Starting phenix.real_space_refine on Sun Aug 24 05:05:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzk_41761/08_2025/8tzk_41761.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzk_41761/08_2025/8tzk_41761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tzk_41761/08_2025/8tzk_41761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzk_41761/08_2025/8tzk_41761.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tzk_41761/08_2025/8tzk_41761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzk_41761/08_2025/8tzk_41761.map" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 27 5.16 5 C 5491 2.51 5 N 1550 2.21 5 O 1535 1.98 5 H 8468 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17077 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3494 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3494 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 4369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4369 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 10, 'TRANS': 293} Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 4, 'HIS:plan': 1, 'ASP:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 118 Chain: "D" Number of atoms: 4359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4359 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 10, 'TRANS': 293} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 9, 'ASP:plan': 8, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 93 Chain: "E" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1305 Classifications: {'peptide': 101} Link IDs: {'TRANS': 100} Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 6, 'ARG:plan': 3, 'GLN:plan1': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.22, per 1000 atoms: 0.19 Number of scatterers: 17077 At special positions: 0 Unit cell: (105.84, 83.16, 149.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 27 16.00 P 4 15.00 Mg 2 11.99 O 1535 8.00 N 1550 7.00 C 5491 6.00 H 8468 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 507.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 62.6% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 49 through 58 removed outlier: 3.651A pdb=" N CYS A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 removed outlier: 3.784A pdb=" N ASN A 89 " --> pdb=" O PHE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Proline residue: A 112 - end of helix removed outlier: 3.739A pdb=" N GLU A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 134 Processing helix chain 'A' and resid 148 through 162 Processing helix chain 'A' and resid 178 through 196 removed outlier: 3.709A pdb=" N ARG A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 212 removed outlier: 3.770A pdb=" N ARG A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 58 removed outlier: 3.648A pdb=" N CYS B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 removed outlier: 3.766A pdb=" N ASN B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 Proline residue: B 112 - end of helix removed outlier: 3.759A pdb=" N GLU B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 134 Processing helix chain 'B' and resid 148 through 162 Processing helix chain 'B' and resid 178 through 196 removed outlier: 3.671A pdb=" N ARG B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 212 removed outlier: 3.766A pdb=" N ARG B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 47 removed outlier: 3.511A pdb=" N ILE C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS C 36 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 86 removed outlier: 3.604A pdb=" N THR C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 58 " --> pdb=" O ASN C 54 " (cutoff:3.500A) Proline residue: C 68 - end of helix removed outlier: 4.217A pdb=" N ALA C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.571A pdb=" N ILE C 104 " --> pdb=" O PRO C 100 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE C 105 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 136 Processing helix chain 'C' and resid 162 through 178 Processing helix chain 'C' and resid 193 through 229 removed outlier: 3.812A pdb=" N HIS C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA C 199 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY C 219 " --> pdb=" O PHE C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 240 Processing helix chain 'C' and resid 242 through 287 Proline residue: C 249 - end of helix removed outlier: 4.651A pdb=" N GLY C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ALA C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR C 287 " --> pdb=" O LEU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 326 removed outlier: 3.909A pdb=" N LEU C 302 " --> pdb=" O TRP C 298 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 47 removed outlier: 3.529A pdb=" N HIS D 36 " --> pdb=" O PHE D 32 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 