Starting phenix.real_space_refine on Wed Mar 12 22:14:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tas_10426/03_2025/6tas_10426.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tas_10426/03_2025/6tas_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_2025/6tas_10426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tas_10426/03_2025/6tas_10426.map" model { file = "/net/cci-nas-00/data/ceres_data/6tas_10426/03_2025/6tas_10426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tas_10426/03_2025/6tas_10426.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.43, per 1000 atoms: 0.63 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: 1.87 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.80 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: 1.85 Time building geometry restraints manager: 2.22 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: 0.03 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: 0.180 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.500 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:13.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.280 ------------------------------------------------------------------------------- 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 8754 Z= 0.404 Angle : 0.866 12.733 11798 Z= 0.593 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (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 TRP 0.017 0.002 TRP B 108 HIS 0.018 0.001 HIS D 118 PHE 0.017 0.001 PHE B 191 TYR 0.016 0.002 TYR A 126 ARG 0.003 0.000 ARG G 233 *********************** 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 : 0.973 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: 0.7366 (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: 1.2773 time to fit residues: 197.4803 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 : 2.337 ------------------------------------------------------------------------------- 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 84 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 186 HIS B 204 ASN C 197 GLN D 44 ASN D 127 GLN D 135 ASN D 137 GLN D 156 GLN D 162 HIS E 99 GLN E 137 GLN E 203 HIS E 204 ASN F 197 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.131611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.117904 restraints weight = 14629.152| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.45 r_work: 0.3633 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8754 Z= 0.312 Angle : 0.620 7.979 11798 Z= 0.348 Chirality : 0.042 0.197 1236 Planarity : 0.004 0.032 1536 Dihedral : 4.796 30.993 1129 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.95 % Allowed : 17.90 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.26), residues: 1028 helix: 0.22 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -0.22 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 108 HIS 0.010 0.001 HIS E 203 PHE 0.031 0.003 PHE F 133 TYR 0.020 0.003 TYR B 126 ARG 0.002 0.000 ARG D 56 *********************** 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 146 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.867 Fit side-chains REVERT: A 48 CYS cc_start: 0.7885 (t) cc_final: 0.7559 (m) REVERT: A 120 SER cc_start: 0.7332 (m) cc_final: 0.7110 (p) REVERT: A 141 ASP cc_start: 0.7775 (m-30) cc_final: 0.7561 (m-30) REVERT: B 102 ARG cc_start: 0.7769 (ttm-80) cc_final: 0.7557 (tmm-80) REVERT: C 130 MET cc_start: 0.7893 (mmm) cc_final: 0.7507 (tpp) REVERT: C 135 ASN cc_start: 0.8867 (p0) cc_final: 0.8662 (p0) REVERT: C 137 GLN cc_start: 0.8344 (tt0) cc_final: 0.8072 (tt0) REVERT: C 141 ASP cc_start: 0.8235 (m-30) cc_final: 0.7990 (m-30) REVERT: C 196 GLU cc_start: 0.7605 (tt0) cc_final: 0.7195 (tt0) REVERT: C 202 GLU cc_start: 0.8333 (tt0) cc_final: 0.7900 (tp30) REVERT: D 48 CYS cc_start: 0.7988 (t) cc_final: 0.7492 (m) REVERT: D 131 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: D 137 GLN cc_start: 0.8279 (pt0) cc_final: 0.8020 (pt0) REVERT: D 141 ASP cc_start: 0.7926 (m-30) cc_final: 0.7611 (m-30) REVERT: F 79 ASP cc_start: 0.8429 (t0) cc_final: 0.8193 (t0) REVERT: F 130 MET cc_start: 0.7699 (mmm) cc_final: 0.7334 (tpp) REVERT: F 169 ASP cc_start: 0.6798 (t0) cc_final: 0.6550 (t0) REVERT: F 181 LYS cc_start: 0.8512 (tmmt) cc_final: 0.8177 (ttpp) outliers start: 27 outliers final: 14 residues processed: 134 average time/residue: 1.0681 time to fit residues: 154.9179 Evaluate side-chains 119 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 237 PHE 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 159 SER Chi-restraints excluded: chain F residue 115 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 0.1980 chunk 13 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 