252 (ttpp) REVERT: F 200 ILE cc_start: 0.6858 (OUTLIER) cc_final: 0.6639 (tp) REVERT: F 202 GLU cc_start: 0.8535 (tt0) cc_final: 0.8326 (tp30) outliers start: 24 outliers final: 9 residues processed: 128 average time/residue: 0.4745 time to fit residues: 65.1297 Evaluate side-chains 104 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain G residue 237 PHE Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain F residue 200 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 0.4980 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 4 optimal weight: 0.0870 chunk 21 optimal weight: 0.2980 chunk 13 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 135 ASN A 137 GLN A 176 ASN B 186 HIS B 203 HIS C 58 HIS D 44 ASN D 135 ASN ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 HIS F 135 ASN H 248 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.137181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.123276 restraints weight = 14073.484| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.55 r_work: 0.3702 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8762 Z= 0.106 Angle : 0.492 9.076 11804 Z= 0.269 Chirality : 0.035 0.130 1236 Planarity : 0.003 0.026 1536 Dihedral : 3.896 17.290 1126 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.29 % Allowed : 19.00 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.27), residues: 1028 helix: 1.20 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -0.18 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 56 TYR 0.009 0.001 TYR C 126 PHE 0.013 0.001 PHE G 237 TRP 0.008 0.001 TRP E 108 HIS 0.009 0.001 HIS B 203 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 8754) covalent geometry : angle 0.47760 (11798) hydrogen bonds : bond 0.04341 ( 343) hydrogen bonds : angle 3.43226 ( 957) metal coordination : bond 0.01308 ( 8) metal coordination : angle 5.32488 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.308 Fit side-chains REVERT: A 120 SER cc_start: 0.7306 (t) cc_final: 0.6891 (p) REVERT: B 102 ARG cc_start: 0.7596 (ttm-80) cc_final: 0.7321 (tmm-80) REVERT: C 56 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.6240 (ttm110) REVERT: C 130 MET cc_start: 0.7911 (mmm) cc_final: 0.7537 (tpp) REVERT: C 141 ASP cc_start: 0.8203 (m-30) cc_final: 0.7946 (m-30) REVERT: C 196 GLU cc_start: 0.7604 (tt0) cc_final: 0.7193 (tt0) REVERT: C 202 GLU cc_start: 0.8404 (tt0) cc_final: 0.7834 (tp30) REVERT: D 131 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: D 137 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7040 (pt0) REVERT: D 141 ASP cc_start: 0.7576 (m-30) cc_final: 0.7248 (m-30) REVERT: F 181 LYS cc_start: 0.8582 (tmmt) cc_final: 0.8224 (ttpp) REVERT: F 202 GLU cc_start: 0.8568 (tt0) cc_final: 0.8341 (tp30) REVERT: H 248 GLN cc_start: 0.7381 (mp10) cc_final: 0.7167 (mp10) outliers start: 21 outliers final: 11 residues processed: 111 average time/residue: 0.4730 time to fit residues: 56.3401 Evaluate side-chains 103 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain F residue 135 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 80 optimal weight: 0.0470 chunk 97 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 186 HIS B 203 HIS D 44 ASN ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN E 203 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.133969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.119868 restraints weight = 14376.506| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.58 r_work: 0.3660 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8762 Z= 0.134 Angle : 0.508 7.461 11804 Z= 0.282 Chirality : 0.037 0.200 1236 Planarity : 0.003 0.027 1536 Dihedral : 3.955 15.449 1126 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.82 % Allowed : 