Starting phenix.real_space_refine on Sun Jun 15 11:03:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6k_28886/06_2025/8f6k_28886.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6k_28886/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8f6k_28886/06_2025/8f6k_28886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6k_28886/06_2025/8f6k_28886.map" model { file = "/net/cci-nas-00/data/ceres_data/8f6k_28886/06_2025/8f6k_28886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6k_28886/06_2025/8f6k_28886.cif" } resolution = 3.46 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= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.71, per 1000 atoms: 0.56 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: 4.56 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.20 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: 6.44 Time building geometry restraints manager: 5.49 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: 0.03 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: 14.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.270 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 47.660 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 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:3.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 67.370 ------------------------------------------------------------------------------- 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 (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: -0.45 (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 TRP 0.006 0.001 TRP A 178 HIS 0.006 0.001 HIS B 73 PHE 0.012 0.001 PHE A 161 TYR 0.016 0.001 TYR A 156 ARG 0.001 0.000 ARG C 210 Details of bonding type rmsd hydrogen bonds : bond 0.17261 ( 567) hydrogen bonds : angle 5.75297 ( 1689) metal coordination : bond 0.00137 ( 4) covalent geometry : bond 0.00229 ( 8872) covalent geometry : angle 0.49915 (12088) *********************** 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 : 1.373 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: 0.7275 (m) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.3769 time to fit residues: 91.7903 Evaluate side-chains 121 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4183 r_free = 0.4183 target = 0.183398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.144498 restraints weight = 35521.642| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.66 r_work: 0.3529 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8876 Z= 0.218 Angle : 0.585 5.078 12088 Z= 0.330 Chirality : 0.038 0.148 1470 Planarity : 0.004 0.043 1512 Dihedral : 4.919 25.167 1214 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.32 % Favored : 93.24 % Rotamer: Outliers : 1.87 % Allowed : 8.26 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.12 (0.27), residues: 1124 helix: 1.34 (0.19), residues: 796 sheet: -4.01 (0.43), residues: 86 loop : -3.39 (0.35), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 178 HIS 0.012 0.002 HIS D 71 PHE 0.012 0.002 PHE D 249 TYR 0.012 0.002 TYR B 102 ARG 0.003 0.000 ARG D 217 Details of bonding type rmsd hydrogen bonds : bond 0.05519 ( 567) hydrogen bonds : angle 4.08022 ( 1689) metal coordination : bond 0.00355 ( 4) covalent geometry : bond 0.00484 ( 8872) covalent geometry : angle 0.58513 (12088) *********************** 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 148 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 ASP cc_start: 0.7609 (t70) cc_final: 0.6962 (t0) outliers start: 17 outliers final: 15 residues processed: 142 average time/residue: 0.4096 time to fit residues: 87.4448 Evaluate side-chains 140 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 1.536 ------------------------------------------------------------------------------- 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 52 THR Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 256 ASN 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 52 THR Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 256 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 92 optimal weight: 0.0040 chunk 77 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 0.0770 chunk 94 optimal weight: 0.4980 overall best weight: 0.4552 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.186737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.148391 restraints weight = 35438.130| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.78 r_work: 0.3576 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8876 Z= 0.114 Angle : 0.504 4.828 12088 Z= 0.277 Chirality : 0.034 0.146 1470 Planarity : 0.004 0.044 1512 Dihedral : 4.574 23.532 1214 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.78 % Favored : 93.95 % Rotamer: Outliers : 1.43 % Allowed : 9.91 % Favored : 88.66 % 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: 0.40 (0.27), residues: 1124 helix: 1.77 (0.20), residues: 788 sheet: -3.70 (0.44), residues: 86 loop : -3.27 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 178 HIS 0.006 0.001 HIS D 71 PHE 0.011 0.001 PHE A 277 TYR 0.009 0.001 TYR B 102 ARG 0.001 0.000 ARG D 74 Details of bonding type rmsd hydrogen bonds : bond 0.04429 ( 567) hydrogen bonds : angle 3.49677 ( 1689) metal coordination : bond 0.00055 ( 4) covalent geometry : bond 0.00230 ( 8872) covalent geometry : angle 0.50397 (12088) *********************** 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 161 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 1.201 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: 0.7579 (t70) cc_final: 0.6947 (t0) outliers start: 13 outliers final: 13 residues processed: 156 average time/residue: 0.3123 time to fit residues: 74.0579 Evaluate side-chains 139 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 66 ILE Chi-restraints excluded: chain D residue 95 SER 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 84 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4210 r_free = 0.4210 target = 0.186014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.141503 restraints weight = 35766.915| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.68 r_work: 0.3562 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.1944 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= 0.152 Angle : 0.520 4.854 12088 Z= 0.291 Chirality : 0.035 0.142 1470 Planarity : 0.004 0.043 1512 Dihedral : 4.631 23.022 1214 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.96 % Favored : 93.77 % Rotamer: Outliers : 1.54 % Allowed : 11.56 % Favored : 86.89 % 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: 0.37 (0.27), residues: 1124 helix: 1.75 (0.20), residues: 786 sheet: -3.66 (0.44), residues: 86 loop : -3.27 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 178 HIS 0.008 0.001 HIS D 71 PHE 0.010 0.001 PHE A 277 TYR 0.010 0.001 TYR B 102 ARG 0.002 0.000 ARG B 217 Details of bonding type rmsd hydrogen bonds : bond 0.04429 ( 567) hydrogen bonds : angle 3.53221 ( 1689) metal coordination : bond 0.00206 ( 4) covalent geometry : bond 0.00333 ( 8872) covalent geometry : angle 0.51970 (12088) *********************** 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 143 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 1.362 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: 0.8789 (m-80) cc_final: 0.8587 (m-80) REVERT: C 156 TYR cc_start: 0.8785 (m-80) cc_final: 0.8581 (m-80) outliers start: 14 outliers final: 14 residues processed: 136 average time/residue: 0.3481 time to fit residues: 72.9304 Evaluate side-chains 133 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 B residue 187 LEU 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 66 ILE Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 187 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 0.0870 chunk 23 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 0.3980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN B 73 HIS C 205 GLN D 73 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.188275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.149410 restraints weight = 36100.074| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.78 r_work: 0.3584 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8876 Z= 0.114 Angle : 0.492 4.647 12088 Z= 0.271 Chirality : 0.034 0.145 1470 Planarity : 0.004 0.044 1512 Dihedral : 4.444 23.405 1214 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.14 % Favored : 93.59 % Rotamer: Outliers : 1.87 % Allowed : 12.00 % Favored : 86.12 % 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: 0.63 (0.27), residues: 1124 helix: 1.91 (0.20), residues: 788 sheet: -3.41 (0.46), residues: 86 loop : -3.18 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 178 HIS 0.005 0.001 HIS D 71 PHE 0.010 0.001 PHE A 277 TYR 0.009 0.001 TYR B 75 ARG 0.001 0.000 ARG C 210 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 567) hydrogen bonds : angle 3.32830 ( 1689) metal coordination : bond 0.00070 ( 4) covalent geometry : bond 0.00238 ( 8872) covalent geometry : angle 0.49247 (12088) *********************** 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 159 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 1.375 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: 0.8793 (m-80) cc_final: 0.8576 (m-80) REVERT: B 73 HIS cc_start: 0.6015 (m-70) cc_final: 0.4984 (m-70) REVERT: C 156 TYR cc_start: 0.8792 (m-80) cc_final: 0.8579 (m-80) REVERT: D 73 HIS cc_start: 0.5987 (m-70) cc_final: 0.5145 (m-70) outliers start: 17 outliers final: 14 residues processed: 152 average time/residue: 0.3706 time to fit residues: 81.8276 Evaluate side-chains 138 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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 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 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 66 ILE Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 187 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 74 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN C 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.186143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.147465 restraints weight = 35912.960| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.68 r_work: 0.3551 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2284 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= 0.148 Angle : 0.519 4.688 12088 Z= 0.288 Chirality : 0.035 0.145 1470 Planarity : 0.004 0.045 1512 Dihedral : 4.519 23.001 1214 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.41 % Favored : 93.24 % Rotamer: Outliers : 2.31 % Allowed : 13.11 % Favored : 84.58 % 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: 