HIS ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN D 44 ASN D 135 ASN F 197 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.130898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.117081 restraints weight = 14933.157| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.57 r_work: 0.3629 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8754 Z= 0.246 Angle : 0.544 6.424 11798 Z= 0.308 Chirality : 0.039 0.189 1236 Planarity : 0.004 0.031 1536 Dihedral : 4.482 16.461 1126 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.37 % Allowed : 19.87 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.27), residues: 1028 helix: 0.84 (0.23), residues: 536 sheet: None (None), residues: 0 loop : -0.38 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 98 HIS 0.011 0.001 HIS B 203 PHE 0.020 0.002 PHE A 132 TYR 0.016 0.002 TYR B 126 ARG 0.002 0.000 ARG D 56 *********************** 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 147 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 0.877 Fit side-chains REVERT: A 48 CYS cc_start: 0.7820 (t) cc_final: 0.7572 (m) REVERT: A 80 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8058 (tm-30) REVERT: A 141 ASP cc_start: 0.7907 (m-30) cc_final: 0.7642 (m-30) REVERT: B 102 ARG cc_start: 0.7802 (ttm-80) cc_final: 0.7585 (tmm-80) REVERT: B 181 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8380 (tttt) REVERT: C 130 MET cc_start: 0.7883 (mmm) cc_final: 0.7504 (tpp) REVERT: C 137 GLN cc_start: 0.8373 (tt0) cc_final: 0.8136 (tt0) REVERT: C 141 ASP cc_start: 0.8214 (m-30) cc_final: 0.7953 (m-30) REVERT: C 196 GLU cc_start: 0.7635 (tt0) cc_final: 0.7224 (tt0) REVERT: C 202 GLU cc_start: 0.8303 (tt0) cc_final: 0.7908 (tp30) REVERT: D 48 CYS cc_start: 0.7901 (t) cc_final: 0.7364 (m) REVERT: D 80 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7727 (tm-30) REVERT: D 131 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: D 141 ASP cc_start: 0.7695 (m-30) cc_final: 0.7376 (m-30) REVERT: F 74 VAL cc_start: 0.7615 (t) cc_final: 0.7334 (t) REVERT: F 130 MET cc_start: 0.7739 (mmm) cc_final: 0.7353 (tpp) REVERT: F 169 ASP cc_start: 0.6977 (t0) cc_final: 0.6681 (t0) outliers start: 40 outliers final: 15 residues processed: 136 average time/residue: 0.8769 time to fit residues: 129.8854 Evaluate side-chains 113 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 B residue 96 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 181 LYS 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 118 HIS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 115 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 55 optimal weight: 0.0770 chunk 62 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 43 optimal weight: 0.4980 chunk 91 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 overall best weight: 2.9144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 HIS ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN D 44 ASN E 134 GLN F 197 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.128536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.114915 restraints weight = 14979.793| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.49 r_work: 0.3606 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8754 Z= 0.267 Angle : 0.552 6.174 11798 Z= 0.311 Chirality : 0.039 0.158 1236 Planarity : 0.004 0.032 1536 Dihedral : 4.468 19.043 1126 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.90 % Allowed : 19.87 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.28), residues: 1028 helix: 1.16 (0.24), residues: 524 sheet: None (None), residues: 0 loop : -0.47 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 98 HIS 0.007 0.001 HIS E 118 PHE 0.024 0.002 PHE H 237 TYR 0.017 0.002 TYR B 126 ARG 0.002 0.000 ARG A 116 *********************** 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 159 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 105 time to evaluate : 1.033 Fit side-chains REVERT: A 48 CYS cc_start: 0.7976 (t) cc_final: 0.7682 (m) REVERT: A 80 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8049 (tm-30) REVERT: A 141 ASP cc_start: 0.7894 (m-30) cc_final: 0.7610 (m-30) REVERT: B 102 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.7591 (tmm-80) REVERT: B 181 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8410 (tttt) REVERT: C 130 MET cc_start: 0.7650 (mmm) cc_final: 0.7380 (tpp) REVERT: C 137 GLN cc_start: 0.8358 (tt0) cc_final: 0.8090 (tt0) REVERT: C 141 ASP cc_start: 0.8221 (m-30) cc_final: 0.7945 (m-30) REVERT: C 202 GLU cc_start: 0.8256 (tt0) cc_final: 0.7813 (tp30) REVERT: D 48 CYS cc_start: 0.7994 (t) cc_final: 0.7350 (m) REVERT: D 80 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7785 (tm-30) REVERT: D 131 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7667 (tt0) REVERT: D 141 ASP cc_start: 0.7658 (m-30) cc_final: 0.7368 (m-30) REVERT: E 42 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7429 (mtpt) REVERT: E 134 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: F 74 VAL cc_start: 0.7711 (t) cc_final: 0.7416 (t) REVERT: F 130 MET cc_start: 0.7655 (mmm) cc_final: 0.7324 (tpp) REVERT: F 169 ASP cc_start: 0.6921 (t0) cc_final: 0.6590 (t0) outliers start: 54 outliers final: 25 residues processed: 147 average time/residue: 0.8532 time to fit residues: 136.7398 Evaluate side-chains 124 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 74 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 200 ILE 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 B residue 181 LYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 122 THR 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 D residue 200 ILE Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 115 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN B 186 HIS ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN D 44 ASN ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 GLN H 248 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.123832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.110714 restraints weight = 15058.505| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.40 r_work: 0.3548 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 8754 Z= 0.472 Angle : 0.687 6.690 11798 Z= 0.383 Chirality : 0.044 0.145 1236 Planarity : 0.005 0.036 1536 Dihedral : 4.995 20.708 1126 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 6.22 % Allowed : 20.85 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.27), residues: 1028 helix: 0.77 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -0.66 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 98 HIS 0.007 0.001 HIS E 203 PHE 0.035 0.003 PHE D 132 TYR 0.027 0.003 TYR B 126 ARG 0.002 0.000 ARG G 247 *********************** 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 165 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 108 time to evaluate : 0.971 Fit side-chains REVERT: A 48 CYS cc_start: 0.7934 (t) cc_final: 0.7622 (m) REVERT: A 80 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8020 (tm-30) REVERT: A 119 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.6522 (m-10) REVERT: A 141 ASP cc_start: 0.7963 (m-30) cc_final: 0.7675 (m-30) REVERT: B 181 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8289 (tttt) REVERT: B 200 ILE cc_start: 0.6660 (OUTLIER) cc_final: 0.6375 (mt) REVERT: C 130 MET cc_start: 0.7680 (mmm) cc_final: 0.7465 (tpp) REVERT: C 137 GLN cc_start: 0.8382 (tt0) cc_final: 0.8081 (tt0) REVERT: C 141 ASP cc_start: 0.8196 (m-30) cc_final: 0.7912 (m-30) REVERT: C 196 GLU cc_start: 0.7769 (tt0) cc_final: 0.7566 (tt0) REVERT: C 202 GLU cc_start: 0.8215 (tt0) cc_final: 0.7793 (tp30) REVERT: D 48 CYS cc_start: 0.8250 (t) cc_final: 0.7467 (m) REVERT: D 131 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: D 141 ASP cc_start: 0.7799 (m-30) cc_final: 0.7517 (m-30) REVERT: E 134 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7411 (tm-30) REVERT: F 130 MET cc_start: 0.7748 (mmm) cc_final: 0.7411 (tpp) REVERT: F 137 GLN cc_start: 0.8134 (tt0) cc_final: 0.7776 (tp40) outliers start: 57 outliers final: 30 residues processed: 148 average time/residue: 0.9455 time to fit residues: 153.0230 Evaluate side-chains 135 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 74 VAL Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 159 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 B residue 181 LYS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 122 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 D residue 184 SER Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 195 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN B 186 HIS ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN E 137 GLN ** E 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.127945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.114639 restraints weight = 14733.505| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.45 r_work: 0.3602 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 8754 Z= 0.258 Angle : 0.561 6.872 11798 Z= 0.313 Chirality : 0.039 0.127 1236 Planarity : 0.004 0.032 1536 Dihedral : 4.575 20.965 1126 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 6.00 % Allowed : 21.40 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.28), residues: 1028 helix: 1.09 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -0.67 (0.30), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 