Starting phenix.real_space_refine on Wed Feb 4 20:30:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wjw_66032/02_2026/9wjw_66032.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wjw_66032/02_2026/9wjw_66032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wjw_66032/02_2026/9wjw_66032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wjw_66032/02_2026/9wjw_66032.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wjw_66032/02_2026/9wjw_66032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wjw_66032/02_2026/9wjw_66032.map" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.103 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: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 8365 2.51 5 N 2097 2.21 5 O 2203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12735 Number of models: 1 Model: "" Number of chains: 10 Chain: "F" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1765 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 9, 'TRANS': 235} Chain: "G" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2342 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 11, 'TRANS': 289} Chain: "S" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1765 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 9, 'TRANS': 235} Chain: "T" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2333 Classifications: {'peptide': 300} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 287} Chain: "A" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 378 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Y" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1769 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 9, 'TRANS': 236} Chain: "Z" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2347 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain: "G" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.19, per 1000 atoms: 0.25 Number of scatterers: 12735 At special positions: 0 Unit cell: (120.31, 122.459, 102.049, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2203 8.00 N 2097 7.00 C 8365 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 745.4 milliseconds 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3034 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 4 sheets defined 74.3% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'F' and resid 2 through 23 removed outlier: 3.753A pdb=" N ILE F 21 " --> pdb=" O GLY F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 41 removed outlier: 4.059A pdb=" N THR F 35 " --> pdb=" O LEU F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 58 Processing helix chain 'F' and resid 73 through 86 Processing helix chain 'F' and resid 92 through 101 Processing helix chain 'F' and resid 103 through 118 removed outlier: 3.976A pdb=" N PHE F 109 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU F 110 " --> pdb=" O ALA F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 132 removed outlier: 3.546A pdb=" N LYS F 131 " --> pdb=" O ARG F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 161 removed outlier: 3.949A pdb=" N VAL F 137 " --> pdb=" O ASN F 133 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU F 138 " --> pdb=" O ILE F 134 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TRP F 139 " --> pdb=" O ARG F 135 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE F 152 " --> pdb=" O GLN F 148 " (cutoff:3.500A) Proline residue: F 155 - end of helix Processing helix chain 'F' and resid 178 through 186 Processing helix chain 'F' and resid 189 through 201 removed outlier: 4.120A pdb=" N GLY F 193 " --> pdb=" O VAL F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 Processing helix chain 'F' and resid 223 through 243 Processing helix chain 'G' and resid 8 through 19 Processing helix chain 'G' and resid 20 through 22 No H-bonds generated for 'chain 'G' and resid 20 through 22' Processing helix chain 'G' and resid 32 through 48 removed outlier: 3.634A pdb=" N TRP G 36 " --> pdb=" O GLN G 32 " (cutoff:3.500A) Proline residue: G 42 - end of helix Processing helix chain 'G' and resid 53 through 61 Processing helix chain 'G' and resid 72 through 88 removed outlier: 3.599A pdb=" N ASN G 88 " --> pdb=" O GLU G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 117 removed outlier: 4.176A pdb=" N GLY G 106 " --> pdb=" O VAL G 102 " (cutoff:3.500A) Proline residue: G 107 - end of helix Proline residue: G 114 - end of helix Processing helix chain 'G' and resid 119 through 133 removed outlier: 3.553A pdb=" N MET G 123 " --> pdb=" O THR G 119 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU G 131 " --> pdb=" O LEU G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 165 Processing helix chain 'G' and resid 168 through 173 Processing helix chain 'G' and resid 176 through 201 removed outlier: 3.782A pdb=" N VAL G 201 " --> pdb=" O VAL G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 242 removed outlier: 3.704A pdb=" N ILE G 232 " --> pdb=" O GLY G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 261 removed outlier: 3.603A pdb=" N LEU G 260 " --> pdb=" O ASN G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 279 Processing helix chain 'G' and resid 282 through 300 removed outlier: 3.578A pdb=" N ILE G 286 " --> pdb=" O SER G 282 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 23 removed outlier: 3.974A pdb=" N ILE S 21 " --> pdb=" O GLY S 17 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 41 removed outlier: 4.541A pdb=" N THR S 35 " --> pdb=" O LEU S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 58 removed outlier: 3.697A pdb=" N ILE S 49 " --> pdb=" O THR S 45 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU S 50 " --> pdb=" O ALA S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 73 through 86 Processing helix chain 'S' and resid 92 through 101 Processing helix chain 'S' and resid 103 through 108 Processing helix chain 'S' and resid 108 through 118 removed outlier: 3.542A pdb=" N MET S 112 " --> pdb=" O LEU S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 118 through 132 removed outlier: 3.686A pdb=" N LYS S 131 " --> pdb=" O ARG S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 133 through 161 removed outlier: 3.829A pdb=" N VAL S 137 " --> pdb=" O ASN S 133 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU S 138 " --> pdb=" O ILE S 134 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE S 152 " --> pdb=" O GLN S 148 " (cutoff:3.500A) Proline residue: S 155 - end of helix Processing helix chain 'S' and resid 163 through 165 No H-bonds generated for 'chain 'S' and resid 163 through 165' Processing helix chain 'S' and resid 166 through 171 removed outlier: 4.066A pdb=" N LEU S 171 " --> pdb=" O VAL S 167 " (cutoff:3.500A) Processing helix chain 