Starting phenix.real_space_refine on Mon May 19 19:45:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzl_41762/05_2025/8tzl_41762_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzl_41762/05_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_41762/05_2025/8tzl_41762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzl_41762/05_2025/8tzl_41762.map" model { file = "/net/cci-nas-00/data/ceres_data/8tzl_41762/05_2025/8tzl_41762_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzl_41762/05_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-5687/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: 10.84, per 1000 atoms: 0.57 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: 5.55 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: 1.64 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: 6.64 Time building geometry restraints manager: 6.55 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: 4.700 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: 0.770 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 43.960 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.300 ------------------------------------------------------------------------------- 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 : 1.456 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: 0.6387 time to fit residues: 157.4865 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 : 1.452 ------------------------------------------------------------------------------- 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 = 62)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.091961 restraints weight = 53416.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.095467 restraints weight = 21630.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.097496 restraints weight = 11975.465| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- 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 : 1.602 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: 0.8744 (mmm) cc_final: 0.8524 (mmt) REVERT: D 223 ARG cc_start: 0.7425 (ttm-80) cc_final: 0.6970 (ttp-170) REVERT: D 306 MET cc_start: 0.6573 (tmm) cc_final: 0.6308 (tmm) REVERT: E 123 LEU cc_start: 0.8932 (tt) cc_final: 0.8465 (mt) REVERT: E 141 ARG cc_start: 0.8039 (mtp180) cc_final: 0.7578 (tpm170) REVERT: E 170 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8280 (tm-30) outliers start: 11 outliers final: 9 residues processed: 125 average time/residue: 0.5054 time to fit residues: 86.7966 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 : 1.430 ------------------------------------------------------------------------------- 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: 0.4980 chunk 10 optimal weight: 0.9980 chunk 130 optimal weight: 50.0000 chunk 117 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 126 optimal weight: 0.0000 chunk 36 optimal weight: 0.6980 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.136219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.091006 restraints weight = 53454.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.094414 restraints weight = 22019.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.096487 restraints weight = 12239.937| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9974 Z= 0.149 Angle : 0.506 5.795 13591 Z= 0.262 Chirality : 0.036 0.156 1652 Planarity : 0.003 0.024 1758 Dihedral : 7.042 124.956 1511 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.20 % Allowed : 9.40 % Favored : 89.40 % 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: 3.24 (0.23), residues: 1388 helix: 3.71 (0.17), residues: 788 sheet: 0.65 (0.47), residues: 126 loop : -0.24 (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 0.022 0.001 PHE C 291 TYR 0.012 0.001 TYR D 252 ARG 0.003 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.04812 ( 677) hydrogen bonds : angle 3.89487 ( 2007) covalent geometry : bond 0.00325 ( 9974) covalent geometry : angle 0.50622 (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 123 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 1.487 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: 0.8034 (mt-10) cc_final: 0.7596 (mt-10) REVERT: B 101 MET cc_start: 0.8738 (mmm) cc_final: 0.8477 (mmt) REVERT: D 223 ARG cc_start: 0.7364 (ttm-80) cc_final: 0.6912 (ttp-170) REVERT: D 306 MET cc_start: 0.6620 (tmm) cc_final: 0.6333 (tmm) REVERT: E 123 LEU cc_start: 0.8913 (tt) cc_final: 0.8470 (mt) REVERT: E 141 ARG cc_start: 0.8058 (mtp180) cc_final: 0.7583 (tpm170) REVERT: E 170 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8363 (tm-30) outliers start: 10 outliers final: 10 residues processed: 119 average time/residue: 0.5520 time to fit residues: 88.5880 Evaluate side-chains 117 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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: 0.9980 chunk 66 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 117 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 119 optimal weight: 50.0000 chunk 75 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.136336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.090580 restraints weight = 53579.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.094021 restraints weight = 22055.