98 HIS 0.007 0.001 HIS E 203 PHE 0.021 0.002 PHE H 237 TYR 0.015 0.002 TYR E 126 ARG 0.002 0.000 ARG A 56 *********************** 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 158 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 103 time to evaluate : 0.854 Fit side-chains REVERT: A 48 CYS cc_start: 0.7997 (t) cc_final: 0.7691 (m) REVERT: A 80 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8038 (tm-30) REVERT: A 119 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.6393 (m-10) REVERT: A 141 ASP cc_start: 0.7805 (m-30) cc_final: 0.7532 (m-30) REVERT: B 181 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8386 (tttt) REVERT: C 130 MET cc_start: 0.7678 (mmm) cc_final: 0.7404 (tpp) REVERT: C 137 GLN cc_start: 0.8364 (tt0) cc_final: 0.8097 (tt0) REVERT: C 141 ASP cc_start: 0.8156 (m-30) cc_final: 0.7898 (m-30) REVERT: C 196 GLU cc_start: 0.7571 (tt0) cc_final: 0.7354 (tt0) REVERT: C 202 GLU cc_start: 0.8208 (tt0) cc_final: 0.7809 (tp30) REVERT: G 231 SER cc_start: 0.6781 (t) cc_final: 0.6396 (p) REVERT: G 246 ASP cc_start: 0.6411 (t70) cc_final: 0.6110 (t70) REVERT: D 48 CYS cc_start: 0.8181 (t) cc_final: 0.7478 (m) REVERT: D 141 ASP cc_start: 0.7668 (m-30) cc_final: 0.7409 (m-30) REVERT: E 134 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: F 74 VAL cc_start: 0.7672 (t) cc_final: 0.7395 (t) REVERT: F 130 MET cc_start: 0.7690 (mmm) cc_final: 0.7363 (tpp) REVERT: F 137 GLN cc_start: 0.8010 (tt0) cc_final: 0.7750 (tp40) outliers start: 55 outliers final: 34 residues processed: 148 average time/residue: 1.2184 time to fit residues: 195.9583 Evaluate side-chains 136 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 119 PHE Chi-restraints excluded: chain A residue 159 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 B residue 181 LYS Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 132 PHE 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 89 LEU Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 137 GLN Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 172 PHE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 195 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 48 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 45 optimal weight: 0.0980 chunk 94 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN A 176 ASN B 134 GLN B 135 ASN B 186 HIS ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN E 182 HIS F 197 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.124137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.111112 restraints weight = 14968.285| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.38 r_work: 0.3556 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 8754 Z= 0.425 Angle : 0.672 9.060 11798 Z= 0.373 Chirality : 0.044 0.302 1236 Planarity : 0.004 0.034 1536 Dihedral : 4.848 20.129 1126 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 6.66 % Allowed : 22.71 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.27), residues: 1028 helix: 0.85 (0.23), residues: 520 sheet: None (None), residues: 0 loop : -0.88 (0.30), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 98 HIS 0.007 0.001 HIS E 203 PHE 0.029 0.003 PHE A 132 TYR 0.024 0.003 TYR B 126 ARG 0.005 0.000 ARG B 102 *********************** 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 162 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 101 time to evaluate : 0.850 Fit side-chains REVERT: A 80 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8044 (tm-30) REVERT: A 119 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.6555 (m-10) REVERT: A 141 ASP cc_start: 0.7890 (m-30) cc_final: 0.7635 (m-30) REVERT: B 181 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8398 (tttt) REVERT: B 200 ILE cc_start: 0.6655 (OUTLIER) cc_final: 0.6323 (mt) REVERT: C 130 MET cc_start: 0.7666 (mmm) cc_final: 0.7451 (tpp) REVERT: C 137 GLN cc_start: 0.8373 (tt0) cc_final: 0.8023 (tt0) REVERT: C 141 ASP cc_start: 0.8184 (m-30) cc_final: 0.7910 (m-30) REVERT: C 202 GLU cc_start: 0.8161 (tt0) cc_final: 0.7795 (tp30) REVERT: G 231 SER cc_start: 0.6860 (t) cc_final: 0.6474 (p) REVERT: G 246 ASP cc_start: 0.6440 (t70) cc_final: 0.6123 (t70) REVERT: D 48 CYS cc_start: 0.8275 (t) cc_final: 0.7508 (m) REVERT: D 119 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.6969 (m-80) REVERT: D 131 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7625 (tt0) REVERT: D 141 ASP cc_start: 0.7739 (m-30) cc_final: 0.7479 (m-30) REVERT: E 134 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7538 (tm-30) REVERT: F 130 MET cc_start: 0.7809 (mmm) cc_final: 0.7476 (tpp) REVERT: F 137 GLN cc_start: 0.8121 (tt0) cc_final: 0.7797 (tp40) outliers start: 61 outliers final: 38 