'S' and resid 178 through 186 Processing helix chain 'S' and resid 189 through 201 removed outlier: 4.290A pdb=" N GLY S 193 " --> pdb=" O VAL S 189 " (cutoff:3.500A) Processing helix chain 'S' and resid 206 through 216 Processing helix chain 'S' and resid 223 through 245 Processing helix chain 'T' and resid 8 through 19 Processing helix chain 'T' and resid 20 through 22 No H-bonds generated for 'chain 'T' and resid 20 through 22' Processing helix chain 'T' and resid 32 through 48 removed outlier: 3.544A pdb=" N ALA T 37 " --> pdb=" O ASN T 33 " (cutoff:3.500A) Proline residue: T 42 - end of helix Processing helix chain 'T' and resid 53 through 61 Processing helix chain 'T' and resid 72 through 88 removed outlier: 3.641A pdb=" N ASN T 88 " --> pdb=" O GLU T 84 " (cutoff:3.500A) Processing helix chain 'T' and resid 95 through 104 Processing helix chain 'T' and resid 105 through 118 removed outlier: 3.553A pdb=" N ALA T 109 " --> pdb=" O MET T 105 " (cutoff:3.500A) Proline residue: T 114 - end of helix Processing helix chain 'T' and resid 119 through 133 removed outlier: 3.678A pdb=" N LEU T 131 " --> pdb=" O LEU T 127 " (cutoff:3.500A) Processing helix chain 'T' and resid 137 through 166 Processing helix chain 'T' and resid 168 through 174 removed outlier: 3.589A pdb=" N ASP T 172 " --> pdb=" O LYS T 168 " (cutoff:3.500A) Processing helix chain 'T' and resid 176 through 201 removed outlier: 3.890A pdb=" N VAL T 201 " --> pdb=" O VAL T 197 " (cutoff:3.500A) Processing helix chain 'T' and resid 229 through 242 removed outlier: 3.638A pdb=" N LYS T 233 " --> pdb=" O ALA T 229 " (cutoff:3.500A) Processing helix chain 'T' and resid 253 through 259 Processing helix chain 'T' and resid 263 through 279 Processing helix chain 'T' and resid 282 through 300 Processing helix chain 'A' and resid 26 through 41 Processing helix chain 'A' and resid 42 through 45 Processing helix chain 'Y' and resid 2 through 23 removed outlier: 3.956A pdb=" N ILE Y 21 " --> pdb=" O GLY Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 41 removed outlier: 3.985A pdb=" N THR Y 35 " --> pdb=" O LEU Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 58 removed outlier: 4.049A pdb=" N ILE Y 49 " --> pdb=" O THR Y 45 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU Y 50 " --> pdb=" O ALA Y 46 " (cutoff:3.500A) Processing helix chain 'Y' and resid 73 through 86 Processing helix chain 'Y' and resid 92 through 101 Processing helix chain 'Y' and resid 103 through 118 removed outlier: 5.163A pdb=" N PHE Y 109 " --> pdb=" O VAL Y 105 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU Y 110 " --> pdb=" O ALA Y 106 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL Y 114 " --> pdb=" O LEU Y 110 " (cutoff:3.500A) Processing helix chain 'Y' and resid 118 through 130 Processing helix chain 'Y' and resid 133 through 160 removed outlier: 3.809A pdb=" N VAL Y 137 " --> pdb=" O ASN Y 133 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE Y 142 " --> pdb=" O GLU Y 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG Y 151 " --> pdb=" O MET Y 147 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE Y 152 " --> pdb=" O GLN Y 148 " (cutoff:3.500A) Proline residue: Y 155 - end of helix removed outlier: 3.582A pdb=" N LEU Y 160 " --> pdb=" O ALA Y 156 " (cutoff:3.500A) Processing helix chain 'Y' and resid 165 through 172 Processing helix chain 'Y' and resid 177 through 187 Processing helix chain 'Y' and resid 188 through 201 removed outlier: 3.924A pdb=" N VAL Y 192 " --> pdb=" O MET Y 188 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL Y 197 " --> pdb=" O GLY Y 193 " (cutoff:3.500A) Processing helix chain 'Y' and resid 206 through 216 Processing helix chain 'Y' and resid 223 through 246 Processing helix chain 'Z' and resid 8 through 19 Processing helix chain 'Z' and resid 20 through 22 No H-bonds generated for 'chain 'Z' and resid 20 through 22' Processing helix chain 'Z' and resid 33 through 48 Proline residue: Z 42 - end of helix Processing helix chain 'Z' and resid 53 through 61 Processing helix chain 'Z' and resid 72 through 87 Processing helix chain 'Z' and resid 95 through 117 removed outlier: 3.518A pdb=" N GLY Z 99 " --> pdb=" O VAL Z 95 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY Z 106 " --> pdb=" O VAL Z 102 " (cutoff:3.500A) Proline residue: Z 107 - end of helix Proline residue: Z 114 - end of helix Processing helix chain 'Z' and resid 119 through 133 removed outlier: 3.539A pdb=" N MET Z 123 " --> pdb=" O THR Z 119 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU Z 131 " --> pdb=" O LEU Z 127 " (cutoff:3.500A) Processing helix chain 'Z' and resid 137 through 165 Processing helix chain 'Z' and resid 169 through 174 removed outlier: 3.593A pdb=" N LEU Z 173 " --> pdb=" O ILE Z 169 " (cutoff:3.500A) Processing helix chain 'Z' and resid 176 through 201 removed outlier: 3.774A pdb=" N ASP Z 180 " --> pdb=" O GLY Z 176 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE Z 181 " --> pdb=" O LEU Z 177 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA Z 195 " --> pdb=" O PHE Z 191 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL Z 201 " --> pdb=" O VAL Z 197 " (cutoff:3.500A) Processing helix chain 'Z' and resid 229 through 242 removed outlier: 3.767A pdb=" N LYS Z 233 " --> pdb=" O ALA Z 229 " (cutoff:3.500A) Processing helix chain 'Z' and resid 253 through 261 Processing helix chain 'Z' and resid 263 through 279 Processing helix chain 'Z' and resid 282 through 300 Processing sheet with id=AA1, first strand: chain 'G' and resid 208 through 213 removed outlier: 3.592A pdb=" N VAL G 212 " --> pdb=" O LYS G 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'T' and resid 208 through 213 removed outlier: 3.620A pdb=" N SER T 210 " --> pdb=" O THR T 251 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 5 through 6 removed outlier: 3.536A pdb=" N MET A 5 " --> pdb=" O LEU A 12 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Z' and resid 208 through 213 removed outlier: 3.572A pdb=" N SER Z 210 " --> pdb=" O THR Z 251 " (cutoff:3.500A) 842 hydrogen bonds defined for protein. 