Starting phenix.real_space_refine on Mon Jun 16 18:04:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzl_41762/06_2025/8tzl_41762_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzl_41762/06_2025/8tzl_41762.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tzl_41762/06_2025/8tzl_41762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzl_41762/06_2025/8tzl_41762.map" model { file = "/net/cci-nas-00/data/ceres_data/8tzl_41762/06_2025/8tzl_41762_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzl_41762/06_2025/8tzl_41762_neut.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 27 5.16 5 C 6217 2.51 5 N 1799 2.21 5 O 1784 1.98 5 H 9042 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18875 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: {'GLU:plan': 2, 'ASP:plan': 1} 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: {'GLU:plan': 2, 'ASP:plan': 1} 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: {'GLN:plan1': 4, 'GLU:plan': 10, 'ASP:plan': 9, 'ARG:plan': 6, 'HIS:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 5, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 93 Chain: "E" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 3103 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 5, 'TRANS': 344} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 896 Unresolved non-hydrogen angles: 1133 Unresolved non-hydrogen dihedrals: 720 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'GLN:plan1': 34, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 18, 'TRP:plan': 3, 'ASP:plan': 10, 'PHE:plan': 5, 'GLU:plan': 24, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 522 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: 11.05, per 1000 atoms: 0.59 Number of scatterers: 18875 At special positions: 0 Unit cell: (183.6, 93.96, 176.04, 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 1784 8.00 N 1799 7.00 C 6217 6.00 H 9042 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: 5.36 Conformation dependent library (CDL) restraints added in 1.7 seconds 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2624 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 12 sheets defined 60.2% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 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 35 through 129 removed outlier: 4.460A pdb=" N GLN E 39 " --> pdb=" O PHE E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 219 Processing helix chain 'E' and resid 221 through 247 Processing helix chain 'E' and resid 254 through 258 Processing helix chain 'E' and resid 375 through 379 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) Processing sheet with id=AB2, first strand: chain 'E' and resid 269 through 271 removed outlier: 6.723A pdb=" N VAL E 287 " --> pdb=" O LEU E 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 286 through 289 current: chain 'E' and resid 314 through 320 removed outlier: 5.561A pdb=" N LEU E 315 " --> pdb=" O PHE E 331 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 325 through 335 current: chain 'E' and resid 372 through 374 Processing sheet with id=AB3, first strand: chain 'E' and resid 276 through 278 removed outlier: 6.926A pdb=" N ILE E 281 " --> pdb=" O GLN E 277 " (cutoff:3.500A) 677 hydrogen bonds defined for protein. 2007 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.58 Time building geometry restraints manager: 6.42 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: 9036 1.03 - 1.23: 6 1.23 - 1.42: 4032 1.42 - 1.61: 5888 1.61 - 1.81: 54 Bond restraints: 19016 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 19011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 32354 2.11 - 4.22: 1782 4.22 - 6.33: 62 6.33 - 8.44: 6 8.44 - 10.55: 10 Bond angle restraints: 34214 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 34209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.87: 8721 24.87 - 49.73: 237 49.73 - 74.60: 71 74.60 - 99.46: 1 99.46 - 124.33: 6 Dihedral angle restraints: 9036 sinusoidal: 4559 harmonic: 4477 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 9033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1365 0.042 - 0.084: 201 0.084 - 0.126: 75 0.126 - 0.168: 5 0.168 - 0.211: 6 Chirality restraints: 1652 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 1649 not shown) Planarity restraints: 3108 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 3105 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 408 2.13 - 2.75: 33702 2.75 - 3.36: 49901 3.36 - 3.98: 59941 3.98 - 4.60: 96654 Nonbonded interactions: 240606 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 240601 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: 6.780 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: 0.360 Extract box with map and model: 0.730 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 44.140 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 9974 Z= 0.178 Angle : 0.510 10.553 13591 Z= 0.250 Chirality : 0.037 0.211 1652 Planarity : 0.002 0.021 1758 Dihedral : 10.725 124.329 3359 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.24), residues: 1388 helix: 4.13 (0.17), residues: 788 sheet: 1.11 (0.50), residues: 129 loop : -0.11 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 298 HIS 0.002 0.001 HIS B 97 PHE 0.006 0.001 PHE C 257 TYR 0.008 0.001 TYR D 252 ARG 0.003 0.000 ARG B 126 Details of bonding type rmsd hydrogen bonds : bond 0.14199 ( 677) hydrogen bonds : angle 4.53754 ( 2007) covalent geometry : bond 0.00363 ( 9974) covalent geometry : angle 0.50999 (13591) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 