85 Proline residue: D 68 - end of helix Processing helix chain 'D' and resid 100 through 114 Processing helix chain 'D' and resid 124 through 135 removed outlier: 4.046A pdb=" N TYR D 135 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 162 through 176 Processing helix chain 'D' and resid 188 through 229 removed outlier: 3.678A pdb=" N LEU D 192 " --> pdb=" O TRP D 188 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY D 219 " --> pdb=" O PHE D 215 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN D 229 " --> pdb=" O ASN D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 239 Processing helix chain 'D' and resid 242 through 286 removed outlier: 3.570A pdb=" N ILE D 246 " --> pdb=" O THR D 242 " (cutoff:3.500A) Proline residue: D 249 - end of helix removed outlier: 3.727A pdb=" N LEU D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 326 removed outlier: 3.632A pdb=" N LEU D 302 " --> pdb=" O TRP D 298 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 129 removed outlier: 3.632A pdb=" N ARG E 96 " --> pdb=" O GLU E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 191 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 removed outlier: 3.945A pdb=" N ILE A 11 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 67 " --> pdb=" O GLN A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 18 removed outlier: 3.605A pdb=" N VAL A 16 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LYS A 18 " --> pdb=" O GLN A 28 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLN A 28 " --> pdb=" O LYS A 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 40 removed outlier: 5.752A pdb=" N ALA A 40 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 170 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLY A 91 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ASP A 171 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A 93 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.570A pdb=" N GLY A 43 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 33 through 34 removed outlier: 3.920A pdb=" N ILE B 11 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 67 " --> pdb=" O GLN B 14 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 16 through 18 removed outlier: 3.622A pdb=" N VAL B 16 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LYS B 18 " --> pdb=" O GLN B 28 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLN B 28 " --> pdb=" O LYS B 18 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 40 removed outlier: 5.745A pdb=" N ALA B 40 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 170 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY B 91 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASP B 171 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL B 93 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.571A pdb=" N GLY B 43 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.633A pdb=" N VAL C 153 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 117 through 123 removed outlier: 3.978A pdb=" N LYS D 119 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL D 153 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP D 181 " --> pdb=" O TYR D 94 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1662 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.71 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8462 1.03 - 1.23: 6 1.23 - 1.42: 3534 1.42 - 1.61: 5162 1.61 - 1.81: 54 Bond restraints: 17218 Sorted by residual: bond pdb=" C6 ADP A 302 " pdb=" N6 ADP A 302 " ideal model delta sigma weight residual 1.355 1.450 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C6 ADP B 302 " pdb=" N6 ADP B 302 " ideal model delta sigma weight residual 1.355 1.449 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C4 ADP A 302 " pdb=" C5 ADP A 302 " ideal model delta sigma weight residual 1.490 1.397 0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" C4 ADP B 302 " pdb=" C5 ADP B 302 " ideal model delta sigma weight residual 1.490 1.397 0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" O3A ADP B 302 " pdb=" PB ADP B 302 " ideal model delta sigma weight residual 1.610 1.684 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 17213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 29309 2.11 - 4.22: 1735 4.22 - 6.33: 56 6.33 - 8.44: 6 8.44 - 10.55: 10 Bond angle restraints: 31116 Sorted by residual: angle pdb=" O2B ADP B 302 " pdb=" PB ADP B 302 " pdb=" O3B ADP B 302 " ideal model delta sigma weight residual 119.90 109.35 10.55 3.00e+00 1.11e-01 1.24e+01 angle pdb=" O2B ADP A 302 " pdb=" PB ADP A 302 " pdb=" O3B ADP A 302 " ideal model delta sigma weight residual 119.90 109.45 10.45 3.00e+00 1.11e-01 1.21e+01 angle pdb=" N ILE D 239 " pdb=" CA ILE D 239 " pdb=" C ILE D 239 " ideal model delta sigma weight residual 110.21 106.30 3.91 1.13e+00 