2517 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: 2.23 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3985 1.34 - 1.46: 2415 1.46 - 1.58: 6469 1.58 - 1.69: 1 1.69 - 1.81: 128 Bond restraints: 12998 Sorted by residual: bond pdb=" CA PRO S 102 " pdb=" CB PRO S 102 " ideal model delta sigma weight residual 1.536 1.499 0.038 1.39e-02 5.18e+03 7.30e+00 bond pdb=" CG PRO S 102 " pdb=" CD PRO S 102 " ideal model delta sigma weight residual 1.503 1.413 0.090 3.40e-02 8.65e+02 7.03e+00 bond pdb=" C ILE Y 101 " pdb=" N PRO Y 102 " ideal model delta sigma weight residual 1.334 1.353 -0.019 8.40e-03 1.42e+04 5.36e+00 bond pdb=" CB PRO F 102 " pdb=" CG PRO F 102 " ideal model delta sigma weight residual 1.492 1.595 -0.103 5.00e-02 4.00e+02 4.26e+00 bond pdb=" N PRO S 102 " pdb=" CD PRO S 102 " ideal model delta sigma weight residual 1.473 1.501 -0.028 1.40e-02 5.10e+03 4.02e+00 ... (remaining 12993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 17362 2.07 - 4.13: 247 4.13 - 6.20: 54 6.20 - 8.26: 10 8.26 - 10.33: 5 Bond angle restraints: 17678 Sorted by residual: angle pdb=" CA PRO F 102 " pdb=" N PRO F 102 " pdb=" CD PRO F 102 " ideal model delta sigma weight residual 112.00 104.33 7.67 1.40e+00 5.10e-01 3.00e+01 angle pdb=" CA PRO S 102 " pdb=" CB PRO S 102 " pdb=" CG PRO S 102 " ideal model delta sigma weight residual 104.50 95.11 9.39 1.90e+00 2.77e-01 2.44e+01 angle pdb=" N TRP F 177 " pdb=" CA TRP F 177 " pdb=" C TRP F 177 " ideal model delta sigma weight residual 114.56 108.39 6.17 1.27e+00 6.20e-01 2.36e+01 angle pdb=" N PRO S 102 " pdb=" CD PRO S 102 " pdb=" CG PRO S 102 " ideal model delta sigma weight residual 103.20 96.10 7.10 1.50e+00 4.44e-01 2.24e+01 angle pdb=" N VAL S 90 " pdb=" CA VAL S 90 " pdb=" C VAL S 90 " ideal model delta sigma weight residual 113.53 108.96 4.57 9.80e-01 1.04e+00 2.18e+01 ... (remaining 17673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 6432 17.74 - 35.48: 887 35.48 - 53.22: 244 53.22 - 70.96: 59 70.96 - 88.70: 20 Dihedral angle restraints: 7642 sinusoidal: 2898 harmonic: 4744 Sorted by residual: dihedral pdb=" CA ILE S 219 " pdb=" C ILE S 219 " pdb=" N SER S 220 " pdb=" CA SER S 220 " ideal model delta harmonic sigma weight residual 180.00 155.88 24.12 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ILE Y 219 " pdb=" C ILE Y 219 " pdb=" N SER Y 220 " pdb=" CA SER Y 220 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ALA T 206 " pdb=" C ALA T 206 " pdb=" N PRO T 207 " pdb=" CA PRO T 207 " ideal model delta harmonic sigma weight residual 180.00 157.43 22.57 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 7639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1698 0.052 - 0.104: 396 0.104 - 0.156: 34 0.156 - 0.208: 2 0.208 - 0.259: 1 Chirality restraints: 2131 Sorted by residual: chirality pdb=" CB ILE T 71 " pdb=" CA ILE T 71 " pdb=" CG1 ILE T 71 " pdb=" CG2 ILE T 71 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CB ILE Z 71 " pdb=" CA ILE Z 71 " pdb=" CG1 ILE Z 71 " pdb=" CG2 ILE Z 71 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CB ILE G 71 " pdb=" CA ILE G 71 " pdb=" CG1 ILE G 71 " pdb=" CG2 ILE G 71 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 2128 not shown) Planarity restraints: 2172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET Y 174 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO Y 175 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO Y 175 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO Y 175 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 101 " -0.043 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO F 102 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO F 102 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 102 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU Z 225 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO Z 226 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO Z 226 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO Z 226 " 0.030 5.00e-02 4.00e+02 ... (remaining 2169 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 246 2.69 - 3.24: 12821 3.24 - 3.79: 20759 3.79 - 4.35: 27038 4.35 - 4.90: 44997 Nonbonded interactions: 105861 Sorted by model distance: nonbonded pdb=" O LEU T 178 " pdb=" OG1 THR T 182 " model vdw 2.132 3.040 nonbonded pdb=" O PHE G 154 " pdb=" OG1 THR G 158 " model vdw 2.216 3.040 nonbonded pdb=" N GLU Z 3 " pdb=" OE1 GLU Z 3 " model vdw 2.237 3.120 nonbonded pdb=" O ASN A 9 " pdb=" OH TYR A 21 " model vdw 2.245 3.040 nonbonded pdb=" O PHE T 154 " pdb=" OG1 THR T 158 " model vdw 2.254 3.040 ... (remaining 105856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'S' selection = (chain 'Y' and resid 1 through 245) } ncs_group { reference = (chain 'G' and resid 4 through 401) selection = chain 'T' selection = (chain 'Z' and resid 4 through 401) } 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.900 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:7.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 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 : 0.003 0.103 12998 Z= 0.147 Angle : 0.656 10.328 17678 Z= 0.355 Chirality : 0.041 0.259 2131 Planarity : 0.005 0.063 2172 Dihedral : 18.200 88.702 4608 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.57 % Favored : 93.31 % Rotamer: Outliers : 4.51 % Allowed : 33.79 % Favored : 61.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.21), residues: 1675 helix: 1.56 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -1.69 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 127 TYR 0.016 0.001 TYR G 219 PHE 0.014 0.001 PHE F 109 TRP 0.015 0.001 TRP F 177 HIS 0.006 0.001 HIS G 224 Details of bonding type rmsd covalent geometry : bond 0.00323 (12998) covalent geometry : angle 0.65557 (17678) hydrogen bonds : bond 0.12665 ( 842) hydrogen bonds : angle 5.26219 ( 2517) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 197 time to evaluate : 0.646 Fit side-chains REVERT: S 102 PRO cc_start: 0.8453 (OUTLIER) cc_final: 0.8195 (Cg_endo) REVERT: T 91 GLU cc_start: 0.4374 (tp30) cc_final: 0.3774 (mp0) REVERT: T 93 ASP cc_start: 0.6534 (OUTLIER) cc_final: 0.6226 (m-30) REVERT: Y 131 LYS cc_start: 0.8565 (mttt) cc_final: 0.7977 (tptm) REVERT: Z 221 ASP cc_start: 0.7844 (t0) cc_final: 0.7208 (p0) outliers start: 59 outliers final: 48 residues processed: 251 average time/residue: 0.5143 time to fit residues: 142.5393 Evaluate side-chains 241 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 191 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 247 GLU Chi-restraints excluded: chain S residue 5 SER Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 45 THR Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 102 PRO Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain S residue 151 ARG Chi-restraints excluded: chain S residue 169 SER Chi-restraints excluded: chain S residue 177 TRP Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 53 ASP Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain T residue 167 SER Chi-restraints excluded: chain T residue 174 SER Chi-restraints excluded: chain A residue 6 ASN Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain Y residue 2 SER Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 114 VAL Chi-restraints excluded: chain Y residue 162 ILE Chi-restraints excluded: chain Y residue 167 VAL Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Z