residues processed: 152 average time/residue: 0.9293 time to fit residues: 155.5197 Evaluate side-chains 140 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 97 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 119 PHE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 181 LYS 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 B residue 166 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 195 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 98 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 33 optimal weight: 0.0870 chunk 52 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN B 134 GLN B 186 HIS B 203 HIS E 134 GLN E 203 HIS F 197 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.131757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.118282 restraints weight = 15091.854| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.51 r_work: 0.3656 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8754 Z= 0.155 Angle : 0.527 9.437 11798 Z= 0.291 Chirality : 0.037 0.238 1236 Planarity : 0.003 0.028 1536 Dihedral : 4.197 19.467 1126 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.37 % Allowed : 25.00 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.28), residues: 1028 helix: 1.29 (0.24), residues: 520 sheet: None (None), residues: 0 loop : -0.70 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 98 HIS 0.006 0.001 HIS E 203 PHE 0.018 0.001 PHE H 237 TYR 0.010 0.001 TYR C 126 ARG 0.004 0.000 ARG B 102 *********************** 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 142 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 0.959 Fit side-chains REVERT: A 48 CYS cc_start: 0.8040 (t) cc_final: 0.7714 (m) REVERT: A 80 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7779 (tm-30) REVERT: A 141 ASP cc_start: 0.7659 (m-30) cc_final: 0.7417 (m-30) REVERT: B 181 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8337 (tttt) REVERT: C 130 MET cc_start: 0.7536 (mmm) cc_final: 0.7284 (tpp) REVERT: C 137 GLN cc_start: 0.8387 (tt0) cc_final: 0.8048 (tt0) REVERT: C 141 ASP cc_start: 0.8044 (m-30) cc_final: 0.7804 (m-30) REVERT: C 202 GLU cc_start: 0.8116 (tt0) cc_final: 0.7764 (tp30) REVERT: G 231 SER cc_start: 0.6554 (t) cc_final: 0.6216 (p) REVERT: G 246 ASP cc_start: 0.6739 (t70) cc_final: 0.6429 (t70) REVERT: D 48 CYS cc_start: 0.8113 (t) cc_final: 0.7507 (m) REVERT: E 42 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7479 (mtpt) REVERT: E 134 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7648 (tm-30) REVERT: F 74 VAL cc_start: 0.7400 (t) cc_final: 0.7129 (t) REVERT: F 130 MET cc_start: 0.7655 (mmm) cc_final: 0.7321 (tpp) REVERT: F 137 GLN cc_start: 0.7933 (tt0) cc_final: 0.7708 (tp40) outliers start: 40 outliers final: 18 residues processed: 132 average time/residue: 0.9316 time to fit residues: 132.9741 Evaluate side-chains 119 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain G residue 235 HIS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 195 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 31 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 75 optimal weight: 0.0170 overall best weight: 0.6222 ------------------------------------------------------------------------------- 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 C 58 HIS C 197 GLN C 203 HIS D 156 GLN E 134 GLN E 137 GLN E 203 HIS F 197 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.135202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.122112 restraints weight = 14630.141| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.37 r_work: 0.3702 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8754 Z= 0.136 Angle : 0.506 7.840 11798 Z= 0.279 Chirality : 0.036 0.219 1236 Planarity : 0.003 0.028 1536 Dihedral : 3.852 16.842 1126 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.73 % Allowed : 26.75 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.28), residues: 1028 helix: 1.48 (0.24), residues: 524 sheet: None (None), residues: 0 loop : -0.62 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 98 HIS 0.007 0.001 HIS E 203 PHE 0.019 0.001 PHE A 64 TYR 0.009 0.001 TYR B 71 ARG 0.004 0.000 ARG B 102 *********************** 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 122 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 1.131 Fit side-chains REVERT: A 48 CYS cc_start: 0.7862 (t) cc_final: 0.7628 (m) REVERT: A 137 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6750 (pp30) REVERT: A 141 ASP cc_start: 0.7596 (m-30) cc_final: 0.7321 (m-30) REVERT: B 181 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8341 (tttt) REVERT: C 130 MET cc_start: 0.7468 (mmm) cc_final: 0.7210 (tpp) REVERT: C 137 GLN cc_start: 0.8308 (tt0) cc_final: 0.7964 (tt0) REVERT: C 141 ASP cc_start: 0.8033 (m-30) cc_final: 0.7787 (m-30) REVERT: C 202 GLU cc_start: 0.8132 (tt0) cc_final: 0.7785 (tp30) REVERT: G 231 SER cc_start: 0.6466 (t) cc_final: 0.6136 (p) REVERT: D 48 CYS cc_start: 0.7953 (t) cc_final: 0.7434 (m) REVERT: E 42 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7336 (mtpt) REVERT: E 134 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: F 74 VAL cc_start: 0.7384 (t) cc_final: 0.7108 (t) REVERT: F 130 MET cc_start: 0.7575 (mmm) cc_final: 0.7235 (tpp) outliers start: 25 outliers final: 16 residues processed: 118 average time/residue: 1.1365 time to fit residues: 143.6284 Evaluate side-chains 108 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain G residue 235 HIS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 0.7980 chunk 58 optimal weight: 0.0270 chunk 4 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 64 optimal weight: 0.0070 chunk 54 optimal weight: 0.0670 chunk 10 optimal weight: 0.0570 chunk 84 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 overall best weight: 0.1712 ------------------------------------------------------------------------------- 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 137 GLN D 176 ASN E 203 HIS F 197 GLN F 203 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.140086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.126928 restraints weight = 14755.331| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.45 r_work: 0.3758 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8754 Z= 0.133 Angle : 0.501 7.200 11798 Z= 0.276 Chirality : 0.035 0.208 1236 Planarity : 0.003 0.028 1536 Dihedral : 3.655 16.868 1126 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.51 % Allowed : 27.18 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.28), residues: 1028 helix: 1.75 (0.24), residues: 514 sheet: None (None), residues: 0 loop : -0.48 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 97 HIS 0.007 0.001 HIS E 203 PHE 0.022 0.001 PHE H 237 TYR 0.008 0.001 TYR B 71 ARG 0.005 0.000 ARG D 102 ********************** 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 115 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 1.002 Fit side-chains REVERT: A 137 GLN cc_start: 0.6971 (OUTLIER) cc_final: 0.6565 (pp30) REVERT: A 139 ASP cc_start: 0.7498 (m-30) cc_final: 0.7179 (m-30) REVERT: A 141 ASP cc_start: 0.7525 (m-30) cc_final: 0.7235 (m-30) REVERT: B 181 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8331 (tttt) REVERT: C 130 MET cc_start: 0.7377 (mmm) cc_final: 0.7172 (tpp) REVERT: C 137 GLN cc_start: 0.8289 (tt0) cc_final: 0.7962 (tt0) REVERT: C 141 ASP cc_start: 0.7971 (m-30) cc_final: 0.7707 (m-30) REVERT: C 202 GLU cc_start: 0.8222 (tt0) cc_final: 0.7827 (tp30) REVERT: D 48 CYS cc_start: 0.7619 (t) cc_final: 0.7288 (m) REVERT: E 42 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7416 (mtpt) REVERT: F 74 VAL cc_start: 0.7287 (t) cc_final: 0.7019 (t) REVERT: F 130 MET cc_start: 0.7516 (mmm) cc_final: 0.7153 (tpp) REVERT: F 181 LYS cc_start: 0.8621 (ttpp) cc_final: 0.8295 (tttm) outliers start: 23 outliers final: 13 residues processed: 111 average time/residue: 1.0551 time to fit residues: 125.9602 Evaluate side-chains 98 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain G residue 235 HIS 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 118 HIS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain F residue 195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 94 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 0.0970 chunk 1 optimal weight: 0.8980 overall best weight: 1.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN B 186 HIS B 203 HIS ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 HIS F 197 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.131218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.117760 restraints weight = 15044.468| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.50 r_work: 0.3648 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8754 Z= 0.205 Angle : 0.539 6.480 11798 Z= 0.299 Chirality : 0.037 0.163 1236 Planarity : 0.003 0.027 1536 Dihedral : 3.865 18.402 1126 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.17 % Allowed : 27.07 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.28), residues: 1028 helix: 1.63 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -0.51 (0.30), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 98 HIS 0.008 0.001 HIS E 203 PHE 0.020 0.002 PHE A 172 TYR 0.016 0.002 TYR B 71 ARG 0.005 0.000 ARG D 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5492.58 seconds wall clock time: 97 minutes 26.57 seconds (5846.57 seconds total)