7.83e-01 1.20e+01 angle pdb=" O1B ADP B 302 " pdb=" PB ADP B 302 " pdb=" O3B ADP B 302 " ideal model delta sigma weight residual 119.90 109.67 10.23 3.00e+00 1.11e-01 1.16e+01 angle pdb=" O1B ADP B 302 " pdb=" PB ADP B 302 " pdb=" O2B ADP B 302 " ideal model delta sigma weight residual 119.90 109.72 10.18 3.00e+00 1.11e-01 1.15e+01 ... (remaining 31111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.87: 7770 24.87 - 49.73: 219 49.73 - 74.60: 65 74.60 - 99.46: 1 99.46 - 124.33: 6 Dihedral angle restraints: 8061 sinusoidal: 4289 harmonic: 3772 Sorted by residual: dihedral pdb=" O2A ADP B 302 " pdb=" O3A ADP B 302 " pdb=" PA ADP B 302 " pdb=" PB ADP B 302 " ideal model delta sinusoidal sigma weight residual -60.00 64.33 -124.33 1 2.00e+01 2.50e-03 3.75e+01 dihedral pdb=" O1B ADP A 302 " pdb=" O3A ADP A 302 " pdb=" PB ADP A 302 " pdb=" PA ADP A 302 " ideal model delta sinusoidal sigma weight residual -60.00 61.90 -121.90 1 2.00e+01 2.50e-03 3.67e+01 dihedral pdb=" O1B ADP B 302 " pdb=" O3A ADP B 302 " pdb=" PB ADP B 302 " pdb=" PA ADP B 302 " ideal model delta sinusoidal sigma weight residual -60.00 59.60 -119.60 1 2.00e+01 2.50e-03 3.59e+01 ... (remaining 8058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1173 0.042 - 0.084: 179 0.084 - 0.126: 61 0.126 - 0.168: 5 0.168 - 0.211: 6 Chirality restraints: 1424 Sorted by residual: chirality pdb=" C2' ADP A 302 " pdb=" C1' ADP A 302 " pdb=" C3' ADP A 302 " pdb=" O2' ADP A 302 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C3' ADP A 302 " pdb=" C2' ADP A 302 " pdb=" C4' ADP A 302 " pdb=" O3' ADP A 302 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C3' ADP B 302 " pdb=" C2' ADP B 302 " pdb=" C4' ADP B 302 " pdb=" O3' ADP B 302 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1421 not shown) Planarity restraints: 2615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 87 " 0.014 5.00e-02 4.00e+02 2.13e-02 7.24e-01 pdb=" N PRO C 88 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO C 88 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 88 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 212 " 0.013 5.00e-02 4.00e+02 2.02e-02 6.54e-01 pdb=" N PRO B 213 " -0.035 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 101 " 0.012 5.00e-02 4.00e+02 1.84e-02 5.40e-01 pdb=" N PRO C 102 " -0.032 5.00e-02 4.00e+02 pdb=" CA PRO C 102 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO C 102 " 0.010 5.00e-02 4.00e+02 ... (remaining 2612 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 379 2.13 - 2.75: 31413 2.75 - 3.36: 46217 3.36 - 3.98: 55796 3.98 - 4.60: 90294 Nonbonded interactions: 224099 Sorted by model distance: nonbonded pdb=" O GLU B 116 " pdb=" HG SER B 117 " model vdw 1.511 2.450 nonbonded pdb=" O LEU E 122 " pdb=" HG1 THR E 125 " model vdw 1.588 2.450 nonbonded pdb=" O GLU A 116 " pdb=" HG SER A 117 " model vdw 1.623 2.450 nonbonded pdb=" HD1 HIS D 36 " pdb=" OH TYR D 252 " model vdw 1.643 2.450 nonbonded pdb="HE21 GLN A 25 " pdb=" OE1 GLN A 28 " model vdw 1.668 2.450 ... (remaining 224094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 27 through 83 or (resid 84 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 85 through 91 or (resid \ 92 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 93 through 99 or (resid 100 and (name N or name CA or name C or name O \ or name CB or name HA )) or resid 101 or (resid 102 and (name N or name CA or n \ ame C or name O or name CB or name HA )) or (resid 103 through 117 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 118 th \ rough 120 or (resid 121 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 122 through 123 or (resid 124 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 125 through \ 152 or (resid 153 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 154 or (resid 155 through 157 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or (resid 158 and (name N o \ r name CA or name C or name O or name CB or name HA )) or resid 159 through 230 \ or (resid 231 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 232 through 241 or (resid 242 through 243 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 244 throug \ h 291 or (resid 292 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 293 or (resid 294 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 295 through 330)) selection = (chain 'D' and (resid 27 or (resid 28 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 29 through 35 or (resid 36 and (nam \ e N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 \ or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD \ 2 or name HE1 or name HE2)) or resid 37 through 82 or (resid 83 through 84 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 85 through 89 or (resid 90 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 91 through 94 or (resid 95 through 96 