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 SER 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LYS 88 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. Residue LEU 191 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue THR 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue SER 220 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue MET 251 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue SER 256 is missing expected H atoms. Skipping. Residue LYS 260 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LEU 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue TYR 292 is missing expected H atoms. Skipping. Residue VAL 296 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue TYR 300 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue ILE 304 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue TYR 313 is missing expected H atoms. Skipping. Residue LEU 315 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue MET 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue THR 334 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LYS 337 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue VAL 343 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Residue THR 345 is missing expected H atoms. Skipping. Residue THR 348 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue SER 359 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue TYR 364 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue SER 371 is missing expected H atoms. Skipping. Residue SER 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.509 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: 0.8668 (mmm) cc_final: 0.8325 (mmt) REVERT: C 63 MET cc_start: 0.8265 (mtm) cc_final: 0.8004 (mtt) REVERT: D 223 ARG cc_start: 0.7460 (ttm-80) cc_final: 0.7216 (ttp-170) REVERT: E 123 LEU cc_start: 0.9023 (tt) cc_final: 0.8551 (mt) REVERT: E 141 ARG cc_start: 0.7897 (mtp180) cc_final: 0.7570 (tpm170) REVERT: E 170 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8426 (tm-30) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.6434 time to fit residues: 159.3030 Evaluate side-chains 114 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 0.9980 chunk 105 optimal weight: 50.0000 chunk 58 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 chunk 71 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 108 optimal weight: 30.0000 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 81 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.136719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.091985 restraints weight = 53416.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.095455 restraints weight = 21629.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.097523 restraints weight = 11975.108| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9974 Z= 0.157 Angle : 0.536 7.250 13591 Z= 0.276 Chirality : 0.037 0.156 1652 Planarity : 0.003 0.023 1758 Dihedral : 7.503 130.499 1511 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.33 % Allowed : 7.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.23), residues: 1388 helix: 3.75 (0.17), residues: 788 sheet: 0.82 (0.49), residues: 126 loop : -0.21 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 256 HIS 0.003 0.001 HIS A 33 PHE 0.017 0.001 PHE C 215 TYR 0.015 0.001 TYR D 252 ARG 0.004 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.05475 ( 677) hydrogen bonds : angle 4.11028 ( 2007) covalent geometry : bond 0.00341 ( 9974) covalent geometry : angle 0.53611 (13591) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 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 SER 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LYS 88 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. Residue LEU 191 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue THR 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue SER 220 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue MET 251 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue SER 256 is missing expected H atoms. Skipping. Residue LYS 260 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LEU 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue TYR 292 is missing expected H atoms. Skipping. Residue VAL 296 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue TYR 300 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue ILE 304 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue TYR 313 is missing expected H atoms. Skipping. Residue LEU 315 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue MET 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue THR 334 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LYS 337 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue VAL 343 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Residue THR 345 is missing expected H atoms. Skipping. Residue THR 348 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue SER 359 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue TYR 364 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue SER 371 is missing expected H atoms. Skipping. Residue SER 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 1.428 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: 0.8745 (mmm) cc_final: 0.8524 (mmt) REVERT: D 223 ARG cc_start: 0.7424 (ttm-80) cc_final: 0.6968 (ttp-170) REVERT: D 306 MET cc_start: 0.6571 (tmm) cc_final: 0.6305 (tmm) REVERT: E 123 LEU cc_start: 0.8929 (tt) cc_final: 0.8463 (mt) REVERT: E 141 ARG cc_start: 0.8039 (mtp180) cc_final: 0.7577 (tpm170) REVERT: E 170 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8281 (tm-30) outliers start: 11 outliers final: 9 residues processed: 125 average time/residue: 0.5058 time to fit residues: 87.5067 Evaluate side-chains 117 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN 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: 139 random chunks: chunk 102 optimal weight: 0.9980 chunk 125 optimal weight: 50.0000 chunk 63 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 130 optimal weight: 50.0000 chunk 117 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.135554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.090049 restraints weight = 53363.