residue 11 ASP Chi-restraints excluded: chain Z residue 73 SER Chi-restraints excluded: chain Z residue 93 ASP Chi-restraints excluded: chain Z residue 148 ASN Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain Z residue 223 SER Chi-restraints excluded: chain Z residue 234 THR Chi-restraints excluded: chain Z residue 250 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 ASN T 23 GLN T 32 GLN T 66 ASN T 255 ASN Y 43 ASN ** Y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 221 GLN ** Z 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 88 ASN Z 237 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.137438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.109005 restraints weight = 18036.296| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.92 r_work: 0.3166 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12998 Z= 0.125 Angle : 0.568 11.008 17678 Z= 0.292 Chirality : 0.040 0.369 2131 Planarity : 0.004 0.061 2172 Dihedral : 6.934 58.886 1903 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.34 % Favored : 92.48 % Rotamer: Outliers : 5.43 % Allowed : 28.90 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.21), residues: 1675 helix: 1.68 (0.15), residues: 1206 sheet: -2.27 (1.92), residues: 10 loop : -1.78 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 86 TYR 0.009 0.001 TYR G 163 PHE 0.010 0.001 PHE F 109 TRP 0.012 0.001 TRP F 177 HIS 0.005 0.001 HIS G 224 Details of bonding type rmsd covalent geometry : bond 0.00260 (12998) covalent geometry : angle 0.56788 (17678) hydrogen bonds : bond 0.03897 ( 842) hydrogen bonds : angle 4.17887 ( 2517) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 203 time to evaluate : 0.470 Fit side-chains REVERT: G 105 MET cc_start: 0.6955 (OUTLIER) cc_final: 0.6319 (mmm) REVERT: S 21 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8396 (tt) REVERT: S 201 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.6776 (pmm) REVERT: T 31 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8209 (ptp) REVERT: T 91 GLU cc_start: 0.4989 (tp30) cc_final: 0.4091 (mp0) REVERT: Y 131 LYS cc_start: 0.8528 (mttt) cc_final: 0.7967 (tptm) REVERT: Z 3 GLU cc_start: 0.6799 (pm20) cc_final: 0.6293 (mm-30) outliers start: 71 outliers final: 25 residues processed: 256 average time/residue: 0.5303 time to fit residues: 149.2522 Evaluate side-chains 206 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain S residue 21 ILE Chi-restraints excluded: chain S residue 138 GLU Chi-restraints excluded: chain S residue 160 LEU Chi-restraints excluded: chain S residue 169 SER Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 201 MET Chi-restraints excluded: chain T residue 31 MET Chi-restraints excluded: chain T residue 167 SER Chi-restraints excluded: chain T residue 174 SER Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 114 VAL Chi-restraints excluded: chain Y residue 162 ILE Chi-restraints excluded: chain Y residue 167 VAL Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain Z residue 250 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 chunk 76 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 chunk 62 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 4 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: G 88 ASN G 237 GLN T 202 ASN T 255 ASN ** Y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 148 GLN ** Z 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 88 ASN Z 237 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.135658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.107032 restraints weight = 18323.328| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.94 r_work: 0.3148 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 12998 Z= 0.136 Angle : 0.564 9.355 17678 Z= 0.291 Chirality : 0.040 0.226 2131 Planarity : 0.004 0.058 2172 Dihedral : 5.589 59.859 1843 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.34 % Favored : 92.54 % Rotamer: Outliers : 5.81 % Allowed : 28.82 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.21), residues: 1675 helix: 1.72 (0.15), residues: 1206 sheet: -1.42 (1.21), residues: 20 loop : -1.78 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 86 TYR 0.007 0.001 TYR Z 48 PHE 0.010 0.001 PHE F 109 TRP 0.014 0.001 TRP S 177 HIS 0.004 0.001 HIS G 224 Details of bonding type rmsd covalent geometry : bond 0.00320 (12998) covalent geometry : angle 0.56384 (17678) hydrogen bonds : bond 0.03903 ( 842) hydrogen bonds : angle 4.07049 ( 2517) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 192 time to evaluate : 0.603 Fit side-chains REVERT: F 166 SER cc_start: 0.5884 (OUTLIER) cc_final: 0.5438 (t) REVERT: F 201 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7202 (pmm) REVERT: G 105 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6446 (mmm) REVERT: S 21 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8373 (tt) REVERT: S 201 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.6890 (pmm) REVERT: T 31 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8209 (ptp) REVERT: T 53 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7840 (p0) REVERT: T 91 GLU cc_start: 0.4680 (tp30) cc_final: 0.3842 (mp0) REVERT: T 138 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7855 (mm) REVERT: Y 131 LYS cc_start: 0.8587 (mttt) cc_final: 0.7968 (tptm) REVERT: Y 201 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.6360 (pp-130) REVERT: Y 244 MET cc_start: 0.7819 (ttm) cc_final: 0.7496 (mtp) outliers start: 76 outliers final: 32 residues processed: 244 average time/residue: 0.5157 time to fit residues: 138.8888 Evaluate side-chains 225 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 201 MET Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain S residue 21 ILE Chi-restraints excluded: chain S residue 138 GLU Chi-restraints excluded: chain S residue 151 ARG Chi-restraints excluded: chain S residue 160 LEU Chi-restraints excluded: chain S residue 169 SER Chi-restraints excluded: chain S residue 174 MET Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 201 MET Chi-restraints excluded: chain T residue 31 MET Chi-restraints excluded: chain T residue 53 ASP Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 169 ILE Chi-restraints excluded: chain T residue 174 SER Chi-restraints excluded: chain T residue 193 LEU Chi-restraints excluded: chain Y residue 2 SER Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 114 VAL Chi-restraints excluded: chain Y residue 162 ILE Chi-restraints excluded: chain Y residue 167 VAL Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 201 MET Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 29 GLU Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain Z residue 148 ASN Chi-restraints excluded: chain Z residue 