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 97 through 110 or (resid 111 through 117 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 118 through 148 or (resid 149 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 150 through 162 or (resid 163 through 169 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 170 through 172 or (resid \ 173 through 174 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 175 through 178 or (resid 179 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 180 or (resid 181 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 182 through 183 or (resid 184 through 187 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 188 through 191 or (resid \ 192 through 193 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 194 through 195 or (resid 196 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 197 through 287 or \ (resid 288 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 289 through 330)) } 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 group one per residue 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: 6.200 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: 0.110 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.920 Find NCS groups from input model: 0.200 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: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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 : 0.004 0.095 8750 Z= 0.187 Angle : 0.527 10.553 11890 Z= 0.246 Chirality : 0.037 0.211 1424 Planarity : 0.002 0.021 1509 Dihedral : 11.132 124.329 3110 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.24 (0.26), residues: 1139 helix: 3.71 (0.19), residues: 672 sheet: 0.47 (0.56), residues: 103 loop : -0.50 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 126 TYR 0.008 0.001 TYR D 252 PHE 0.006 0.001 PHE C 257 TRP 0.004 0.001 TRP C 298 HIS 0.002 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8750) covalent geometry : angle 0.52734 (11890) hydrogen bonds : bond 0.12861 ( 558) hydrogen bonds : angle 4.69838 ( 1662) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.8660 (mmm) cc_final: 0.8316 (mmt) REVERT: C 41 LYS cc_start: 0.8721 (tttt) cc_final: 0.8507 (ttmm) REVERT: C 63 MET cc_start: 0.8253 (mtm) cc_final: 0.7979 (mtt) REVERT: D 223 ARG cc_start: 0.7435 (ttm-80) cc_final: 0.7216 (ttp-170) REVERT: E 123 LEU cc_start: 0.9022 (tt) cc_final: 0.8528 (mt) REVERT: E 141 ARG cc_start: 0.7904 (mtp180) cc_final: 0.7581 (tpm170) REVERT: E 170 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8414 (tm-30) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.3346 time to fit residues: 81.2361 Evaluate side-chains 114 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.0030 chunk 100 optimal weight: 0.6980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN B 80 ASN E 111 GLN E 161 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.112763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.089225 restraints weight = 48636.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.093337 restraints weight = 19766.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.096017 restraints weight = 10919.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.097427 restraints weight = 7118.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.098597 restraints weight = 5437.438| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8750 Z= 0.159 Angle : 0.565 6.949 11890 Z= 0.286 Chirality : 0.037 0.166 1424 Planarity : 0.003 0.034 1509 Dihedral : 8.174 130.453 1262 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.20 % Allowed : 8.07 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.94 (0.26), residues: 1139 helix: 3.47 (0.19), residues: 680 sheet: 0.12 (0.54), residues: 100 loop : -0.66 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 126 TYR 0.015 0.001 TYR D 252 PHE 0.016 0.001 PHE C 215 TRP 0.003 0.001 TRP D 256 HIS 0.003 0.001 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8750) covalent geometry : angle 0.56454 (11890) hydrogen bonds : bond 0.04998 ( 558) hydrogen bonds : angle 4.23477 ( 1662) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7599 (mt-10) REVERT: B 101 MET cc_start: 0.8694 (mmm) cc_final: 0.8422 (mmt) REVERT: C 41 LYS cc_start: 0.8701 (tttt) cc_final: 0.8486 (ttmm) REVERT: C 127 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7950 (mm-40) REVERT: D 223 ARG cc_start: 0.7457 (ttm-80) cc_final: 0.7169 (ttp-170) REVERT: D 306 MET cc_start: 0.6643 (tmm) cc_final: 0.6396 (tmm) REVERT: E 123 LEU cc_start: 0.8967 (tt) cc_final: 0.8482 (mt) REVERT: E 141 ARG cc_start: 0.7968 (mtp180) cc_final: 0.7603 (tpm170) REVERT: E 170 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8344 (tm-30) outliers start: 10 outliers final: 8 residues processed: 130 average time/residue: 0.2890 time to fit residues: 48.7687 Evaluate side-chains 120 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 99 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.110076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.086323 restraints weight = 49168.