Starting phenix.real_space_refine on Sun Aug 24 05:18:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6k_28886/08_2025/8f6k_28886.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6k_28886/08_2025/8f6k_28886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8f6k_28886/08_2025/8f6k_28886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6k_28886/08_2025/8f6k_28886.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f6k_28886/08_2025/8f6k_28886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6k_28886/08_2025/8f6k_28886.map" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 S 12 5.16 5 C 5630 2.51 5 N 1470 2.21 5 O 1596 1.98 5 H 8586 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17298 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 4226 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 6, 'TRANS': 272} Chain: "B" Number of atoms: 4421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 4421 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "C" Number of atoms: 4226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 4226 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 6, 'TRANS': 272} Chain: "D" Number of atoms: 4421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 4421 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.09, per 1000 atoms: 0.18 Number of scatterers: 17298 At special positions: 0 Unit cell: (137.033, 102.505, 102.505, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 12 16.00 O 1596 8.00 N 1470 7.00 C 5630 6.00 H 8586 1.00 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: 1.25 Conformation dependent library (CDL) restraints added in 525.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 155 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 155 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 155 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 155 " 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 67.8% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 12 through 34 removed outlier: 3.659A pdb=" N ARG A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 63 removed outlier: 3.706A pdb=" N ILE A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 109 removed outlier: 4.149A pdb=" N ALA A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLN A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 142 removed outlier: 3.662A pdb=" N GLY A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 175 removed outlier: 4.414A pdb=" N PHE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 180 through 208 removed outlier: 3.767A pdb=" N PHE A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 removed outlier: 3.544A pdb=" N LEU A 222 " --> pdb=" O GLN A 218 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'B' and resid 15 through 23 Processing helix chain 'B' and resid 24 through 35 Processing helix chain 'B' and resid 38 through 65 removed outlier: 3.591A pdb=" N ILE B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 109 removed outlier: 3.719A pdb=" N LEU B 86 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 140 Processing helix chain 'B' and resid 141 through 144 Processing helix chain 'B' and resid 149 through 176 removed outlier: 3.667A pdb=" N LEU B 160 " --> pdb=" O TYR B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 217 removed outlier: 4.165A pdb=" N ASP B 181 " --> pdb=" O TRP B 177 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 269 removed outlier: 3.539A pdb=" N THR B 268 " --> pdb=" O SER B 264 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B 269 " --> pdb=" O ILE B 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 34 removed outlier: 3.664A pdb=" N ARG C 16 " --> pdb=" O LYS C 12 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 31 " --> pdb=" O THR C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 63 removed outlier: 3.703A pdb=" N ILE C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE C 60 " --> pdb=" O ILE C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 109 removed outlier: 4.125A pdb=" N ALA C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE C 92 " --> pdb=" O GLN C 88 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE C 101 " --> pdb=" O PHE C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 142 removed outlier: 3.666A pdb=" N GLY C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 175 removed outlier: 4.418A pdb=" N PHE C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C 162 " --> pdb=" O SER C 158 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 166 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 180 through 208 removed outlier: 3.767A pdb=" N PHE C 184 " --> pdb=" O ALA C 180 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA C 185 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER C 203 " --> pdb=" O LEU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 224 removed outlier: 3.539A pdb=" N LEU C 222 " --> pdb=" O GLN C 218 