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.095967 restraints weight = 12387.007| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2424 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= 0.130 Angle : 0.482 5.952 13591 Z= 0.247 Chirality : 0.036 0.155 1652 Planarity : 0.002 0.025 1758 Dihedral : 6.585 120.685 1511 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.33 % Allowed : 9.40 % Favored : 89.28 % 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: 3.27 (0.23), residues: 1388 helix: 3.71 (0.17), residues: 790 sheet: 0.59 (0.46), residues: 128 loop : -0.18 (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 0.010 0.001 TYR D 252 ARG 0.003 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 677) hydrogen bonds : angle 3.70988 ( 2007) covalent geometry : bond 0.00283 ( 9974) covalent geometry : angle 0.48203 (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 : 1.623 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: 0.8008 (mt-10) cc_final: 0.7570 (mt-10) REVERT: B 101 MET cc_start: 0.8738 (mmm) cc_final: 0.8521 (mmt) REVERT: C 41 LYS cc_start: 0.8674 (tttt) cc_final: 0.8426 (ttmm) REVERT: C 291 PHE cc_start: 0.7345 (t80) cc_final: 0.6758 (t80) REVERT: D 223 ARG cc_start: 0.7291 (ttm-80) cc_final: 0.6876 (ttp-170) REVERT: D 306 MET cc_start: 0.6757 (tmm) cc_final: 0.6425 (tmm) REVERT: E 123 LEU cc_start: 0.8946 (tt) cc_final: 0.8538 (mt) REVERT: E 141 ARG cc_start: 0.8075 (mtp180) cc_final: 0.7593 (tpm170) REVERT: E 170 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8327 (tm-30) outliers start: 11 outliers final: 9 residues processed: 126 average time/residue: 0.5283 time to fit residues: 90.5778 Evaluate side-chains 121 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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: 0.9980 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 0.0870 chunk 23 optimal weight: 0.7980 chunk 26 optimal weight: 0.0980 chunk 82 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 80 ASN B 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.135770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.090461 restraints weight = 53865.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.093889 restraints weight = 22145.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.095872 restraints weight = 12346.067| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9974 Z= 0.138 Angle : 0.487 6.041 13591 Z= 0.250 Chirality : 0.036 0.156 1652 Planarity : 0.002 0.026 1758 Dihedral : 6.528 120.608 1511 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.57 % Allowed : 9.40 % 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: 3.27 (0.23), residues: 1388 helix: 3.70 (0.17), residues: 790 sheet: 0.75 (0.49), residues: 108 loop : -0.18 (0.29), residues: 490 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 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 0.04311 ( 677) hydrogen bonds : angle 3.66488 ( 2007) covalent geometry : bond 0.00307 ( 9974) covalent geometry : angle 0.48750 (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 127 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 1.565 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: 0.7991 (mt-10) cc_final: 0.7581 (mt-10) REVERT: B 101 MET cc_start: 0.8731 (mmm) cc_final: 0.8481 (mmt) REVERT: C 41 LYS cc_start: 0.8679 (tttt) cc_final: 0.8427 (ttmm) REVERT: C 291 PHE cc_start: 0.7377 (t80) cc_final: 0.6819 (t80) REVERT: D 223 ARG cc_start: 0.7246 (ttm-80) cc_final: 0.6854 (ttp-170) REVERT: D 306 MET cc_start: 0.6757 (tmm) cc_final: 0.6404 (tmm) REVERT: E 123 LEU cc_start: 0.8944 (tt) cc_final: 0.8539 (mt) REVERT: E 141 ARG cc_start: 0.8047 (mtp180) cc_final: 0.7579 (tpm170) REVERT: E 170 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8321 (tm-30) outliers start: 13 outliers final: 10 residues processed: 122 average time/residue: 0.5174 time to fit residues: 85.7054 Evaluate side-chains 122 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 1.544 ------------------------------------------------------------------------------- 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: 0.8980 chunk 100 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 74 optimal weight: 0.0470 overall best weight: 0.7678 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.134138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.089284 restraints weight = 53256.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.092551 restraints weight = 22111.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.094608 restraints weight = 12337.004| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9974 Z= 0.165 Angle : 0.505 5.895 13591 Z= 0.262 Chirality : 0.037 0.161 1652 Planarity : 0.003 0.026 1758 Dihedral : 6.543 120.733 1511 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.57 % Allowed : 10.48 % Favored : 87.95 % 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: 3.18 (0.23), residues: 1388 helix: 3.66 (0.17), residues: 788 sheet: 0.62 (0.49), residues: 108 loop : -0.23 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 256 HIS 0.005 0.001 HIS B 97 PHE 0.011 0.001 PHE A 32 TYR 0.010 0.001 TYR D 252 ARG 0.003 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 677) hydrogen bonds : angle 3.68347 ( 2007) covalent geometry : bond 0.00375 ( 9974) covalent geometry : angle 0.50505 (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 : 1.549 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: 0.8076 (mt-10) cc_final: 0.7679 (mt-10) REVERT: B 101 MET cc_start: 0.8737 (mmm) cc_final: 0.8491 (mmt) REVERT: C 41 LYS cc_start: 0.8701 (tttt) cc_final: 