20.63 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.27), residues: 1028 helix: 1.46 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -0.27 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 56 TYR 0.013 0.002 TYR E 126 PHE 0.027 0.002 PHE F 133 TRP 0.008 0.001 TRP E 108 HIS 0.006 0.001 HIS E 203 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8754) covalent geometry : angle 0.49840 (11798) hydrogen bonds : bond 0.05165 ( 343) hydrogen bonds : angle 3.49279 ( 957) metal coordination : bond 0.01055 ( 8) metal coordination : angle 4.32210 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 0.368 Fit side-chains REVERT: A 120 SER cc_start: 0.7767 (t) cc_final: 0.7446 (p) REVERT: B 102 ARG cc_start: 0.7640 (ttm-80) cc_final: 0.7361 (tmm-80) REVERT: B 172 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7535 (m-10) REVERT: C 56 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.6264 (ttm110) REVERT: C 130 MET cc_start: 0.7933 (mmm) cc_final: 0.7582 (tpp) REVERT: C 141 ASP cc_start: 0.8216 (m-30) cc_final: 0.7944 (m-30) REVERT: C 202 GLU cc_start: 0.8405 (tt0) cc_final: 0.7854 (tp30) REVERT: D 48 CYS cc_start: 0.7951 (t) cc_final: 0.7503 (m) REVERT: D 131 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: D 137 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7202 (pt0) REVERT: D 141 ASP cc_start: 0.7542 (m-30) cc_final: 0.7201 (m-30) REVERT: F 137 GLN cc_start: 0.8257 (tp40) cc_final: 0.7808 (tp40) REVERT: F 181 LYS cc_start: 0.8580 (tmmt) cc_final: 0.8280 (ttpp) REVERT: F 202 GLU cc_start: 0.8596 (tt0) cc_final: 0.8367 (tp30) outliers start: 35 outliers final: 13 residues processed: 117 average time/residue: 0.4624 time to fit residues: 58.2352 Evaluate side-chains 105 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 159 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 76 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 73 optimal weight: 0.0970 chunk 93 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 186 HIS B 203 HIS ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.133852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.119850 restraints weight = 14331.955| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.59 r_work: 0.3664 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8762 Z= 0.120 Angle : 0.485 6.915 11804 Z= 0.269 Chirality : 0.036 0.171 1236 Planarity : 0.003 0.029 1536 Dihedral : 3.902 15.714 1126 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.38 % Allowed : 20.74 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.27), residues: 1028 helix: 1.60 (0.24), residues: 524 sheet: None (None), residues: 0 loop : -0.35 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 56 TYR 0.011 0.001 TYR B 126 PHE 0.028 0.002 PHE E 133 TRP 0.008 0.001 TRP F 98 HIS 0.006 0.001 HIS E 203 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8754) covalent geometry : angle 0.47618 (11798) hydrogen bonds : bond 0.04750 ( 343) hydrogen bonds : angle 3.42590 ( 957) metal coordination : bond 0.00944 ( 8) metal coordination : angle 3.99998 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.292 Fit side-chains REVERT: A 120 SER cc_start: 0.7898 (t) cc_final: 0.7600 (p) REVERT: B 102 ARG cc_start: 0.7705 (ttm-80) cc_final: 0.7379 (tmm-80) REVERT: C 56 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.6283 (ttm110) REVERT: C 130 MET cc_start: 0.7884 (mmm) cc_final: 0.7507 (tpp) REVERT: C 141 ASP cc_start: 0.8219 (m-30) cc_final: 0.7953 (m-30) REVERT: C 196 GLU cc_start: 0.7761 (tt0) cc_final: 0.7385 (tt0) REVERT: C 202 GLU cc_start: 0.8394 (tt0) cc_final: 0.7833 (tp30) REVERT: D 48 CYS cc_start: 0.7977 (t) cc_final: 0.7489 (m) REVERT: D 131 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: D 137 