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 275 Processing helix chain 'D' and resid 15 through 23 Processing helix chain 'D' and resid 24 through 35 Processing helix chain 'D' and resid 38 through 65 removed outlier: 3.591A pdb=" N ILE D 57 " --> pdb=" O LEU D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 109 removed outlier: 3.732A pdb=" N LEU D 86 " --> pdb=" O PRO D 82 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 140 Processing helix chain 'D' and resid 141 through 144 Processing helix chain 'D' and resid 149 through 176 removed outlier: 3.667A pdb=" N LEU D 160 " --> pdb=" O TYR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 217 removed outlier: 4.165A pdb=" N ASP D 181 " --> pdb=" O TRP D 177 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY D 182 " --> pdb=" O TRP D 178 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP D 209 " --> pdb=" O GLN D 205 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 269 removed outlier: 3.535A pdb=" N THR D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR D 269 " --> pdb=" O ILE D 265 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 239 through 241 removed outlier: 4.026A pdb=" N THR A 244 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 244 through 246 removed outlier: 6.297A pdb=" N VAL B 245 " --> pdb=" O GLU B 281 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 252 through 254 Processing sheet with id=AA4, first strand: chain 'C' and resid 239 through 240 Processing sheet with id=AA5, first strand: chain 'D' and resid 244 through 246 removed outlier: 6.294A pdb=" N VAL D 245 " --> pdb=" O GLU D 281 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 252 through 254 567 hydrogen bonds defined for protein. 1689 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: 3.46 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8582 1.03 - 1.23: 8 1.23 - 1.42: 3670 1.42 - 1.62: 5178 1.62 - 1.81: 20 Bond restraints: 17458 Sorted by residual: bond pdb=" N VAL A 11 " pdb=" CA VAL A 11 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.74e+00 bond pdb=" N VAL C 11 " pdb=" CA VAL C 11 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.68e+00 bond pdb=" N VAL A 11 " pdb=" H VAL A 11 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" N VAL C 11 " pdb=" H VAL C 11 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" N ASP C 279 " pdb=" CA ASP C 279 " ideal model delta sigma weight residual 1.457 1.469 -0.011 1.29e-02 6.01e+03 7.73e-01 ... (remaining 17453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 28497 0.95 - 1.91: 2796 1.91 - 2.86: 128 2.86 - 3.82: 45 3.82 - 4.77: 8 Bond angle restraints: 31474 Sorted by residual: angle pdb=" N VAL B 273 " pdb=" CA VAL B 273 " pdb=" C VAL B 273 " ideal model delta sigma weight residual 112.80 109.64 3.16 1.15e+00 7.56e-01 7.54e+00 angle pdb=" N VAL D 273 " pdb=" CA VAL D 273 " pdb=" C VAL D 273 " ideal model delta sigma weight residual 112.80 109.65 3.15 1.15e+00 7.56e-01 7.51e+00 angle pdb=" N HIS C 73 " pdb=" CA HIS C 73 " pdb=" CB HIS C 73 " ideal model delta sigma weight residual 114.27 110.56 3.71 1.64e+00 3.72e-01 5.12e+00 angle pdb=" N ALA D 116 " pdb=" CA ALA D 116 " pdb=" CB ALA D 116 " ideal model delta sigma weight residual 113.65 110.37 3.28 1.47e+00 4.63e-01 4.98e+00 angle pdb=" N HIS A 73 " pdb=" CA HIS A 73 " pdb=" CB HIS A 73 " ideal model delta sigma weight residual 114.27 110.64 3.63 1.64e+00 3.72e-01 4.91e+00 ... (remaining 31469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 7389 16.81 - 33.62: 540 33.62 - 50.43: 127 50.43 - 67.24: 72 67.24 - 84.05: 18 Dihedral angle restraints: 8146 sinusoidal: 4338 harmonic: 3808 Sorted by residual: dihedral pdb=" CA ASP B 70 " pdb=" C ASP B 70 " pdb=" N HIS B 71 " pdb=" CA HIS B 71 " ideal model delta harmonic sigma weight residual -180.00 -157.56 -22.44 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ASP D 70 " pdb=" C ASP D 70 " pdb=" N HIS D 71 " pdb=" CA HIS D 71 " ideal model delta harmonic sigma weight residual 180.00 -157.93 -22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA HIS D 71 " pdb=" C HIS D 71 " pdb=" N ASP D 72 " pdb=" CA ASP D 72 " ideal model delta harmonic sigma weight residual -180.00 -159.68 -20.32 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 8143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1012 0.029 - 0.059: 319 0.059 - 0.088: 101 0.088 - 0.117: 26 0.117 - 0.147: 12 Chirality restraints: 1470 Sorted by residual: chirality pdb=" CA VAL A 67 " pdb=" N VAL A 67 " pdb=" C VAL A 67 " pdb=" CB VAL A 67 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CA VAL C 67 " pdb=" N VAL C 67 " pdb=" C VAL C 67 " pdb=" CB VAL C 67 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA ILE D 283 " pdb=" N ILE D 283 " pdb=" C ILE D 283 " pdb=" CB ILE D 283 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 1467 not shown) Planarity restraints: 2582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 