167 SER Chi-restraints excluded: chain Z residue 221 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 58 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 125 optimal weight: 0.5980 chunk 48 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 8 optimal weight: 0.0970 chunk 146 optimal weight: 0.0270 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 ASN G 224 HIS G 237 GLN T 202 ASN T 255 ASN ** Y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 88 ASN Z 237 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.135603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.107506 restraints weight = 18635.226| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.76 r_work: 0.3124 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12998 Z= 0.115 Angle : 0.548 9.095 17678 Z= 0.282 Chirality : 0.040 0.393 2131 Planarity : 0.004 0.055 2172 Dihedral : 5.285 59.951 1840 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.22 % Favored : 92.66 % Rotamer: Outliers : 5.43 % Allowed : 29.59 % Favored : 64.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.21), residues: 1675 helix: 1.79 (0.15), residues: 1211 sheet: -1.34 (1.21), residues: 20 loop : -1.83 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 86 TYR 0.018 0.001 TYR G 219 PHE 0.010 0.001 PHE F 109 TRP 0.015 0.001 TRP S 177 HIS 0.008 0.001 HIS Z 224 Details of bonding type rmsd covalent geometry : bond 0.00251 (12998) covalent geometry : angle 0.54763 (17678) hydrogen bonds : bond 0.03570 ( 842) hydrogen bonds : angle 3.95140 ( 2517) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 192 time to evaluate : 0.490 Fit side-chains REVERT: F 201 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7141 (pmm) REVERT: G 105 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6438 (mmm) REVERT: S 201 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.6816 (pmm) REVERT: T 31 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8241 (ptp) REVERT: T 91 GLU cc_start: 0.4375 (tp30) cc_final: 0.3589 (mp0) REVERT: T 93 ASP cc_start: 0.6582 (OUTLIER) cc_final: 0.6288 (m-30) REVERT: T 138 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7870 (mm) REVERT: T 174 SER cc_start: 0.7472 (OUTLIER) cc_final: 0.7192 (t) REVERT: Y 131 LYS cc_start: 0.8591 (mttt) cc_final: 0.7812 (tptm) REVERT: Y 201 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.6452 (pp-130) REVERT: Y 244 MET cc_start: 0.7803 (ttm) cc_final: 0.7522 (mtp) REVERT: Z 3 GLU cc_start: 0.6421 (pm20) cc_final: 0.5917 (tp30) outliers start: 71 outliers final: 26 residues processed: 244 average time/residue: 0.5642 time to fit residues: 150.5538 Evaluate side-chains 210 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 201 MET Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain S residue 45 THR Chi-restraints excluded: chain S residue 138 GLU Chi-restraints excluded: chain S residue 151 ARG Chi-restraints excluded: chain S residue 169 SER Chi-restraints excluded: chain S residue 174 MET Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 201 MET Chi-restraints excluded: chain T residue 31 MET Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 169 ILE Chi-restraints excluded: chain T residue 174 SER Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 114 VAL Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Y residue 162 ILE Chi-restraints excluded: chain Y residue 167 VAL Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 201 MET Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain Z residue 167 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 0.0050 chunk 159 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 132 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 ASN G 237 GLN T 202 ASN T 255 ASN ** Y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 88 ASN Z 237 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107960 restraints weight = 18840.452| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.76 r_work: 0.3134 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12998 Z= 0.114 Angle : 0.546 9.315 17678 Z= 0.281 Chirality : 0.040 0.251 2131 Planarity : 0.004 0.055 2172 Dihedral : 5.115 59.445 1840 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.16 % Favored : 92.78 % Rotamer: Outliers : 4.82 % Allowed : 30.28 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.21), residues: 1675 helix: 1.83 (0.15), residues: 1212 sheet: -1.32 (1.21), residues: 20 loop : -1.81 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 127 TYR 0.007 0.001 TYR G 219 PHE 0.010 0.001 PHE G 144 TRP 0.015 0.001 TRP S 177 HIS 0.004 0.001 HIS G 224 Details of bonding type rmsd covalent geometry : bond 0.00253 (12998) covalent geometry : angle 0.54627 (17678) hydrogen bonds : bond 0.03450 ( 842) hydrogen bonds : angle 3.89095 ( 2517) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 184 time to evaluate : 0.497 Fit side-chains REVERT: F 151 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7870 (ptt-90) REVERT: F 201 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7243 (pmm) REVERT: G 97 ILE cc_start: 0.6563 (OUTLIER) cc_final: 0.6137 (mt) REVERT: G 105 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6517 (mmm) REVERT: S 21 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8374 (tt) REVERT: T 84 GLU cc_start: 0.7695 (tt0) cc_final: 0.7427 (tt0) REVERT: T 91 GLU cc_start: 0.4245 (tp30) cc_final: 0.3439 (mp0) REVERT: T 93 ASP cc_start: 0.6518 (OUTLIER) cc_final: 0.6165 (m-30) REVERT: T 138 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7897 (mm) REVERT: Y 131 LYS cc_start: 0.8488 (mttt) cc_final: 0.7969 (tptm) REVERT: Y 201 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.6520 (pp-130) REVERT: Y 244 MET cc_start: 0.7804 (ttm) cc_final: 0.7536 (mtp) REVERT: Z 3 GLU cc_start: 0.6484 (pm20) cc_final: 0.5954 (tp30) REVERT: Z 30 ARG cc_start: 0.7919 (mtm-85) cc_final: 0.7621 (mtm-85) outliers start: 63 outliers final: 27 residues processed: 226 average time/residue: 0.5609 time to fit residues: 139.1936 Evaluate side-chains 216 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 201 MET Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain S residue 21 ILE Chi-restraints excluded: chain S residue 45 THR Chi-restraints excluded: chain S residue 138 GLU Chi-restraints excluded: chain S residue 151 ARG Chi-restraints excluded: chain S residue 169 SER Chi-restraints excluded: chain S residue 174 MET Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 169 ILE Chi-restraints excluded: chain Y residue 8 LEU Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 114 VAL Chi-restraints excluded: chain Y residue 162 ILE Chi-restraints excluded: chain Y residue 167 VAL Chi-restraints excluded: chain Y residue 201 MET Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain Z residue 167 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 145 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 ASN G 224 HIS G 237 GLN T 202 ASN T 255 ASN ** Y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 88 ASN Z 237 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.107793 restraints weight = 18679.817| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.77 r_work: 0.3125 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12998 Z= 0.121 Angle : 0.551 9.666 17678 Z= 0.282 Chirality : 0.041 0.450 2131 Planarity : 0.004 0.055 2172 Dihedral : 5.020 58.988 1838 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.16 % Favored : 92.78 % Rotamer: Outliers : 5.12 % Allowed : 30.58 % Favored : 64.