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7212 (pt0) REVERT: D 141 ASP cc_start: 0.7584 (m-30) cc_final: 0.7256 (m-30) REVERT: F 130 MET cc_start: 0.7713 (mmm) cc_final: 0.7288 (tpp) REVERT: F 137 GLN cc_start: 0.8293 (tp40) cc_final: 0.7846 (tp40) REVERT: F 181 LYS cc_start: 0.8552 (tmmt) cc_final: 0.8245 (ttpp) REVERT: F 202 GLU cc_start: 0.8593 (tt0) cc_final: 0.8319 (tp30) outliers start: 31 outliers final: 15 residues processed: 116 average time/residue: 0.4703 time to fit residues: 58.5993 Evaluate side-chains 105 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 172 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 58 optimal weight: 0.0030 chunk 28 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 99 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 overall best weight: 2.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 186 HIS B 203 HIS ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.132290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.118600 restraints weight = 14951.824| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.49 r_work: 0.3648 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8762 Z= 0.154 Angle : 0.530 6.288 11804 Z= 0.294 Chirality : 0.038 0.121 1236 Planarity : 0.004 0.030 1536 Dihedral : 4.108 16.302 1126 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.60 % Allowed : 21.07 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.28), residues: 1028 helix: 1.58 (0.24), residues: 524 sheet: None (None), residues: 0 loop : -0.48 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 226 TYR 0.016 0.002 TYR E 126 PHE 0.019 0.002 PHE F 133 TRP 0.008 0.002 TRP C 98 HIS 0.006 0.001 HIS E 203 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8754) covalent geometry : angle 0.52364 (11798) hydrogen bonds : bond 0.05744 ( 343) hydrogen bonds : angle 3.56770 ( 957) metal coordination : bond 0.00789 ( 8) metal coordination : angle 3.55014 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.311 Fit side-chains REVERT: A 48 CYS cc_start: 0.7930 (t) cc_final: 0.7575 (m) REVERT: A 120 SER cc_start: 0.7769 (t) cc_final: 0.7518 (p) REVERT: B 102 ARG cc_start: 0.7635 (ttm-80) cc_final: 0.7380 (tmm-80) REVERT: B 135 ASN cc_start: 0.7990 (m-40) cc_final: 0.7689 (m110) REVERT: C 56 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.6652 (ttm110) REVERT: C 130 MET cc_start: 0.7677 (mmm) cc_final: 0.7406 (tpp) REVERT: C 141 ASP cc_start: 0.8243 (m-30) cc_final: 0.7984 (m-30) REVERT: C 196 GLU cc_start: 0.7773 (tt0) cc_final: 0.7393 (tt0) REVERT: C 202 GLU cc_start: 0.8192 (tt0) cc_final: 0.7703 (tp30) REVERT: G 226 ARG cc_start: 0.7732 (mtt90) cc_final: 0.7350 (mtp85) REVERT: D 48 CYS cc_start: 0.8059 (t) cc_final: 0.7479 (m) REVERT: D 131 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7770 (tt0) REVERT: D 137 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7381 (pt0) REVERT: E 42 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7362 (mtpt) REVERT: E 134 GLN cc_start: 0.7395 (tt0) cc_final: 0.7068 (tm-30) REVERT: F 130 MET cc_start: 0.7739 (mmm) cc_final: 0.7293 (tpp) REVERT: F 137 GLN cc_start: 0.8258 (tp40) cc_final: 0.7853 (tp40) REVERT: F 181 LYS cc_start: 0.8467 (tmmt) cc_final: 0.8196 (ttpp) REVERT: F 202 GLU cc_start: 0.8496 (tt0) cc_final: 0.8291 (tp30) outliers start: 33 outliers final: 18 residues processed: 118 average time/residue: 0.4821 time to fit residues: 60.8201 Evaluate side-chains 116 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 172 PHE Chi-restraints excluded: chain F residue 118 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 1.9990 chunk 17 optimal weight: 0.0370 chunk 20 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 73 optimal weight: 0.4980 chunk 