67 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.27e+00 pdb=" N PRO A 68 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 67 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO B 68 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 68 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 68 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 287 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.10e+00 pdb=" N PRO D 288 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 288 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 288 " -0.020 5.00e-02 4.00e+02 ... (remaining 2579 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 941 2.20 - 2.80: 35960 2.80 - 3.40: 47133 3.40 - 4.00: 58732 4.00 - 4.60: 91886 Nonbonded interactions: 234652 Sorted by model distance: nonbonded pdb=" HE2 HIS D 71 " pdb=" O TYR D 75 " model vdw 1.595 2.450 nonbonded pdb=" O LEU D 251 " pdb=" H ALA D 287 " model vdw 1.597 2.450 nonbonded pdb=" O LEU B 251 " pdb=" H ALA B 287 " model vdw 1.608 2.450 nonbonded pdb=" OD1 ASP B 51 " pdb=" HE2 HIS B 155 " model vdw 1.617 2.450 nonbonded pdb=" OD1 ASP D 51 " pdb=" HE2 HIS D 155 " model vdw 1.618 2.450 ... (remaining 234647 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 11 through 65 or (resid 66 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 67 and (n \ ame N or name CA or name C or name O or name CB or name CG1 or name CG2)) or (re \ sid 68 and (name N or name CA or name C or name O or name CB or name CG or name \ CD )) or (resid 69 and (name N or name CA or name C or name O or name CB )) or ( \ resid 70 and (name N or name CA or name C or name O or name CB or name CG or nam \ e OD1 or name OD2)) or (resid 71 and (name N or name CA or name C or name O or n \ ame CB or name CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid 72 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name OD2)) or (resid 73 and (name N or name CA or name C or name O or name CB o \ r name CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid 74 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name CZ or name NH1 or name NH2)) or (resid 75 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ or name OH )) or (resid 76 and (name N or name CA or name C or nam \ e O )) or (resid 77 and (name N or name CA or name C or name O or name CB or nam \ e CG or name ND1 or name CD2 or name CE1 or name NE2)) or resid 78 through 287 o \ r (resid 288 and (name N or name CA or name C or name O or name CB or name CG or \ name CD )) or (resid 289 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2)) or resid 301)) selection = chain 'C' selection = (chain 'D' and (resid 11 through 65 or (resid 66 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 67 and (n \ ame N or name CA or name C or name O or name CB or name CG1 or name CG2)) or (re \ sid 68 and (name N or name CA or name C or name O or name CB or name CG or name \ CD )) or (resid 69 and (name N or name CA or name C or name O or name CB )) or ( \ resid 70 and (name N or name CA or name C or name O or name CB or name CG or nam \ e OD1 or name OD2)) or (resid 71 and (name N or name CA or name C or name O or n \ ame CB or name CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid 72 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name OD2)) or (resid 73 and (name N or name CA or name C or name O or name CB o \ r name CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid 74 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name CZ or name NH1 or name NH2)) or (resid 75 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ or name OH )) or (resid 76 and (name N or name CA or name C or nam \ e O )) or (resid 77 and (name N or name CA or name C or name O or name CB or nam \ e CG or name ND1 or name CD2 or name CE1 or name NE2)) or resid 78 through 287 o \ r (resid 288 and (name N or name CA or name C or name O or name CB or name CG or \ name CD )) or (resid 289 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2)) or resid 301)) } 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: 2.590 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: 0.070 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.910 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8876 Z= 0.116 Angle : 0.499 4.773 12088 Z= 0.285 Chirality : 0.034 0.147 1470 Planarity : 0.003 0.038 1512 Dihedral : 14.249 84.047 3098 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.96 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.26), residues: 1124 helix: 1.06 (0.20), residues: 776 sheet: -4.09 (0.45), residues: 76 loop : -3.13 (0.33), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 210 TYR 0.016 0.001 TYR A 156 PHE 0.012 0.001 PHE A 161 TRP 0.006 0.001 TRP A 178 HIS 0.006 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8872) covalent geometry : angle 0.49915 (12088) hydrogen bonds : bond 0.17261 ( 567) hydrogen bonds : angle 5.75297 ( 1689) metal