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.21), residues: 1675 helix: 1.84 (0.15), residues: 1213 sheet: -1.34 (1.21), residues: 20 loop : -1.78 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 127 TYR 0.018 0.001 TYR G 219 PHE 0.010 0.001 PHE F 109 TRP 0.013 0.001 TRP S 177 HIS 0.004 0.001 HIS G 298 Details of bonding type rmsd covalent geometry : bond 0.00274 (12998) covalent geometry : angle 0.55141 (17678) hydrogen bonds : bond 0.03502 ( 842) hydrogen bonds : angle 3.87559 ( 2517) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 190 time to evaluate : 0.490 Fit side-chains REVERT: F 19 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: F 151 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7982 (ptt-90) REVERT: F 201 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7297 (pmm) REVERT: G 85 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8077 (tp30) REVERT: G 97 ILE cc_start: 0.6612 (OUTLIER) cc_final: 0.6154 (mt) REVERT: G 105 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6494 (mmm) REVERT: G 174 SER cc_start: 0.6444 (OUTLIER) cc_final: 0.6232 (t) REVERT: S 99 ILE cc_start: 0.8007 (mt) cc_final: 0.7554 (mp) REVERT: T 138 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7875 (mm) REVERT: T 221 ASP cc_start: 0.8429 (t70) cc_final: 0.7511 (p0) REVERT: Y 8 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8358 (mt) REVERT: Y 131 LYS cc_start: 0.8481 (mttt) cc_final: 0.7959 (tptm) REVERT: Y 201 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.6501 (pp-130) REVERT: Y 243 LYS cc_start: 0.7731 (mtpt) cc_final: 0.7470 (mptt) REVERT: Y 244 MET cc_start: 0.7796 (ttm) cc_final: 0.7524 (mtp) REVERT: Z 3 GLU cc_start: 0.6419 (pm20) cc_final: 0.5931 (tp30) REVERT: Z 30 ARG cc_start: 0.7921 (mtm-85) cc_final: 0.7677 (mtm-85) outliers start: 67 outliers final: 29 residues processed: 239 average time/residue: 0.5599 time to fit residues: 146.6051 Evaluate side-chains 214 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 201 MET Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain S residue 45 THR Chi-restraints excluded: chain S residue 138 GLU Chi-restraints excluded: chain S residue 151 ARG Chi-restraints excluded: chain S residue 169 SER Chi-restraints excluded: chain S residue 174 MET Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 169 ILE Chi-restraints excluded: chain Y residue 2 SER Chi-restraints excluded: chain Y residue 8 LEU Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 114 VAL Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Y residue 162 ILE Chi-restraints excluded: chain Y residue 167 VAL Chi-restraints excluded: chain Y residue 201 MET Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain Z residue 148 ASN Chi-restraints excluded: chain Z residue 167 SER Chi-restraints excluded: chain Z residue 221 ASP Chi-restraints excluded: chain Z residue 250 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 119 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 117 optimal weight: 0.0870 chunk 81 optimal weight: 0.5980 chunk 82 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 70 optimal weight: 0.0770 chunk 40 optimal weight: 9.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 ASN G 224 HIS G 237 GLN T 202 ASN T 255 ASN ** Y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 88 ASN Z 237 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.108881 restraints weight = 18729.537| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.74 r_work: 0.3145 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12998 Z= 0.115 Angle : 0.557 9.943 17678 Z= 0.285 Chirality : 0.040 0.274 2131 Planarity : 0.004 0.055 2172 Dihedral : 4.924 59.079 1838 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.04 % Favored : 92.90 % Rotamer: Outliers : 4.36 % Allowed : 31.65 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.21), residues: 1675 helix: 1.91 (0.15), residues: 1209 sheet: -1.27 (1.22), residues: 20 loop : -1.77 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 127 TYR 0.008 0.001 TYR Z 48 PHE 0.010 0.001 PHE G 144 TRP 0.014 0.001 TRP S 177 HIS 0.004 0.001 HIS G 224 Details of bonding type rmsd covalent geometry : bond 0.00252 (12998) covalent geometry : angle 0.55705 (17678) hydrogen bonds : bond 0.03344 ( 842) hydrogen bonds : angle 3.83510 ( 2517) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 186 time to evaluate : 0.486 Fit side-chains REVERT: F 19 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: F 151 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7971 (ptt-90) REVERT: F 201 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8036 (ptt) REVERT: G 85 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7840 (tp30) REVERT: G 97 ILE cc_start: 0.6597 (OUTLIER) cc_final: 0.6143 (mt) REVERT: G 102 VAL cc_start: 0.8693 (t) cc_final: 0.8387 (m) REVERT: G 105 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6537 (mmm) REVERT: G 174 SER cc_start: 0.6491 (OUTLIER) cc_final: 0.6261 (t) REVERT: S 99 ILE cc_start: 0.8014 (mt) cc_final: 0.7544 (mp) REVERT: T 138 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7895 (mm) REVERT: T 221 ASP cc_start: 0.8441 (t70) cc_final: 0.7547 (p0) REVERT: Y 131 LYS cc_start: 0.8493 (mttt) cc_final: 0.7969 (tptm) REVERT: Y 201 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7600 (ptt) REVERT: Y 243 LYS cc_start: 0.7659 (mtpt) cc_final: 0.7408 (mptt) REVERT: Y 244 MET cc_start: 0.7778 (ttm) cc_final: 0.7518 (mtp) REVERT: Z 3 GLU cc_start: 0.6365 (pm20) cc_final: 0.5895 (tp30) outliers start: 57 outliers final: 27 residues processed: 221 average time/residue: 0.5532 time to fit residues: 133.8988 Evaluate side-chains 214 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 201 MET Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain G residue 279 LYS Chi-restraints excluded: chain S residue 45 THR Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 138 GLU Chi-restraints excluded: chain S residue 151 ARG Chi-restraints excluded: chain