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.093420 restraints weight = 22168.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.095385 restraints weight = 12475.556| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9974 Z= 0.168 Angle : 0.513 5.702 13591 Z= 0.268 Chirality : 0.037 0.154 1652 Planarity : 0.003 0.028 1758 Dihedral : 7.048 124.065 1511 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.20 % Allowed : 9.28 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.23), residues: 1388 helix: 3.66 (0.17), residues: 788 sheet: 0.62 (0.47), residues: 126 loop : -0.25 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 256 HIS 0.003 0.001 HIS B 97 PHE 0.023 0.001 PHE C 291 TYR 0.012 0.001 TYR D 252 ARG 0.007 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.04845 ( 677) hydrogen bonds : angle 3.92141 ( 2007) covalent geometry : bond 0.00364 ( 9974) covalent geometry : angle 0.51342 (13591) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 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 SER 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LYS 88 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. Residue LEU 191 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue THR 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue SER 220 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue MET 251 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue SER 256 is missing expected H atoms. Skipping. Residue LYS 260 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LEU 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue TYR 292 is missing expected H atoms. Skipping. Residue VAL 296 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue TYR 300 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue ILE 304 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue TYR 313 is missing expected H atoms. Skipping. Residue LEU 315 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue MET 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue THR 334 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LYS 337 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue VAL 343 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Residue THR 345 is missing expected H atoms. Skipping. Residue THR 348 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue SER 359 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue TYR 364 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue SER 371 is missing expected H atoms. Skipping. Residue SER 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 1.476 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: 0.8040 (mt-10) cc_final: 0.7605 (mt-10) REVERT: B 101 MET cc_start: 0.8727 (mmm) cc_final: 0.8475 (mmt) REVERT: C 41 LYS cc_start: 0.8689 (tttt) cc_final: 0.8436 (ttmm) REVERT: D 223 ARG cc_start: 0.7367 (ttm-80) cc_final: 0.6911 (ttp-170) REVERT: D 306 MET cc_start: 0.6634 (tmm) cc_final: 0.6340 (tmm) REVERT: E 123 LEU cc_start: 0.8935 (tt) cc_final: 0.8486 (mt) REVERT: E 141 ARG cc_start: 0.8064 (mtp180) cc_final: 0.7592 (tpm170) REVERT: E 170 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8350 (tm-30) outliers start: 10 outliers final: 10 residues processed: 120 average time/residue: 0.5561 time to fit residues: 89.9674 Evaluate side-chains 118 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 1.476 ------------------------------------------------------------------------------- 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 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 D residue 324 LEU Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 94 optimal weight: 0.9980 chunk 123 optimal weight: 50.0000 chunk 43 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 69 optimal weight: 0.2980 chunk 119 optimal weight: 50.0000 chunk 75 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.135799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.091034 restraints weight = 53580.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.094473 restraints weight = 22017.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.096475 restraints weight = 12210.227| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9974 Z= 0.134 Angle : 0.486 6.017 13591 Z= 0.250 Chirality : 0.036 0.152 1652 Planarity : 0.003 0.025 1758 Dihedral : 6.607 120.408 1511 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.33 % Allowed : 9.