60 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 186 HIS B 203 HIS ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.135707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.122042 restraints weight = 14952.330| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.49 r_work: 0.3698 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8762 Z= 0.107 Angle : 0.484 8.115 11804 Z= 0.264 Chirality : 0.036 0.270 1236 Planarity : 0.003 0.028 1536 Dihedral : 3.833 17.747 1126 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.17 % Allowed : 21.83 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.28), residues: 1028 helix: 1.74 (0.24), residues: 524 sheet: None (None), residues: 0 loop : -0.49 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 102 TYR 0.009 0.001 TYR C 126 PHE 0.012 0.001 PHE D 64 TRP 0.009 0.001 TRP C 98 HIS 0.006 0.001 HIS E 203 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8754) covalent geometry : angle 0.47701 (11798) hydrogen bonds : bond 0.04177 ( 343) hydrogen bonds : angle 3.40663 ( 957) metal coordination : bond 0.00824 ( 8) metal coordination : angle 3.56872 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.280 Fit side-chains REVERT: A 48 CYS cc_start: 0.7626 (t) cc_final: 0.7419 (m) REVERT: A 101 VAL cc_start: 0.9158 (t) cc_final: 0.8936 (m) REVERT: A 120 SER cc_start: 0.7537 (t) cc_final: 0.7274 (p) REVERT: B 134 GLN cc_start: 0.7634 (tm-30) cc_final: 0.7388 (tm-30) REVERT: C 130 MET cc_start: 0.7554 (mmm) cc_final: 0.7274 (tpp) REVERT: C 141 ASP cc_start: 0.8132 (m-30) cc_final: 0.7864 (m-30) REVERT: C 196 GLU cc_start: 0.7722 (tt0) cc_final: 0.7368 (tt0) REVERT: C 202 GLU cc_start: 0.8291 (tt0) cc_final: 0.7810 (tp30) REVERT: G 226 ARG cc_start: 0.7785 (mtt90) cc_final: 0.7403 (mtp85) REVERT: D 48 CYS cc_start: 0.7829 (t) cc_final: 0.7399 (m) REVERT: D 137 GLN cc_start: 0.7935 (pp30) cc_final: 0.7255 (pt0) REVERT: F 130 MET cc_start: 0.7664 (mmm) cc_final: 0.7264 (tpp) REVERT: F 137 GLN cc_start: 0.8168 (tp40) cc_final: 0.7829 (tp40) REVERT: F 181 LYS cc_start: 0.8457 (tmmt) cc_final: 0.8219 (ttpp) outliers start: 29 outliers final: 15 residues processed: 112 average time/residue: 0.4736 time to fit residues: 56.9882 Evaluate side-chains 105 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 172 PHE Chi-restraints excluded: chain F residue 118 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 60 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 64 optimal weight: 0.0770 chunk 1 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 137 GLN B 186 HIS B 203 HIS ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.132746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.119226 restraints weight = 14802.968| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.45 r_work: 0.3653 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8762 Z= 0.150 Angle : 0.521 8.401 11804 Z= 0.286 Chirality : 0.037 0.118 1236 Planarity : 0.003 0.028 1536 Dihedral : 3.977 16.645 1126 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.62 % Allowed : 23.25 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.28), residues: 1028 helix: 1.67 (0.24), residues: 524 sheet: None (None), residues: 0 loop : -0.53 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 102 TYR 0.015 0.002 TYR E 126 PHE 0.017 0.002 PHE D 132 TRP 0.008 0.001 TRP F 98 HIS 0.007 0.001 HIS E 203 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8754) covalent geometry : angle 0.51498 (11798) hydrogen bonds : bond 0.05454 ( 343) hydrogen bonds : angle 3.52927 ( 957) metal coordination : bond 0.00784 ( 8) metal coordination : angle 3.46349 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.341 Fit side-chains REVERT: A 48 CYS cc_start: 0.7864 (t) cc_final: 0.7532 (m) REVERT: A 120 SER cc_start: 0.7784 (t) cc_final: 0.7551 (p) REVERT: B 134 GLN cc_start: 0.7709 (tm-30) cc_final: 0.7420 (tm-30) REVERT: C 130 MET cc_start: 0.7619 (mmm) cc_final: 0.7362 (tpp) REVERT: C 141 ASP cc_start: 0.8236 (m-30) cc_final: 0.7952 (m-30) REVERT: C 196 GLU cc_start: 0.7753 (tt0) cc_final: 0.7383 (tt0) REVERT: C 202 GLU cc_start: 0.8171 (tt0) cc_final: 0.7717 (tp30) REVERT: G 226 ARG cc_start: 0.7787 (mtt90) cc_final: 0.7489 (mtp85) REVERT: D 48 CYS cc_start: 0.8031 (t) cc_final: 0.7480 (m) REVERT: D 137 GLN cc_start: 0.7969 (pp30) cc_final: 0.7322 (pt0) REVERT: F 130 MET cc_start: 0.7663 (mmm) cc_final: 0.7271 (tpp) REVERT: F 137 GLN cc_start: 0.8045 (tp40) cc_final: 0.7707 (tp40) REVERT: F 181 LYS cc_start: 0.8418 (tmmt) cc_final: 0.8182 (ttpp) outliers start: 24 outliers final: 18 residues processed: 111 average time/residue: 0.4727 time to fit residues: 56.3579 Evaluate side-chains 110 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 172 PHE Chi-restraints excluded: chain F residue 118 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 14 optimal weight: 0.0970 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 73 optimal weight: 0.5980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 135 ASN B 186 HIS B 203 HIS ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.134898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.121355 restraints weight = 14897.346| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.46 r_work: 0.3679 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8762 Z= 0.110 Angle : 0.485 7.948 11804 Z= 0.267 Chirality : 0.037 0.329 1236 Planarity : 0.003 0.027 1536 Dihedral : 3.772 18.034 1126 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.62 % Allowed : 23.25 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.28), residues: 1028 helix: 1.77 (0.24), residues: 526 sheet: None (None), residues: 0 loop : -0.49 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 102 TYR 0.010 0.001 TYR C 126 PHE 0.016 0.001 PHE H 237 TRP 0.009 0.001 TRP C 98 HIS 0.006 0.001 HIS E 203 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8754) covalent geometry : angle 0.47866 (11798) hydrogen bonds : bond 0.04198 ( 343) hydrogen bonds : angle 3.39800 ( 957) metal coordination : bond 0.00831 ( 8) metal coordination : angle 3.48115 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.320 Fit side-chains REVERT: A 48 CYS cc_start: 0.7810 (t) cc_final: 0.7247 (m) REVERT: A 120 SER cc_start: 0.7606 (t) cc_final: 0.7367 (p) REVERT: B 134 GLN cc_start: 0.7690 (tm-30) cc_final: 0.7366 (tm-30) REVERT: C 130 MET cc_start: 0.7524 (mmm) cc_final: 0.7279 (tpp) REVERT: C 141 ASP cc_start: 0.8187 (m-30) cc_final: 0.7918 (m-30) REVERT: C 196 GLU cc_start: 0.7614 (tt0) cc_final: 0.7239 (mt-10) REVERT: C 202 GLU cc_start: 0.8202 (tt0) cc_final: 0.7762 (tp30) REVERT: G 226 ARG cc_start: 0.7833 (mtt90) cc_final: 0.7562 (mtp85) REVERT: D 48 CYS cc_start: 0.7975 (t) cc_final: 0.7465 (m) REVERT: D 131 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7458 (tt0) REVERT: D 137 GLN cc_start: 0.7875 (pp30) cc_final: 0.7205 (pt0) REVERT: F 130 MET cc_start: 0.7703 (mmm) cc_final: 0.7261 (tpp) REVERT: F 137 GLN cc_start: 0.7933 (tp40) cc_final: 0.7660 (tp40) REVERT: F 181 LYS cc_start: 0.8405 (tmmt) cc_final: 0.8188 (ttpp) outliers start: 24 outliers final: 18 residues processed: 108 average time/residue: 0.5072 time to fit residues: 58.5775 Evaluate side-chains 110 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 172 PHE Chi-restraints excluded: chain F residue 118 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 156 GLN B 186 HIS B 203 HIS ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.132230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.118689 