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.090433 restraints weight = 20404.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.092920 restraints weight = 11377.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.094693 restraints weight = 7627.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.095560 restraints weight = 5666.107| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8750 Z= 0.211 Angle : 0.565 5.735 11890 Z= 0.294 Chirality : 0.038 0.156 1424 Planarity : 0.003 0.029 1509 Dihedral : 7.692 122.191 1262 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.45 % Allowed : 9.52 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.53 (0.25), residues: 1139 helix: 3.22 (0.19), residues: 682 sheet: -0.19 (0.52), residues: 102 loop : -0.97 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 126 TYR 0.013 0.002 TYR D 252 PHE 0.026 0.001 PHE C 291 TRP 0.004 0.001 TRP D 256 HIS 0.004 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 8750) covalent geometry : angle 0.56507 (11890) hydrogen bonds : bond 0.04959 ( 558) hydrogen bonds : angle 4.19606 ( 1662) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7607 (mt-10) REVERT: B 101 MET cc_start: 0.8701 (mmm) cc_final: 0.8377 (mmt) REVERT: C 41 LYS cc_start: 0.8749 (tttt) cc_final: 0.8531 (ttmm) REVERT: D 223 ARG cc_start: 0.7371 (ttm-80) cc_final: 0.7160 (ttp-170) REVERT: D 306 MET cc_start: 0.6707 (tmm) cc_final: 0.6416 (tmm) REVERT: E 123 LEU cc_start: 0.8978 (tt) cc_final: 0.8494 (mt) REVERT: E 141 ARG cc_start: 0.7936 (mtp180) cc_final: 0.7618 (tpm170) REVERT: E 170 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8359 (tm-30) outliers start: 12 outliers final: 11 residues processed: 125 average time/residue: 0.2955 time to fit residues: 47.7190 Evaluate side-chains 120 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 77 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 113 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.110382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.086600 restraints weight = 48720.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.090566 restraints weight = 20215.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.093253 restraints weight = 11362.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.094673 restraints weight = 7486.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.095869 restraints weight = 5736.320| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8750 Z= 0.158 Angle : 0.523 5.974 11890 Z= 0.266 Chirality : 0.037 0.157 1424 Planarity : 0.003 0.028 1509 Dihedral : 7.310 119.197 1262 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.57 % Allowed : 9.88 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.25), residues: 1139 helix: 3.26 (0.19), residues: 682 sheet: -0.25 (0.51), residues: 102 loop : -0.86 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 24 TYR 0.011 0.001 TYR D 252 PHE 0.009 0.001 PHE A 32 TRP 0.004 0.001 TRP D 256 HIS 0.004 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8750) covalent geometry : angle 0.52294 (11890) hydrogen bonds : bond 0.04641 ( 558) hydrogen bonds : angle 4.03741 ( 1662) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7598 (mt-10) REVERT: B 101 MET cc_start: 0.8703 (mmm) cc_final: 0.8441 (mmt) REVERT: C 41 LYS cc_start: 0.8743 (tttt) cc_final: 0.8523 (ttmm) REVERT: C 291 PHE cc_start: 0.7329 (t80) cc_final: 0.6814 (t80) REVERT: D 223 ARG cc_start: 0.7342 (ttm-80) cc_final: 0.7095 (ttp-170) REVERT: D 306 MET cc_start: 0.6739 (tmm) cc_final: 0.6435 (tmm) REVERT: E 123 LEU cc_start: 0.8970 (tt) cc_final: 0.8506 (mt) REVERT: E 141 ARG cc_start: 0.7974 (mtp180) cc_final: 0.7624 (tpm170) REVERT: E 170 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8423 (tm-30) outliers start: 13 outliers final: 11 residues processed: 125 average time/residue: 0.2759 time to fit residues: 44.4601 Evaluate side-chains 122 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 4 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 80 ASN B 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.105650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.081340 restraints weight = 50152.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.085318 restraints weight = 21353.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.087793 restraints weight = 12125.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.089490 restraints weight = 8201.