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.23), residues: 1388 helix: 3.68 (0.17), residues: 790 sheet: 0.56 (0.46), residues: 128 loop : -0.20 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 298 HIS 0.004 0.001 HIS B 97 PHE 0.008 0.001 PHE D 138 TYR 0.011 0.001 TYR D 252 ARG 0.003 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.04439 ( 677) hydrogen bonds : angle 3.74032 ( 2007) covalent geometry : bond 0.00295 ( 9974) covalent geometry : angle 0.48613 (13591) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 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 SER 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LYS 88 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. Residue LEU 191 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue THR 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue SER 220 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue MET 251 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue SER 256 is missing expected H atoms. Skipping. Residue LYS 260 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LEU 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue TYR 292 is missing expected H atoms. Skipping. Residue VAL 296 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue TYR 300 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue ILE 304 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue TYR 313 is missing expected H atoms. Skipping. Residue LEU 315 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue MET 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue THR 334 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LYS 337 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue VAL 343 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Residue THR 345 is missing expected H atoms. Skipping. Residue THR 348 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue SER 359 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue TYR 364 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue SER 371 is missing expected H atoms. Skipping. Residue SER 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 1.655 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: symmetry clash REVERT: A 61 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7574 (mt-10) REVERT: B 101 MET cc_start: 0.8741 (mmm) cc_final: 0.8487 (mmt) REVERT: C 41 LYS cc_start: 0.8682 (tttt) cc_final: 0.8431 (ttmm) REVERT: C 291 PHE cc_start: 0.7366 (t80) cc_final: 0.6787 (t80) REVERT: D 223 ARG cc_start: 0.7293 (ttm-80) cc_final: 0.6869 (ttp-170) REVERT: D 306 MET cc_start: 0.6730 (tmm) cc_final: 0.6402 (tmm) REVERT: E 123 LEU cc_start: 0.8946 (tt) cc_final: 0.8538 (mt) REVERT: E 141 ARG cc_start: 0.8045 (mtp180) cc_final: 0.7580 (tpm170) REVERT: E 170 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8340 (tm-30) outliers start: 11 outliers final: 9 residues processed: 126 average time/residue: 0.5273 time to fit residues: 90.6723 Evaluate side-chains 122 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 1.469 ------------------------------------------------------------------------------- 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 174 THR Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL 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: 139 random chunks: chunk 22 optimal weight: 0.9990 chunk 130 optimal weight: 50.0000 chunk 72 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 0.0970 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 82 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.135936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.090089 restraints weight = 53919.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.093408 restraints weight = 22078.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.095482 restraints weight = 12407.423| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9974 Z= 0.131 Angle : 0.484 6.078 13591 Z= 0.247 Chirality : 0.036 0.160 1652 Planarity : 0.002 0.026 1758 Dihedral : 6.500 120.066 1511 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.57 % Allowed : 9.76 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.23), residues: 1388 helix: 3.72 (0.17), residues: 790 sheet: 0.47 (0.46), residues: 128 loop : -0.21 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 298 HIS 0.004 0.001 HIS B 97 PHE 0.008 0.001 PHE A 32 TYR 0.011 0.001 TYR D 252 ARG 0.003 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 677) hydrogen bonds : angle 3.64672 ( 2007) covalent geometry : bond 0.00286 ( 9974) covalent geometry : angle 0.48352 (13591) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 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 SER 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LYS 88 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. Residue LEU 191 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue THR 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue SER 220 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue MET 251 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue SER 256 is missing expected H atoms. Skipping. Residue LYS 260 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LEU 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue TYR 292 is missing expected H atoms. Skipping. Residue VAL 296 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue TYR 300 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue ILE 304 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue TYR 313 is missing expected H atoms. Skipping. Residue LEU 315 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue MET 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue THR 334 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LYS 337 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue VAL 343 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Residue THR 345 is missing expected H atoms. Skipping. Residue THR 348 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue SER 359 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue TYR 364 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue SER 371 is missing expected H atoms. Skipping. Residue SER 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 1.557 