coordination : bond 0.00137 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 THR cc_start: 0.7696 (m) cc_final: 0.7276 (m) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1302 time to fit residues: 32.5300 Evaluate side-chains 120 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.3980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.189336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.150795 restraints weight = 35621.696| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.53 r_work: 0.3636 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8876 Z= 0.120 Angle : 0.514 4.800 12088 Z= 0.284 Chirality : 0.035 0.143 1470 Planarity : 0.004 0.042 1512 Dihedral : 4.432 20.775 1214 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.98 % Favored : 94.57 % Rotamer: Outliers : 1.32 % Allowed : 7.82 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.27), residues: 1124 helix: 1.76 (0.20), residues: 780 sheet: -3.89 (0.46), residues: 76 loop : -3.00 (0.33), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 16 TYR 0.011 0.001 TYR C 156 PHE 0.015 0.001 PHE B 249 TRP 0.006 0.001 TRP A 178 HIS 0.009 0.001 HIS D 71 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8872) covalent geometry : angle 0.51406 (12088) hydrogen bonds : bond 0.04805 ( 567) hydrogen bonds : angle 3.74385 ( 1689) metal coordination : bond 0.00037 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 ASP cc_start: 0.7780 (t70) cc_final: 0.7132 (t0) REVERT: D 214 GLU cc_start: 0.8038 (tp30) cc_final: 0.7828 (tp30) REVERT: D 249 PHE cc_start: 0.8652 (m-80) cc_final: 0.8449 (m-80) outliers start: 12 outliers final: 11 residues processed: 156 average time/residue: 0.1534 time to fit residues: 36.7503 Evaluate side-chains 142 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 175 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 76 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN C 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.186337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.146986 restraints weight = 35925.876| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.89 r_work: 0.3562 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8876 Z= 0.165 Angle : 0.536 4.898 12088 Z= 0.299 Chirality : 0.036 0.144 1470 Planarity : 0.004 0.043 1512 Dihedral : 4.623 22.124 1214 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.05 % Favored : 93.51 % Rotamer: Outliers : 1.21 % Allowed : 10.24 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.27), residues: 1124 helix: 1.70 (0.20), residues: 788 sheet: -3.56 (0.45), residues: 86 loop : -3.25 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 217 TYR 0.010 0.001 TYR B 102 PHE 0.013 0.001 PHE D 249 TRP 0.005 0.001 TRP A 178 HIS 0.009 0.002 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8872) covalent geometry : angle 0.53561 (12088) hydrogen bonds : bond 0.04735 ( 567) hydrogen bonds : angle 3.64991 ( 1689) metal coordination : bond 0.00143 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 ASP cc_start: 0.7655 (t70) cc_final: 0.7034 (t0) outliers start: 11 outliers final: 10 residues processed: 143 average time/residue: 0.1584 time to fit residues: 34.9960 Evaluate side-chains 133 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 175 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN C 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.186745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.148050 restraints weight = 35806.662| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.65 r_work: 0.3574 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8876 Z= 0.136 Angle : 0.507 4.721 12088 Z= 0.282 Chirality : 0.035 0.147 1470 Planarity : 0.004 0.044 1512 Dihedral : 4.565 22.767 1214 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.58 % Favored : 93.15 % Rotamer: Outliers : 1.54 % Allowed : 11.23 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.27), residues: 1124 helix: 1.80 (0.20), residues: 788 sheet: -3.49 (0.45), residues: 86 loop : -3.22 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 217 TYR 0.010 0.001 TYR B 102 PHE 0.011 0.001 PHE A 277 TRP 0.005 0.001 TRP A 178 HIS 0.007 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8872) covalent geometry : angle 0.50651 (12088) hydrogen bonds : bond 0.04330 ( 567) hydrogen bonds : angle 3.47559 ( 1689) metal coordination : bond 0.00119 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 146 average time/residue: 0.1594 time to fit residues: 35.8936 Evaluate side-chains 133 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 175 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN C 163 ASN C 205 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.186627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.148051 restraints weight = 35822.279| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.70 r_work: 0.3578 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8876 Z= 0.142 Angle : 