S residue 174 MET Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 169 ILE Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 114 VAL Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Y residue 162 ILE Chi-restraints excluded: chain Y residue 167 VAL Chi-restraints excluded: chain Y residue 201 MET Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain Z residue 167 SER Chi-restraints excluded: chain Z residue 250 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 62 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 50 optimal weight: 0.0170 chunk 79 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 ASN G 237 GLN T 202 ASN T 255 ASN ** Y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 88 ASN Z 237 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.140544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.113432 restraints weight = 18109.749| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.78 r_work: 0.3231 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12998 Z= 0.117 Angle : 0.558 10.069 17678 Z= 0.285 Chirality : 0.042 0.486 2131 Planarity : 0.004 0.055 2172 Dihedral : 4.845 58.921 1835 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.43 % Allowed : 31.80 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.21), residues: 1675 helix: 1.93 (0.15), residues: 1207 sheet: -1.30 (1.22), residues: 20 loop : -1.70 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 60 TYR 0.020 0.001 TYR G 219 PHE 0.010 0.001 PHE G 144 TRP 0.012 0.001 TRP S 177 HIS 0.004 0.001 HIS G 298 Details of bonding type rmsd covalent geometry : bond 0.00262 (12998) covalent geometry : angle 0.55781 (17678) hydrogen bonds : bond 0.03378 ( 842) hydrogen bonds : angle 3.81323 ( 2517) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 179 time to evaluate : 0.442 Fit side-chains REVERT: F 19 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: F 115 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8265 (mtt90) REVERT: F 151 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8000 (ptt-90) REVERT: F 166 SER cc_start: 0.6113 (OUTLIER) cc_final: 0.5628 (t) REVERT: F 201 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8073 (ptt) REVERT: G 85 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8010 (tp30) REVERT: G 97 ILE cc_start: 0.6654 (OUTLIER) cc_final: 0.6189 (mt) REVERT: G 102 VAL cc_start: 0.8646 (t) cc_final: 0.8333 (m) REVERT: G 105 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6540 (mmm) REVERT: G 174 SER cc_start: 0.6479 (OUTLIER) cc_final: 0.6214 (t) REVERT: S 99 ILE cc_start: 0.8042 (mt) cc_final: 0.7573 (mp) REVERT: T 138 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7922 (mm) REVERT: T 221 ASP cc_start: 0.8484 (t70) cc_final: 0.7698 (p0) REVERT: Y 19 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7877 (mm-30) REVERT: Y 131 LYS cc_start: 0.8485 (mttt) cc_final: 0.7951 (tptm) REVERT: Y 201 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.6575 (pp-130) REVERT: Y 243 LYS cc_start: 0.7729 (mtpt) cc_final: 0.7462 (mptt) REVERT: Y 244 MET cc_start: 0.7781 (ttm) cc_final: 0.7486 (mtp) REVERT: Z 3 GLU cc_start: 0.6391 (pm20) cc_final: 0.5896 (tp30) outliers start: 58 outliers final: 27 residues processed: 214 average time/residue: 0.5309 time to fit residues: 123.6745 Evaluate side-chains 211 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 201 MET Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain G residue 279 LYS Chi-restraints excluded: chain S residue 45 THR Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 138 GLU Chi-restraints excluded: chain S residue 151 ARG Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 142 LEU Chi-restraints excluded: chain T residue 169 ILE Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 114 VAL Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Y residue 162 ILE Chi-restraints excluded: chain Y residue 167 VAL Chi-restraints excluded: chain Y residue 201 MET Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain Z residue 167 SER Chi-restraints excluded: chain Z residue 250 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 145 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 ASN G 224 HIS G 237 GLN T 202 ASN T 255 ASN ** Y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 88 ASN Z 237 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.141240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.114464 restraints weight = 18112.764| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.76 r_work: 0.3217 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12998 Z= 0.128 Angle : 0.570 10.215 17678 Z= 0.292 Chirality : 0.041 0.409 2131 Planarity : 0.004 0.055 2172 Dihedral : 4.876 58.449 1835 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.43 % Allowed : 31.65 % Favored : 63.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.21), residues: 1675 helix: 1.90 (0.15), residues: 1210 sheet: -1.31 (1.22), residues: 20 loop : -1.71 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 60 TYR 0.009 0.001 TYR T 219 PHE 0.010 0.001 PHE G 144 TRP 0.012 0.001 TRP S 177 HIS 0.005 0.001 HIS G 224 Details of bonding type rmsd covalent geometry : bond 0.00297 (12998) covalent geometry : angle 0.57022 (17678) hydrogen bonds : bond 0.03493 ( 842) hydrogen bonds : angle 3.83673 ( 2517) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 178 time to evaluate : 0.344 Fit side-chains REVERT: F 19 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: F 115 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8259 (mtt90) REVERT: F 130 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8216 (tm-30) REVERT: F 151 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8024 (ptt-90) REVERT: F 166 SER cc_start: 0.6096 (OUTLIER) cc_final: 0.5619 (t) REVERT: F 201 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8086 (ptt) REVERT: G 97 ILE cc_start: 0.6698 (OUTLIER) cc_final: 0.6246 (mt) REVERT: G 105 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6573 (mmm) REVERT: G 174 SER cc_start: 0.6461 (OUTLIER) cc_final: 0.6200 (t) REVERT: S 99 ILE cc_start: 0.8056 (mt) cc_final: 0.7580 (mp) REVERT: S 125 MET cc_start: 0.8641 (mtm) cc_final: 0.8438 (mtp) REVERT: T 53 ASP cc_start: 0.7992 (p0) cc_final: 0.7755 (p0) REVERT: T 91 GLU cc_start: 0.4077 (tp30) cc_final: 0.3441 (mp0) REVERT: T 138 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7929 (mm) REVERT: T 221 ASP cc_start: 0.8495 (t70) cc_final: 0.7730 (p0) REVERT: Y 19 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7877 (mm-30) REVERT: Y 131 LYS cc_start: 0.8487 (mttt) cc_final: 0.7944 (tptm) REVERT: Y 201 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7615 (ptt) REVERT: Y 243 LYS cc_start: 0.7758 (mtpt) cc_final: 0.7494 (mptt) REVERT: Y 244 