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.090371 restraints weight = 6130.512| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8750 Z= 0.205 Angle : 0.554 5.796 11890 Z= 0.287 Chirality : 0.037 0.155 1424 Planarity : 0.003 0.047 1509 Dihedral : 7.348 119.226 1262 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.81 % Allowed : 10.96 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.25), residues: 1139 helix: 3.15 (0.19), residues: 682 sheet: -0.43 (0.50), residues: 102 loop : -1.00 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 103 TYR 0.012 0.001 TYR C 250 PHE 0.011 0.001 PHE A 32 TRP 0.011 0.001 TRP C 298 HIS 0.006 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 8750) covalent geometry : angle 0.55442 (11890) hydrogen bonds : bond 0.04814 ( 558) hydrogen bonds : angle 4.06760 ( 1662) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7656 (mt-10) REVERT: B 101 MET cc_start: 0.8717 (mmm) cc_final: 0.8460 (mmt) REVERT: C 41 LYS cc_start: 0.8769 (tttt) cc_final: 0.8518 (ttmm) REVERT: C 291 PHE cc_start: 0.7521 (t80) cc_final: 0.6864 (t80) REVERT: D 223 ARG cc_start: 0.7314 (ttm-80) cc_final: 0.7028 (ttp-170) REVERT: D 306 MET cc_start: 0.6742 (tmm) cc_final: 0.6398 (tmm) REVERT: E 123 LEU cc_start: 0.8925 (tt) cc_final: 0.8492 (mt) REVERT: E 141 ARG cc_start: 0.8035 (mtp180) cc_final: 0.7663 (tpm170) REVERT: E 170 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8392 (tm-30) outliers start: 15 outliers final: 12 residues processed: 124 average time/residue: 0.2833 time to fit residues: 45.4217 Evaluate side-chains 122 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 18 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 37 optimal weight: 0.0980 chunk 7 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.110363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.086463 restraints weight = 48507.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.090468 restraints weight = 20153.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.093071 restraints weight = 11330.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.094688 restraints weight = 7538.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.095536 restraints weight = 5678.431| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8750 Z= 0.128 Angle : 0.510 6.197 11890 Z= 0.257 Chirality : 0.036 0.160 1424 Planarity : 0.003 0.043 1509 Dihedral : 7.108 117.950 1262 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.33 % Allowed : 11.08 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.62 (0.25), residues: 1139 helix: 3.35 (0.19), residues: 678 sheet: -0.45 (0.50), residues: 102 loop : -0.90 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 50 TYR 0.011 0.001 TYR D 252 PHE 0.008 0.001 PHE A 32 TRP 0.005 0.001 TRP C 298 HIS 0.005 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8750) covalent geometry : angle 0.51029 (11890) hydrogen bonds : bond 0.04437 ( 558) hydrogen bonds : angle 3.85605 ( 1662) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7574 (mt-10) REVERT: B 101 MET cc_start: 0.8676 (mmm) cc_final: 0.8358 (mmt) REVERT: C 41 LYS cc_start: 0.8743 (tttt) cc_final: 0.8512 (ttmm) REVERT: C 291 PHE cc_start: 0.7421 (t80) cc_final: 0.6814 (t80) REVERT: D 223 ARG cc_start: 0.7289 (ttm-80) cc_final: 0.7056 (ttp-170) REVERT: D 306 MET cc_start: 0.6823 (tmm) cc_final: 0.6472 (tmm) REVERT: D 326 GLU cc_start: 0.8500 (pp20) cc_final: 0.8169 (pp20) REVERT: E 123 LEU cc_start: 0.8939 (tt) cc_final: 0.8516 (mt) REVERT: E 141 ARG cc_start: 0.7993 (mtp180) cc_final: 0.7659 (tpm170) REVERT: E 170 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8403 (tm-30) outliers start: 11 outliers final: 11 residues processed: 124 average time/residue: 0.2777 time to fit residues: 44.5855 Evaluate side-chains 123 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 80 optimal weight: 0.6980 chunk 39 optimal weight: 0.2980 chunk 102 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 60 optimal weight: 0.0870 chunk 1 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN B 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.110271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.086372 restraints weight = 48780.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.090362 restraints weight = 20218.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.093045 restraints weight = 11386.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.094605 restraints weight = 7517.