0.517 5.363 12088 Z= 0.286 Chirality : 0.035 0.146 1470 Planarity : 0.004 0.044 1512 Dihedral : 4.560 23.115 1214 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.41 % Favored : 93.33 % Rotamer: Outliers : 2.31 % Allowed : 11.12 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.27), residues: 1124 helix: 1.82 (0.20), residues: 790 sheet: -3.45 (0.46), residues: 86 loop : -3.12 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 217 TYR 0.010 0.001 TYR B 102 PHE 0.011 0.001 PHE D 249 TRP 0.005 0.001 TRP A 178 HIS 0.007 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8872) covalent geometry : angle 0.51657 (12088) hydrogen bonds : bond 0.04273 ( 567) hydrogen bonds : angle 3.43759 ( 1689) metal coordination : bond 0.00132 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 16 residues processed: 148 average time/residue: 0.1661 time to fit residues: 37.3183 Evaluate side-chains 134 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 273 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 106 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.185820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.147187 restraints weight = 35764.339| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.69 r_work: 0.3565 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8876 Z= 0.154 Angle : 0.527 5.080 12088 Z= 0.292 Chirality : 0.036 0.149 1470 Planarity : 0.004 0.047 1512 Dihedral : 4.604 23.425 1214 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.03 % Favored : 92.79 % Rotamer: Outliers : 1.87 % Allowed : 13.66 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.27), residues: 1124 helix: 1.76 (0.19), residues: 794 sheet: -3.51 (0.45), residues: 86 loop : -3.26 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 217 TYR 0.010 0.001 TYR B 75 PHE 0.011 0.001 PHE D 249 TRP 0.005 0.001 TRP A 178 HIS 0.007 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8872) covalent geometry : angle 0.52708 (12088) hydrogen bonds : bond 0.04344 ( 567) hydrogen bonds : angle 3.45332 ( 1689) metal coordination : bond 0.00167 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 144 average time/residue: 0.1637 time to fit residues: 35.7641 Evaluate side-chains 132 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 273 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 0.0010 chunk 5 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN C 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.187653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.149056 restraints weight = 35871.868| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.67 r_work: 0.3578 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8876 Z= 0.124 Angle : 0.510 4.869 12088 Z= 0.280 Chirality : 0.035 0.148 1470 Planarity : 0.004 0.045 1512 Dihedral : 4.480 23.924 1214 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.49 % Favored : 93.15 % Rotamer: Outliers : 2.09 % Allowed : 13.55 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.27), residues: 1124 helix: 1.96 (0.19), residues: 792 sheet: -3.40 (0.46), residues: 86 loop : -3.16 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 210 TYR 0.010 0.001 TYR C 156 PHE 0.010 0.001 PHE A 277 TRP 0.005 0.001 TRP C 178 HIS 0.006 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8872) covalent geometry : angle 0.51032 (12088) hydrogen bonds : bond 0.04083 ( 567) hydrogen bonds : angle 3.31330 ( 1689) metal coordination : bond 0.00099 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 16 residues processed: 142 average time/residue: 0.1660 time to fit residues: 35.6649 Evaluate side-chains 130 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain D residue 8 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 187 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 100 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.187061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.147961 restraints weight = 35766.526| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.71 r_work: 0.3577 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8876 Z= 0.121 Angle : 0.506 4.759 12088 Z= 0.277 Chirality : 0.035 0.146 1470 Planarity : 0.004 0.044 1512 Dihedral : 4.412 23.463 1214 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.85 % Favored : 92.79 % Rotamer: Outliers : 2.42 % Allowed : 13.66 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.27), residues: 1124 helix: 2.07 (0.19), residues: 786 sheet: -3.35 (0.47), residues: 86 loop : -3.07 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 217 TYR 0.010 0.001 TYR B 75 PHE 0.009 0.001 PHE A 161 TRP 0.005 0.001 TRP A 178 HIS 0.005 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8872) covalent geometry : angle 0.50592 (12088) hydrogen bonds : bond 0.03969 ( 567) hydrogen bonds : angle 3.26330 ( 1689) metal coordination : bond 0.00098 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ARG cc_start: 0.7023 (mtp180) cc_final: 0.6810 (mtm-85) REVERT: B 249 PHE cc_start: 0.8388 (m-10) cc_final: 0.8149 (m-10) outliers start: 22 outliers final: 17 residues processed: 143 average time/residue: 0.1511 time to fit residues: 31.6904 Evaluate side-chains 139 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain D residue 8 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 175 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 0.3980 chunk 1 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN B 256 ASN C 205 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.187470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.148827 restraints weight = 35909.096| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.66 r_work: 0.3569 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8876 Z= 0.132 Angle : 0.518 4.644 12088 Z= 0.284 Chirality : 0.035 0.146 1470 Planarity : 0.004 0.044 1512 Dihedral : 4.437 23.458 1214 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.76 % Favored : 92.88 % Rotamer: Outliers : 2.42 % Allowed : 13.99 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.27), residues: 1124 helix: 2.05 (0.19), residues: 792 sheet: -3.36 (0.47), residues: 86 loop : -3.16 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 210 TYR 0.010 0.001 TYR B 75 PHE 0.009 0.001 PHE D 249 TRP 0.005 0.001 TRP C 178 HIS 0.006 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8872) covalent geometry : angle 0.51759 (12088) hydrogen bonds : bond 0.04006 ( 567) hydrogen bonds : angle 3.26527 ( 1689) metal coordination : bond 0.00128 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 TYR cc_start: 0.8743 (m-80) cc_final: 0.8511 (m-80) REVERT: B 210 ARG cc_start: 0.7147 (mtp180) cc_final: 0.6923 (mtm-85) REVERT: B 213 ASP cc_start: 0.7454 (t70) cc_final: 0.6821 (t0) outliers start: 22 outliers final: 19 residues processed: 143 average time/residue: 0.1548 time to fit residues: 32.3022 Evaluate side-chains 139 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain D residue 8 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 187 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 64 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 88 optimal weight: 0.0870 chunk 95 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.188291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.149890 restraints weight = 35707.453| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.97 r_work: 0.3564 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8876 Z= 0.120 Angle : 0.514 4.927 12088 Z= 0.280 Chirality : 0.035 0.148 1470 Planarity : 0.004 0.043 1512 Dihedral : 4.392 23.642 1214 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.58 % Favored : 93.06 % Rotamer: Outliers : 2.09 % Allowed : 14.65 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.27), residues: 1124 helix: 2.12 (0.19), residues: 792 sheet: -3.31 (0.47), residues: 86 loop : -3.12 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 210 TYR 0.011 0.001 TYR C 156 PHE 0.009 0.001 PHE B 249 TRP 0.004 0.001 TRP A 178 HIS 0.006 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8872) covalent geometry : angle 0.51395 (12088) hydrogen bonds : bond 0.03906 ( 567) hydrogen bonds : angle 3.22421 ( 1689) metal coordination : bond 0.00099 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 TYR cc_start: 0.8741 (m-80) cc_final: 0.8501 (m-80) REVERT: B 210 ARG cc_start: 0.7150 (mtp180) cc_final: 0.6906 (mtm-85) REVERT: B 213 ASP cc_start: 0.7416 (t70) cc_final: 0.6797 (t0) outliers start: 19 outliers final: 17 residues processed: 138 average time/residue: 0.1387 time to fit residues: 28.2344 Evaluate side-chains 140 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain D residue 8 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 175 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.185831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.147072 restraints weight = 36113.383| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.95 r_work: 0.3544 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8876 Z= 0.141 Angle : 0.530 4.659 12088 Z= 0.290 Chirality : 0.035 0.147 1470 Planarity : 0.004 0.044 1512 Dihedral : 4.466 23.282 1214 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.67 % Favored : 92.97 % Rotamer: Outliers : 2.20 % Allowed : 14.65 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.27), residues: 1124 helix: 2.12 (0.19), residues: 792 sheet: -3.39 (0.47), residues: 86 loop : -3.15 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 210 TYR 0.012 0.001 TYR C 156 PHE 0.013 0.001 PHE B 249 TRP 0.004 0.001 TRP A 178 HIS 0.006 0.001 HIS D 71 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8872) covalent geometry : angle 0.53014 (12088) hydrogen bonds : bond 0.04056 ( 567) hydrogen bonds : angle 3.27173 ( 1689) metal coordination : bond 0.00148 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4003.76 seconds wall clock time: 68 minutes 49.68 seconds (4129.68 seconds total)