MET cc_start: 0.7789 (ttm) cc_final: 0.7497 (mtp) REVERT: Z 3 GLU cc_start: 0.6397 (pm20) cc_final: 0.5891 (tp30) outliers start: 58 outliers final: 32 residues processed: 216 average time/residue: 0.5255 time to fit residues: 124.1272 Evaluate side-chains 222 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 201 MET Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain G residue 279 LYS Chi-restraints excluded: chain S residue 45 THR Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 138 GLU Chi-restraints excluded: chain S residue 151 ARG Chi-restraints excluded: chain S residue 174 MET Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 142 LEU Chi-restraints excluded: chain T residue 169 ILE Chi-restraints excluded: chain Y residue 2 SER Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 114 VAL Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Y residue 162 ILE Chi-restraints excluded: chain Y residue 167 VAL Chi-restraints excluded: chain Y residue 201 MET Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 41 ILE Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain Z residue 148 ASN Chi-restraints excluded: chain Z residue 167 SER Chi-restraints excluded: chain Z residue 250 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 42 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 56 optimal weight: 0.0070 chunk 82 optimal weight: 0.8980 chunk 64 optimal weight: 0.0010 chunk 85 optimal weight: 0.8980 chunk 159 optimal weight: 0.3980 chunk 73 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 overall best weight: 0.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 ASN G 237 GLN T 202 ASN T 255 ASN ** Y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 237 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.143109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.116505 restraints weight = 18161.291| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.76 r_work: 0.3250 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12998 Z= 0.112 Angle : 0.558 10.479 17678 Z= 0.285 Chirality : 0.042 0.465 2131 Planarity : 0.004 0.055 2172 Dihedral : 4.812 58.747 1835 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.59 % Allowed : 32.11 % Favored : 64.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.21), residues: 1675 helix: 1.98 (0.15), residues: 1204 sheet: -1.29 (1.24), residues: 20 loop : -1.59 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 60 TYR 0.021 0.001 TYR G 219 PHE 0.011 0.001 PHE G 144 TRP 0.014 0.001 TRP S 177 HIS 0.003 0.000 HIS G 298 Details of bonding type rmsd covalent geometry : bond 0.00243 (12998) covalent geometry : angle 0.55764 (17678) hydrogen bonds : bond 0.03269 ( 842) hydrogen bonds : angle 3.80037 ( 2517) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 191 time to evaluate : 0.498 Fit side-chains REVERT: F 19 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: F 115 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8242 (mtt90) REVERT: F 130 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8163 (tm-30) REVERT: F 151 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7996 (ptt-90) REVERT: F 166 SER cc_start: 0.6169 (OUTLIER) cc_final: 0.5745 (t) REVERT: F 201 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8090 (ptt) REVERT: G 97 ILE cc_start: 0.6660 (OUTLIER) cc_final: 0.6201 (mt) REVERT: G 102 VAL cc_start: 0.8703 (t) cc_final: 0.8408 (m) REVERT: G 105 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6518 (mmm) REVERT: G 142 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8141 (pp) REVERT: G 174 SER cc_start: 0.6428 (OUTLIER) cc_final: 0.6154 (t) REVERT: G 224 HIS cc_start: 0.7981 (m-70) cc_final: 0.7763 (m170) REVERT: S 99 ILE cc_start: 0.8043 (mt) cc_final: 0.7567 (mp) REVERT: T 53 ASP cc_start: 0.7996 (p0) cc_final: 0.7771 (p0) REVERT: T 91 GLU cc_start: 0.4016 (tp30) cc_final: 0.3415 (mp0) REVERT: T 138 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7914 (mm) REVERT: T 221 ASP cc_start: 0.8572 (t70) cc_final: 0.7824 (p0) REVERT: Y 44 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8338 (tt) REVERT: Y 131 LYS cc_start: 0.8462 (mttt) cc_final: 0.7930 (tptm) REVERT: Y 201 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7650 (ptt) REVERT: Y 243 LYS cc_start: 0.7811 (mtpt) cc_final: 0.7463 (mptt) REVERT: Y 244 MET cc_start: 0.7768 (ttm) cc_final: 0.7507 (mtp) outliers start: 47 outliers final: 26 residues processed: 218 average time/residue: 0.5419 time to fit residues: 129.1980 Evaluate side-chains 220 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 201 MET Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain G residue 279 LYS Chi-restraints excluded: chain S residue 45 THR Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 138 GLU Chi-restraints excluded: chain S residue 151 ARG Chi-restraints excluded: chain S residue 174 MET Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 169 ILE Chi-restraints excluded: chain Y residue 2 SER Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 114 VAL Chi-restraints excluded: chain Y residue 162 ILE Chi-restraints excluded: chain Y residue 167 VAL Chi-restraints excluded: chain Y residue 201 MET Chi-restraints excluded: chain Y residue 203 THR Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain Z residue 167 SER Chi-restraints excluded: chain Z residue 250 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 6 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 161 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 ASN G 237 GLN T 255 ASN ** Y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 88 ASN Z 237 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.139418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111088 restraints weight = 18126.627| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.92 r_work: 0.3195 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12998 Z= 0.125 Angle : 0.573 10.466 17678 Z= 0.293 Chirality : 0.041 0.397 2131 Planarity : 0.004 0.056 2172 Dihedral : 4.780 58.249 1834 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.29 % Allowed : 32.57 % Favored : 64.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.21), residues: 1675 helix: 1.96 (0.15), residues: 1204 sheet: -1.32 (1.24), residues: 20 loop : -1.57 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 60 TYR 0.009 0.001 TYR Z 48 PHE 0.010 0.001 PHE G 144 TRP 0.014 0.001 TRP F 177 HIS 0.004 0.001 HIS G 298 Details of bonding type rmsd covalent geometry : bond 0.00289 (12998) covalent geometry : angle 0.57331 (17678) hydrogen bonds : bond 0.03388 ( 842) hydrogen bonds : angle 3.80726 ( 2517) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4450.57 seconds wall clock time: 76 minutes 37.10 seconds (4597.10 seconds total)