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.095567 restraints weight = 5695.456| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8750 Z= 0.140 Angle : 0.516 6.055 11890 Z= 0.261 Chirality : 0.037 0.165 1424 Planarity : 0.003 0.032 1509 Dihedral : 7.002 117.643 1262 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.57 % Allowed : 11.08 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.25), residues: 1139 helix: 3.33 (0.19), residues: 678 sheet: -0.12 (0.51), residues: 92 loop : -1.00 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 50 TYR 0.011 0.001 TYR D 252 PHE 0.009 0.001 PHE A 32 TRP 0.004 0.001 TRP C 298 HIS 0.005 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8750) covalent geometry : angle 0.51591 (11890) hydrogen bonds : bond 0.04391 ( 558) hydrogen bonds : angle 3.82232 ( 1662) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7597 (mt-10) REVERT: B 101 MET cc_start: 0.8676 (mmm) cc_final: 0.8369 (mmt) REVERT: C 41 LYS cc_start: 0.8739 (tttt) cc_final: 0.8506 (ttmm) REVERT: C 291 PHE cc_start: 0.7432 (t80) cc_final: 0.6858 (t80) REVERT: D 223 ARG cc_start: 0.7298 (ttm-80) cc_final: 0.7065 (ttp-170) REVERT: D 326 GLU cc_start: 0.8566 (pp20) cc_final: 0.8192 (pp20) REVERT: E 123 LEU cc_start: 0.8961 (tt) cc_final: 0.8549 (mt) REVERT: E 141 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7642 (tpm170) REVERT: E 170 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8389 (tm-30) outliers start: 13 outliers final: 10 residues processed: 123 average time/residue: 0.2948 time to fit residues: 46.6826 Evaluate side-chains 122 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 66 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 29 optimal weight: 0.0870 chunk 104 optimal weight: 30.0000 chunk 9 optimal weight: 0.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 193 ASN B 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.110633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.086754 restraints weight = 48497.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.090797 restraints weight = 20133.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.093193 restraints weight = 11260.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.095028 restraints weight = 7625.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.095882 restraints weight = 5644.810| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8750 Z= 0.121 Angle : 0.511 6.186 11890 Z= 0.255 Chirality : 0.036 0.168 1424 Planarity : 0.003 0.029 1509 Dihedral : 6.875 117.058 1262 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.69 % Allowed : 11.45 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.70 (0.25), residues: 1139 helix: 3.39 (0.19), residues: 681 sheet: -0.09 (0.51), residues: 92 loop : -0.97 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 126 TYR 0.010 0.001 TYR D 252 PHE 0.008 0.001 PHE A 32 TRP 0.003 0.000 TRP C 298 HIS 0.005 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8750) covalent geometry : angle 0.51141 (11890) hydrogen bonds : bond 0.04217 ( 558) hydrogen bonds : angle 3.73060 ( 1662) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7578 (mt-10) REVERT: A 113 MET cc_start: 0.7700 (mtp) cc_final: 0.7270 (mtp) REVERT: B 101 MET cc_start: 0.8656 (mmm) cc_final: 0.8344 (mmt) REVERT: C 41 LYS cc_start: 0.8730 (tttt) cc_final: 0.8501 (ttmm) REVERT: C 291 PHE cc_start: 0.7426 (t80) cc_final: 0.6864 (t80) REVERT: D 223 ARG cc_start: 0.7272 (ttm-80) cc_final: 0.7063 (ttp-170) REVERT: D 326 GLU cc_start: 0.8560 (pp20) cc_final: 0.8177 (pp20) REVERT: E 119 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8163 (tp) REVERT: E 123 LEU cc_start: 0.8984 (tt) cc_final: 0.8569 (mt) REVERT: E 141 ARG cc_start: 0.7974 (mtp180) cc_final: 0.7644 (tpm170) REVERT: E 170 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8438 (tm-30) outliers start: 14 outliers final: 12 residues processed: 123 average time/residue: 0.2826 time to fit residues: 45.0474 Evaluate side-chains 125 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 1 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN E 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.105611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.081292 restraints weight = 49983.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.085225 restraints weight = 21210.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.087750 restraints weight = 12082.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.089283 restraints weight = 8163.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.090476 restraints weight = 6222.868| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8750 Z= 0.189 Angle : 0.547 6.397 11890 Z= 0.280 Chirality : 0.037 0.166 1424 Planarity : 0.003 0.030 1509 Dihedral : 7.006 119.301 1262 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.81 % Allowed : 11.57 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.51 (0.25), residues: 1139 helix: 3.24 (0.19), residues: 679 sheet: 0.07 (0.55), residues: 72 loop : -1.04 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 50 TYR 0.011 0.001 TYR C 250 PHE 0.013 0.001 PHE A 32 TRP 0.005 0.001 TRP C 298 HIS 0.006 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 8750) covalent geometry : angle 0.54749 (11890) hydrogen bonds : bond 0.04506 ( 558) hydrogen bonds : angle 3.88186 ( 1662) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7645 (mt-10) REVERT: A 113 MET cc_start: 0.7710 (mtp) cc_final: 0.7275 (mtp) REVERT: B 101 MET cc_start: 0.8701 (mmm) cc_final: 0.8408 (mmt) REVERT: C 41 LYS cc_start: 0.8754 (tttt) cc_final: 0.8511 (ttmm) REVERT: C 291 PHE cc_start: 0.7526 (t80) cc_final: 0.6977 (t80) REVERT: D 223 ARG cc_start: 0.7290 (ttm-80) cc_final: 0.7020 (ttp-170) REVERT: D 324 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8694 (mp) REVERT: D 326 GLU cc_start: 0.8631 (pp20) cc_final: 0.8266 (pp20) REVERT: E 119 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8108 (tp) REVERT: E 123 LEU cc_start: 0.8937 (tt) cc_final: 0.8559 (mt) REVERT: E 141 ARG cc_start: 0.8045 (mtp180) cc_final: 0.7644 (tpm170) REVERT: E 167 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8563 (mm-30) REVERT: E 170 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8374 (tm-30) outliers start: 15 outliers final: 11 residues processed: 122 average time/residue: 0.2660 time to fit residues: 42.1716 Evaluate side-chains 125 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 5 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.109015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.085217 restraints weight = 48688.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.089242 restraints weight = 20211.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.091852 restraints weight = 11339.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.093291 restraints weight = 7520.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.094489 restraints weight = 5753.807| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8750 Z= 0.169 Angle : 0.538 7.022 11890 Z= 0.274 Chirality : 0.037 0.168 1424 Planarity : 0.003 0.032 1509 Dihedral : 7.022 118.909 1262 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.69 % Allowed : 11.57 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.25), residues: 1139 helix: 3.22 (0.19), residues: 679 sheet: 0.10 (0.56), residues: 70 loop : -1.05 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 50 TYR 0.010 0.001 TYR C 250 PHE 0.011 0.001 PHE A 32 TRP 0.007 0.001 TRP C 298 HIS 0.005 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8750) covalent geometry : angle 0.53761 (11890) hydrogen bonds : bond 0.04474 ( 558) hydrogen bonds : angle 3.84703 ( 1662) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7650 (mt-10) REVERT: A 113 MET cc_start: 0.7887 (mtp) cc_final: 0.7525 (mtp) REVERT: B 101 MET cc_start: 0.8708 (mmm) cc_final: 0.8402 (mmt) REVERT: C 41 LYS cc_start: 0.8763 (tttt) cc_final: 0.8539 (ttmm) REVERT: C 291 PHE cc_start: 0.7526 (t80) cc_final: 0.6991 (t80) REVERT: D 223 ARG cc_start: 0.7296 (ttm-80) cc_final: 0.7073 (ttp-170) REVERT: D 324 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8788 (mp) REVERT: D 326 GLU cc_start: 0.8560 (pp20) cc_final: 0.8226 (pp20) REVERT: E 119 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8158 (tp) REVERT: E 123 LEU cc_start: 0.8976 (tt) cc_final: 0.8587 (mt) REVERT: E 141 ARG cc_start: 0.8020 (mtp180) cc_final: 0.7656 (tpm170) REVERT: E 167 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8510 (mm-30) REVERT: E 170 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8380 (tm-30) outliers start: 14 outliers final: 11 residues processed: 122 average time/residue: 0.2744 time to fit residues: 43.0843 Evaluate side-chains 125 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 77 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN E 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.108826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.085053 restraints weight = 48844.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.089101 restraints weight = 20231.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.091703 restraints weight = 11335.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.093109 restraints weight = 7516.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.094321 restraints weight = 5788.601| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8750 Z= 0.169 Angle : 0.545 6.534 11890 Z= 0.278 Chirality : 0.037 0.168 1424 Planarity : 0.003 0.031 1509 Dihedral : 6.996 118.883 1262 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.69 % Allowed : 11.69 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.25), residues: 1139 helix: 3.23 (0.19), residues: 676 sheet: 0.04 (0.55), residues: 70 loop : -1.08 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 50 TYR 0.010 0.001 TYR C 250 PHE 0.011 0.001 PHE A 32 TRP 0.005 0.001 TRP C 298 HIS 0.005 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8750) covalent geometry : angle 0.54526 (11890) hydrogen bonds : bond 0.04477 ( 558) hydrogen bonds : angle 3.83856 ( 1662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3247.59 seconds wall clock time: 56 minutes 1.40 seconds (3361.40 seconds total)