restraints weight = 14887.425| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.48 r_work: 0.3629 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8762 Z= 0.158 Angle : 0.535 8.022 11804 Z= 0.295 Chirality : 0.038 0.119 1236 Planarity : 0.004 0.028 1536 Dihedral : 3.997 17.413 1126 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.62 % Allowed : 23.47 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.28), residues: 1028 helix: 1.70 (0.24), residues: 524 sheet: None (None), residues: 0 loop : -0.54 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 102 TYR 0.015 0.002 TYR E 126 PHE 0.017 0.002 PHE D 132 TRP 0.008 0.001 TRP F 98 HIS 0.007 0.001 HIS E 203 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 8754) covalent geometry : angle 0.52963 (11798) hydrogen bonds : bond 0.05575 ( 343) hydrogen bonds : angle 3.56745 ( 957) metal coordination : bond 0.00764 ( 8) metal coordination : angle 3.41148 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.309 Fit side-chains REVERT: A 48 CYS cc_start: 0.7886 (t) cc_final: 0.7543 (m) REVERT: A 120 SER cc_start: 0.7793 (t) cc_final: 0.7587 (p) REVERT: B 134 GLN cc_start: 0.7787 (tm-30) cc_final: 0.7486 (tm-30) REVERT: C 130 MET cc_start: 0.7612 (mmm) cc_final: 0.7384 (tpp) REVERT: C 141 ASP cc_start: 0.8222 (m-30) cc_final: 0.7928 (m-30) REVERT: C 196 GLU cc_start: 0.7758 (tt0) cc_final: 0.7372 (tt0) REVERT: C 202 GLU cc_start: 0.8145 (tt0) cc_final: 0.7726 (tp30) REVERT: G 226 ARG cc_start: 0.7784 (mtt90) cc_final: 0.7501 (mtp85) REVERT: D 48 CYS cc_start: 0.8041 (t) cc_final: 0.7466 (m) REVERT: D 131 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7522 (tt0) REVERT: D 137 GLN cc_start: 0.7968 (pp30) cc_final: 0.7354 (pt0) REVERT: E 42 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7399 (mtpt) REVERT: F 130 MET cc_start: 0.7738 (mmm) cc_final: 0.7271 (tpp) REVERT: F 137 GLN cc_start: 0.8028 (tp40) cc_final: 0.7721 (tp40) REVERT: F 181 LYS cc_start: 0.8418 (tmmt) cc_final: 0.8187 (ttpp) outliers start: 24 outliers final: 16 residues processed: 111 average time/residue: 0.4586 time to fit residues: 54.8748 Evaluate side-chains 111 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 172 PHE Chi-restraints excluded: chain F residue 118 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 0.0270 chunk 58 optimal weight: 0.1980 chunk 94 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 156 GLN B 186 HIS B 203 HIS D 44 ASN ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN E 203 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.136915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.123625 restraints weight = 14686.306| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.44 r_work: 0.3731 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8762 Z= 0.098 Angle : 0.471 7.385 11804 Z= 0.259 Chirality : 0.035 0.300 1236 Planarity : 0.003 0.026 1536 Dihedral : 3.594 17.813 1126 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.97 % Allowed : 24.34 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.28), residues: 1028 helix: 1.76 (0.24), residues: 538 sheet: None (None), residues: 0 loop : -0.52 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 102 TYR 0.008 0.001 TYR C 126 PHE 0.012 0.001 PHE A 64 TRP 0.010 0.001 TRP C 98 HIS 0.006 0.001 HIS E 203 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 8754) covalent geometry : angle 0.46384 (11798) hydrogen bonds : bond 0.03420 ( 343) hydrogen bonds : angle 3.34029 ( 957) metal coordination : bond 0.00918 ( 8) metal coordination : angle 3.55221 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2325.26 seconds wall clock time: 40 minutes 18.52 seconds (2418.52 seconds total)