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: 0.7983 (mt-10) cc_final: 0.7574 (mt-10) REVERT: B 101 MET cc_start: 0.8728 (mmm) cc_final: 0.8489 (mmt) REVERT: C 41 LYS cc_start: 0.8682 (tttt) cc_final: 0.8429 (ttmm) REVERT: C 291 PHE cc_start: 0.7425 (t80) cc_final: 0.6808 (t80) REVERT: D 223 ARG cc_start: 0.7264 (ttm-80) cc_final: 0.6876 (ttp-170) REVERT: D 306 MET cc_start: 0.6754 (tmm) cc_final: 0.6398 (tmm) REVERT: E 123 LEU cc_start: 0.8941 (tt) cc_final: 0.8537 (mt) REVERT: E 141 ARG cc_start: 0.8060 (mtp180) cc_final: 0.7581 (tpm170) REVERT: E 170 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8306 (tm-30) outliers start: 13 outliers final: 10 residues processed: 124 average time/residue: 0.5687 time to fit residues: 95.5439 Evaluate side-chains 123 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 1.518 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 0.0370 chunk 100 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.133968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.088219 restraints weight = 53113.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.091424 restraints weight = 22357.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.093510 restraints weight = 12542.159| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9974 Z= 0.163 Angle : 0.508 5.888 13591 Z= 0.263 Chirality : 0.037 0.165 1652 Planarity : 0.003 0.037 1758 Dihedral : 6.516 120.372 1511 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.57 % Allowed : 10.60 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.23), residues: 1388 helix: 3.67 (0.17), residues: 784 sheet: 0.38 (0.45), residues: 128 loop : -0.26 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 298 HIS 0.005 0.001 HIS B 97 PHE 0.011 0.001 PHE A 32 TYR 0.011 0.001 TYR D 252 ARG 0.004 0.000 ARG C 50 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 677) hydrogen bonds : angle 3.67548 ( 2007) covalent geometry : bond 0.00367 ( 9974) covalent geometry : angle 0.50771 (13591) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 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 SER 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LYS 88 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. Residue LEU 191 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue THR 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue SER 220 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue MET 251 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue SER 256 is missing expected H atoms. Skipping. Residue LYS 260 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LEU 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue TYR 292 is missing expected H atoms. Skipping. Residue VAL 296 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue TYR 300 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue ILE 304 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue TYR 313 is missing expected H atoms. Skipping. Residue LEU 315 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue MET 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue THR 334 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LYS 337 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue VAL 343 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Residue THR 345 is missing expected H atoms. Skipping. Residue THR 348 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue SER 359 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue TYR 364 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue SER 371 is missing expected H atoms. Skipping. Residue SER 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 1.501 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: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7674 (mt-10) REVERT: B 101 MET cc_start: 0.8732 (mmm) cc_final: 0.8492 (mmt) REVERT: C 41 LYS cc_start: 0.8706 (tttt) cc_final: 0.8436 (ttmm) REVERT: C 291 PHE cc_start: 0.7497 (t80) cc_final: 0.6882 (t80) REVERT: D 223 ARG cc_start: 0.7269 (ttm-80) cc_final: 0.6859 (ttp-170) REVERT: D 326 GLU cc_start: 0.8632 (pp20) cc_final: 0.8264 (pp20) REVERT: E 123 LEU cc_start: 0.8968 (tt) cc_final: 0.8548 (mt) REVERT: E 141 ARG cc_start: 0.8045 (mtp180) cc_final: 0.7651 (tpm170) outliers start: 13 outliers final: 11 residues processed: 123 average time/residue: 0.5364 time to fit residues: 90.1669 Evaluate side-chains 124 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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 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 139 GLU 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: 139 random chunks: chunk 68 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 125 optimal weight: 30.0000 chunk 29 optimal weight: 0.1980 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 126 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 3 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3909 r_free = 0.3909 target = 0.133864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.087953 restraints weight = 52960.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.091242 restraints weight = 22163.