0.55 (0.27), residues: 1124 helix: 1.86 (0.19), residues: 792 sheet: -3.52 (0.45), residues: 86 loop : -3.27 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 178 HIS 0.007 0.001 HIS B 71 PHE 0.010 0.001 PHE D 249 TYR 0.010 0.001 TYR B 75 ARG 0.004 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.04223 ( 567) hydrogen bonds : angle 3.38004 ( 1689) metal coordination : bond 0.00168 ( 4) covalent geometry : bond 0.00325 ( 8872) covalent geometry : angle 0.51884 (12088) *********************** 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 153 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 HIS cc_start: 0.6033 (m-70) cc_final: 0.5122 (m-70) REVERT: B 210 ARG cc_start: 0.7123 (mtp180) cc_final: 0.6791 (mtm-85) REVERT: B 213 ASP cc_start: 0.7609 (t70) cc_final: 0.6968 (t0) REVERT: D 73 HIS cc_start: 0.5978 (m-70) cc_final: 0.5078 (m-70) outliers start: 21 outliers final: 17 residues processed: 146 average time/residue: 0.3743 time to fit residues: 79.7037 Evaluate side-chains 136 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 B residue 187 LEU Chi-restraints excluded: chain C residue 207 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 175 TYR Chi-restraints excluded: chain D residue 187 LEU 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 8 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.184952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.146174 restraints weight = 35809.236| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.89 r_work: 0.3524 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8876 Z= 0.166 Angle : 0.539 4.661 12088 Z= 0.299 Chirality : 0.036 0.150 1470 Planarity : 0.004 0.048 1512 Dihedral : 4.646 23.856 1214 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.85 % Favored : 92.79 % Rotamer: Outliers : 2.97 % Allowed : 12.89 % Favored : 84.14 % 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: 0.49 (0.27), residues: 1124 helix: 1.81 (0.19), residues: 794 sheet: -3.58 (0.45), residues: 86 loop : -3.27 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 178 HIS 0.007 0.002 HIS B 71 PHE 0.013 0.001 PHE D 249 TYR 0.011 0.001 TYR B 75 ARG 0.005 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 567) hydrogen bonds : angle 3.43604 ( 1689) metal coordination : bond 0.00204 ( 4) covalent geometry : bond 0.00365 ( 8872) covalent geometry : angle 0.53858 (12088) *********************** 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 151 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 HIS cc_start: 0.5877 (m-70) cc_final: 0.5015 (m-70) REVERT: B 210 ARG cc_start: 0.7159 (mtp180) cc_final: 0.6854 (mtm-85) REVERT: B 213 ASP cc_start: 0.7524 (t70) cc_final: 0.6892 (t0) REVERT: D 73 HIS cc_start: 0.6039 (m-70) cc_final: 0.5055 (m-70) REVERT: D 74 ARG cc_start: 0.7960 (ttt180) cc_final: 0.7725 (ttt180) outliers start: 27 outliers final: 19 residues processed: 144 average time/residue: 0.3780 time to fit residues: 79.4615 Evaluate side-chains 135 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain D residue 273 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 48 optimal weight: 0.1980 chunk 105 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 89 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.187819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.148953 restraints weight = 35940.877| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.70 r_work: 0.3576 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2448 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= 0.119 Angle : 0.508 4.630 12088 Z= 0.277 Chirality : 0.034 0.146 1470 Planarity : 0.004 0.044 1512 Dihedral : 4.449 23.960 1214 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.85 % Favored : 92.79 % Rotamer: Outliers : 1.98 % Allowed : 13.55 % 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 (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: 0.76 (0.27), residues: 1124 helix: 2.01 (0.19), residues: 792 sheet: -3.42 (0.46), residues: 86 loop : -3.16 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 178 HIS 0.006 0.001 HIS B 71 PHE 0.009 0.001 PHE D 249 TYR 0.010 0.001 TYR B 75 ARG 0.004 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 567) hydrogen bonds : angle 3.25522 ( 1689) metal coordination : bond 0.00090 ( 4) covalent geometry : bond 0.00252 ( 8872) covalent geometry : angle 0.50760 (12088) *********************** 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 142 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 HIS cc_start: 0.5868 (m-70) cc_final: 0.5007 (m-70) REVERT: B 210 ARG cc_start: 0.7061 (mtp180) cc_final: 0.6775 (mtm-85) REVERT: B 213 ASP cc_start: 0.7475 (t70) cc_final: 0.6827 (t0) REVERT: B 249 PHE cc_start: 0.8364 (m-10) cc_final: 0.8140 (m-10) REVERT: D 73 HIS cc_start: 0.5920 (m-70) cc_final: 0.5082 (m-70) outliers start: 18 outliers final: 15 residues processed: 138 average time/residue: 0.3682 time to fit residues: 74.5687 Evaluate side-chains 129 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 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 16 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 108 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.186544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.147823 restraints weight = 35912.460| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.71 