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.093270 restraints weight = 12504.244| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9974 Z= 0.156 Angle : 0.500 5.985 13591 Z= 0.258 Chirality : 0.037 0.169 1652 Planarity : 0.003 0.026 1758 Dihedral : 6.479 120.279 1511 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.23), residues: 1388 helix: 3.69 (0.17), residues: 785 sheet: 0.28 (0.45), residues: 128 loop : -0.26 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.005 0.001 HIS B 97 PHE 0.011 0.001 PHE A 32 TYR 0.010 0.001 TYR C 250 ARG 0.003 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.04321 ( 677) hydrogen bonds : angle 3.62204 ( 2007) covalent geometry : bond 0.00352 ( 9974) covalent geometry : angle 0.49985 (13591) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 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 SER 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LYS 88 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. Residue LEU 191 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue THR 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue SER 220 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue MET 251 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue SER 256 is missing expected H atoms. Skipping. Residue LYS 260 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LEU 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue TYR 292 is missing expected H atoms. Skipping. Residue VAL 296 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue TYR 300 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue ILE 304 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue TYR 313 is missing expected H atoms. Skipping. Residue LEU 315 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue MET 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue THR 334 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LYS 337 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue VAL 343 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Residue THR 345 is missing expected H atoms. Skipping. Residue THR 348 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue SER 359 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue TYR 364 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue SER 371 is missing expected H atoms. Skipping. Residue SER 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 1.432 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: 0.8055 (mt-10) cc_final: 0.7663 (mt-10) REVERT: B 101 MET cc_start: 0.8727 (mmm) cc_final: 0.8472 (mmt) REVERT: C 41 LYS cc_start: 0.8713 (tttt) cc_final: 0.8442 (ttmm) REVERT: C 291 PHE cc_start: 0.7535 (t80) cc_final: 0.6932 (t80) REVERT: D 223 ARG cc_start: 0.7236 (ttm-80) cc_final: 0.6847 (ttp-170) REVERT: D 306 MET cc_start: 0.6573 (tmm) cc_final: 0.6288 (tmm) REVERT: E 123 LEU cc_start: 0.8954 (tt) cc_final: 0.8559 (mt) REVERT: E 141 ARG cc_start: 0.8050 (mtp180) cc_final: 0.7634 (tpm170) outliers start: 13 outliers final: 10 residues processed: 125 average time/residue: 0.5478 time to fit residues: 92.3210 Evaluate side-chains 127 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 1.595 ------------------------------------------------------------------------------- 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: 139 random chunks: chunk 129 optimal weight: 50.0000 chunk 76 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 125 optimal weight: 50.0000 chunk 71 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.132718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.086581 restraints weight = 53589.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.089868 restraints weight = 22506.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.091938 restraints weight = 12738.769| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9974 Z= 0.190 Angle : 0.531 5.789 13591 Z= 0.277 Chirality : 0.037 0.165 1652 Planarity : 0.003 0.034 1758 Dihedral : 6.556 120.930 1511 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.93 % Allowed : 11.08 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.23), residues: 1388 helix: 3.56 (0.17), residues: 785 sheet: 0.53 (0.48), residues: 108 loop : -0.35 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 298 HIS 0.006 0.001 HIS B 97 PHE 0.013 0.001 PHE A 32 TYR 0.011 0.001 TYR C 250 ARG 0.004 0.000 ARG C 50 Details of bonding type rmsd hydrogen bonds : bond 0.04473 ( 677) hydrogen bonds : angle 3.69732 ( 2007) covalent geometry : bond 0.00433 ( 9974) covalent geometry : angle 0.53127 (13591) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 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 SER 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LYS 88 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. Residue LEU 191 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue THR 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue SER 220 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue MET 251 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue SER 256 is missing expected H atoms. Skipping. Residue LYS 260 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LEU 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue TYR 292 is missing expected H atoms. Skipping. Residue VAL 296 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue TYR 300 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue ILE 304 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue TYR 313 is missing expected H atoms. Skipping. Residue LEU 315 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue MET 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue THR 334 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LYS 337 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue VAL 343 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Residue THR 345 is missing expected H atoms. Skipping. Residue THR 348 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue SER 359 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue TYR 364 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue SER 