r_work: 0.3553 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8876 Z= 0.138 Angle : 0.526 4.643 12088 Z= 0.288 Chirality : 0.035 0.147 1470 Planarity : 0.004 0.045 1512 Dihedral : 4.488 23.295 1214 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.85 % Favored : 92.79 % Rotamer: Outliers : 2.09 % Allowed : 14.10 % Favored : 83.81 % 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: 0.74 (0.27), residues: 1124 helix: 2.00 (0.19), residues: 792 sheet: -3.44 (0.46), residues: 86 loop : -3.19 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 178 HIS 0.006 0.001 HIS B 71 PHE 0.011 0.001 PHE D 249 TYR 0.011 0.001 TYR B 75 ARG 0.005 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 567) hydrogen bonds : angle 3.30057 ( 1689) metal coordination : bond 0.00152 ( 4) covalent geometry : bond 0.00301 ( 8872) covalent geometry : angle 0.52552 (12088) *********************** 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 140 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 HIS cc_start: 0.5779 (m-70) cc_final: 0.4897 (m-70) REVERT: B 210 ARG cc_start: 0.7148 (mtp180) cc_final: 0.6876 (mtm180) REVERT: B 213 ASP cc_start: 0.7382 (t70) cc_final: 0.6767 (t0) REVERT: D 73 HIS cc_start: 0.5951 (m-70) cc_final: 0.5066 (m-70) outliers start: 19 outliers final: 17 residues processed: 136 average time/residue: 0.4689 time to fit residues: 93.8758 Evaluate side-chains 130 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 1.553 ------------------------------------------------------------------------------- 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 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 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 64 optimal weight: 0.0050 chunk 57 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 83 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 88 optimal weight: 0.0980 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- 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** C 205 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.190042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.151081 restraints weight = 35471.574| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.91 r_work: 0.3584 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8876 Z= 0.106 Angle : 0.507 4.971 12088 Z= 0.274 Chirality : 0.034 0.149 1470 Planarity : 0.004 0.043 1512 Dihedral : 4.314 22.874 1214 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.85 % Favored : 92.79 % Rotamer: Outliers : 1.76 % Allowed : 15.09 % 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 (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: 1.05 (0.28), residues: 1124 helix: 2.24 (0.19), residues: 790 sheet: -3.29 (0.48), residues: 86 loop : -3.12 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 178 HIS 0.005 0.001 HIS B 71 PHE 0.009 0.001 PHE A 161 TYR 0.010 0.001 TYR B 75 ARG 0.005 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 567) hydrogen bonds : angle 3.16144 ( 1689) metal coordination : bond 0.00050 ( 4) covalent geometry : bond 0.00223 ( 8872) covalent geometry : angle 0.50741 (12088) ********************** 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 143 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 HIS cc_start: 0.5853 (m-70) cc_final: 0.5038 (m-70) REVERT: B 213 ASP cc_start: 0.7360 (t70) cc_final: 0.6752 (t0) REVERT: D 73 HIS cc_start: 0.5857 (m-70) cc_final: 0.5031 (m-70) outliers start: 16 outliers final: 13 residues processed: 139 average time/residue: 0.4575 time to fit residues: 95.3569 Evaluate side-chains 133 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 52 THR 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 207 LEU Chi-restraints excluded: chain D residue 52 THR 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 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 69 optimal weight: 0.0770 chunk 73 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 81 optimal weight: 0.2980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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** 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 = 0.188932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.149581 restraints weight = 35605.369| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.79 r_work: 0.3585 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8876 Z= 0.114 Angle : 0.513 4.682 12088 Z= 0.278 Chirality : 0.035 0.146 1470 Planarity : 0.004 0.043 1512 Dihedral : 4.303 22.168 1214 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.49 % Favored : 93.15 % Rotamer: Outliers : 1.76 % Allowed : 15.64 % Favored : 82.60 % 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: 1.11 (0.27), residues: 1124 helix: 2.29 (0.19), residues: 790 sheet: -3.27 (0.48), residues: 86 loop : -3.12 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 33 HIS 0.005 0.001 HIS B 71 PHE 0.009 0.001 PHE B 249 TYR 0.011 0.001 TYR B 75 ARG 0.005 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 567) hydrogen bonds : angle 3.16300 ( 1689) metal coordination : bond 0.00084 ( 4) covalent geometry : bond 0.00245 ( 8872) covalent geometry : angle 0.51297 (12088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8805.17 seconds wall clock time: 153 minutes 24.44 seconds (9204.44 seconds total)