371 is missing expected H atoms. Skipping. Residue SER 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 1.535 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: 0.8058 (mt-10) cc_final: 0.7685 (mt-10) REVERT: B 101 MET cc_start: 0.8781 (mmm) cc_final: 0.8519 (mmt) REVERT: C 41 LYS cc_start: 0.8744 (tttt) cc_final: 0.8481 (ttmm) REVERT: C 291 PHE cc_start: 0.7552 (t80) cc_final: 0.6972 (t80) REVERT: D 306 MET cc_start: 0.6596 (tmm) cc_final: 0.6296 (tmm) REVERT: E 119 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8053 (tp) REVERT: E 123 LEU cc_start: 0.8967 (tt) cc_final: 0.8556 (mt) REVERT: E 141 ARG cc_start: 0.8071 (mtp180) cc_final: 0.7641 (tpm170) outliers start: 16 outliers final: 12 residues processed: 124 average time/residue: 0.5372 time to fit residues: 91.5397 Evaluate side-chains 124 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 1.528 ------------------------------------------------------------------------------- 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 E residue 119 LEU Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 163 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 105 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 7 optimal weight: 0.0020 chunk 78 optimal weight: 0.9990 chunk 127 optimal weight: 0.0370 chunk 77 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 overall best weight: 0.3666 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.134771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.088443 restraints weight = 53182.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.091743 restraints weight = 22123.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.093750 restraints weight = 12364.720| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 9974 Z= 0.111 Angle : 0.491 6.326 13591 Z= 0.250 Chirality : 0.036 0.172 1652 Planarity : 0.002 0.029 1758 Dihedral : 6.342 118.826 1511 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.45 % Allowed : 11.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.23), residues: 1388 helix: 3.77 (0.17), residues: 785 sheet: 0.26 (0.45), residues: 128 loop : -0.23 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 298 HIS 0.004 0.001 HIS B 97 PHE 0.007 0.001 PHE A 32 TYR 0.010 0.001 TYR D 252 ARG 0.006 0.000 ARG B 126 Details of bonding type rmsd hydrogen bonds : bond 0.04117 ( 677) hydrogen bonds : angle 3.49251 ( 2007) covalent geometry : bond 0.00243 ( 9974) covalent geometry : angle 0.49126 (13591) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 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 SER 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LYS 88 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. Residue LEU 191 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue THR 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue SER 220 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue MET 251 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue SER 256 is missing expected H atoms. Skipping. Residue LYS 260 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LEU 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue TYR 292 is missing expected H atoms. Skipping. Residue VAL 296 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue TYR 300 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue ILE 304 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue TYR 313 is missing expected H atoms. Skipping. Residue LEU 315 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue MET 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue THR 334 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LYS 337 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue VAL 343 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Residue THR 345 is missing expected H atoms. Skipping. Residue THR 348 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue SER 359 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue TYR 364 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue SER 371 is missing expected H atoms. Skipping. Residue SER 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 1.586 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: 0.7956 (mt-10) cc_final: 0.7599 (mt-10) REVERT: B 101 MET cc_start: 0.8719 (mmm) cc_final: 0.8448 (mmt) REVERT: C 41 LYS cc_start: 0.8704 (tttt) cc_final: 0.8437 (ttmm) REVERT: C 291 PHE cc_start: 0.7565 (t80) cc_final: 0.6962 (t80) REVERT: D 306 MET cc_start: 0.6545 (tmm) cc_final: 0.6250 (tmm) REVERT: E 123 LEU cc_start: 0.8950 (tt) cc_final: 0.8562 (mt) REVERT: E 141 ARG cc_start: 0.8058 (mtp180) cc_final: 0.7643 (tpm170) REVERT: E 167 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8659 (mm-30) outliers start: 12 outliers final: 11 residues processed: 125 average time/residue: 0.5630 time to fit residues: 95.3595 Evaluate side-chains 125 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 1.778 ------------------------------------------------------------------------------- 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 E residue 163 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 51 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 135 optimal weight: 50.0000 chunk 77 optimal weight: 0.9980 chunk 101 optimal weight: 0.3980 chunk 136 optimal weight: 40.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3899 r_free = 0.3899 target = 0.133003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.087401 restraints weight = 53390.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.090361 restraints weight = 22590.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.092414 restraints weight = 12748.222| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9974 Z= 0.178 Angle : 0.535 6.547 13591 Z= 0.276 Chirality : 0.037 0.171 1652 Planarity : 0.003 0.067 1758 Dihedral : 6.441 121.332 1511 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.57 % Allowed : 11.93 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.23), residues: 1388 helix: 3.64 (0.17), residues: 785 sheet: 1.10 (0.48), residues: 96 loop : -0.44 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 298 HIS 0.005 0.001 HIS B 97 PHE 0.013 0.001 PHE A 32 TYR 0.011 0.001 TYR C 250 ARG 0.010 0.000 ARG B 103 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 677) hydrogen bonds : angle 3.61159 ( 2007) covalent geometry : bond 0.00407 ( 9974) covalent geometry : angle 0.53459 (13591) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 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 SER 33 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue VAL 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 47 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue ILE 80 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LYS 88 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. Residue LEU 191 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue THR 211 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue SER 218 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue SER 220 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue THR 224 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue MET 251 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue SER 256 is missing expected H atoms. Skipping. Residue LYS 260 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LEU 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue TYR 292 is missing expected H atoms. Skipping. Residue VAL 296 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 299 is missing expected H atoms. Skipping. Residue TYR 300 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue ILE 304 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue TYR 309 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue TYR 313 is missing expected H atoms. Skipping. Residue LEU 315 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue MET 326 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LEU 328 is missing expected H atoms. Skipping. Residue TYR 329 is missing expected H atoms. Skipping. Residue THR 334 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LYS 337 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue VAL 343 is missing expected H atoms. Skipping. Residue THR 344 is missing expected H atoms. Skipping. Residue THR 345 is missing expected H atoms. Skipping. Residue THR 348 is missing expected H atoms. Skipping. Residue ILE 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue THR 355 is missing expected H atoms. Skipping. Residue SER 359 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue TYR 364 is missing expected H atoms. Skipping. Residue ILE 367 is missing expected H atoms. Skipping. Residue SER 371 is missing expected H atoms. Skipping. Residue SER 377 is missing expected H atoms. Skipping. Residue LEU 380 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 1.540 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: 0.8100 (mt-10) cc_final: 0.7722 (mt-10) REVERT: B 101 MET cc_start: 0.8742 (mmm) cc_final: 0.8454 (mmt) REVERT: C 41 LYS cc_start: 0.8722 (tttt) cc_final: 0.8456 (ttmm) REVERT: C 291 PHE cc_start: 0.7620 (t80) cc_final: 0.7039 (t80) REVERT: D 306 MET cc_start: 0.6567 (tmm) cc_final: 0.6264 (tmm) REVERT: E 119 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8039 (tp) REVERT: E 123 LEU cc_start: 0.8957 (tt) cc_final: 0.8550 (mt) REVERT: E 141 ARG cc_start: 0.8098 (mtp180) cc_final: 0.7640 (tpm170) outliers start: 13 outliers final: 10 residues processed: 123 average time/residue: 0.5344 time to fit residues: 89.3002 Evaluate side-chains 122 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 1.731 ------------------------------------------------------------------------------- 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 E residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 67 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 80 optimal weight: 0.0970 chunk 38 optimal weight: 0.5980 chunk 46 optimal weight: 0.2980 chunk 128 optimal weight: 50.0000 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.134046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.089188 restraints weight = 51792.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.092446 restraints weight = 21492.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.094363 restraints weight = 12023.456| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9974 Z= 0.126 Angle : 0.508 6.542 13591 Z= 0.259 Chirality : 0.036 0.173 1652 Planarity : 0.003 0.030 1758 Dihedral : 6.321 119.510 1511 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.45 % Allowed : 12.41 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.23), residues: 1388 helix: 3.75 (0.17), residues: 785 sheet: 1.15 (0.48), residues: 96 loop : -0.38 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 298 HIS 0.005 0.001 HIS B 97 PHE 0.009 0.001 PHE A 32 TYR 0.010 0.001 TYR D 252 ARG 0.009 0.000 ARG B 103 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 677) hydrogen bonds : angle 3.49059 ( 2007) covalent geometry : bond 0.00281 ( 9974) covalent geometry : angle 0.50792 (13591) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7860.60 seconds wall clock time: 137 minutes 31.05 seconds (8251.05 seconds total)