0.8435 (ttmm) REVERT: C 291 PHE cc_start: 0.7481 (t80) cc_final: 0.6868 (t80) REVERT: D 223 ARG cc_start: 0.7266 (ttm-80) cc_final: 0.6860 (ttp-170) REVERT: D 306 MET cc_start: 0.6744 (tmm) cc_final: 0.6376 (tmm) REVERT: E 123 LEU cc_start: 0.8959 (tt) cc_final: 0.8544 (mt) REVERT: E 141 ARG cc_start: 0.8044 (mtp180) cc_final: 0.7611 (tpm170) REVERT: E 170 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8335 (tm-30) outliers start: 13 outliers final: 11 residues processed: 123 average time/residue: 0.5566 time to fit residues: 92.4029 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 : 1.866 ------------------------------------------------------------------------------- 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: 0.9990 chunk 84 optimal weight: 1.9990 chunk 125 optimal weight: 50.0000 chunk 29 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 3 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.133462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.087393 restraints weight = 53093.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.090581 restraints weight = 22250.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.092655 restraints weight = 12637.632| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9974 Z= 0.173 Angle : 0.521 5.869 13591 Z= 0.271 Chirality : 0.037 0.171 1652 Planarity : 0.003 0.042 1758 Dihedral : 6.567 120.829 1511 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.93 % Allowed : 10.48 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.08 (0.23), residues: 1388 helix: 3.61 (0.17), residues: 785 sheet: 0.58 (0.49), residues: 108 loop : -0.32 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 0.006 0.000 ARG C 50 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 677) hydrogen bonds : angle 3.68822 ( 2007) covalent geometry : bond 0.00396 ( 9974) covalent geometry : angle 0.52063 (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: 16 poor density : 115 time to evaluate : 1.434 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: 0.8070 (mt-10) cc_final: 0.7683 (mt-10) REVERT: B 101 MET cc_start: 0.8737 (mmm) cc_final: 0.8494 (mmt) REVERT: C 41 LYS cc_start: 0.8721 (tttt) cc_final: 0.8449 (ttmm) REVERT: C 291 PHE cc_start: 0.7528 (t80) cc_final: 0.6954 (t80) REVERT: D 326 GLU cc_start: 0.8676 (pp20) cc_final: 0.8320 (pp20) REVERT: E 123 LEU cc_start: 0.8951 (tt) cc_final: 0.8550 (mt) REVERT: E 141 ARG cc_start: 0.8055 (mtp180) cc_final: 0.7635 (tpm170) REVERT: E 170 GLN cc_start: 0.8532 (tm-30) cc_final: 0.8297 (tm-30) outliers start: 16 outliers final: 11 residues processed: 124 average time/residue: 0.5187 time to fit residues: 86.7615 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 : 1.463 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 21 optimal weight: 0.9980 chunk 125 optimal weight: 40.0000 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 113 optimal weight: 0.0570 chunk 41 optimal weight: 0.3980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.133912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.087938 restraints weight = 53272.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.091176 restraints weight = 22186.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.093288 restraints weight = 12516.603| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9974 Z= 0.138 Angle : 0.501 6.089 13591 Z= 0.257 Chirality : 0.036 0.167 1652 Planarity : 0.003 0.026 1758 Dihedral : 6.459 119.843 1511 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.69 % Allowed : 10.96 % 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: 3.19 (0.23), residues: 1388 helix: 3.69 (0.17), residues: 785 sheet: 0.59 (0.49), residues: 108 loop : -0.26 (0.29), residues: 495 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 0.009 0.001 PHE A 32 TYR 0.011 0.001 TYR D 252 ARG 0.003 0.000 ARG C 50 Details of bonding type rmsd hydrogen bonds : bond 0.04274 ( 677) hydrogen bonds : angle 3.58750 ( 2007) covalent geometry : bond 0.00310 ( 9974) covalent geometry : angle 0.50123 (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: 14 poor density : 117 time to evaluate : 1.582 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: 0.8056 (mt-10) cc_final: 0.7667 (mt-10) REVERT: B 101 MET cc_start: 0.8724 (mmm) cc_final: 0.8441 (mmt) REVERT: C 41 LYS cc_start: 0.8708 (tttt) cc_final: 0.8437 (ttmm) REVERT: C 291 PHE cc_start: 0.7572 (t80) cc_final: 0.6956 (t80) REVERT: D 326 GLU cc_start: 0.8654 (pp20) cc_final: 0.8270 (pp20) REVERT: E 119 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8066 (tp) REVERT: E 123 LEU cc_start: 0.8939 (tt) cc_final: 0.8546 (mt) REVERT: E 141 ARG cc_start: 0.8065 (mtp180) cc_final: 0.7634 (tpm170) REVERT: E 170 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8327 (tm-30) outliers start: 14 outliers final: 11 residues processed: 124 average time/residue: 0.5309 time to fit residues: 89.7476 Evaluate side-chains 127 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLN 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 119 LEU Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 105 optimal weight: 8.9990 chunk 46 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 7 optimal weight: 0.0060 chunk 78 optimal weight: 0.9980 chunk 127 optimal weight: 0.0010 chunk 77 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 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 = 0.3921 r_free = 0.3921 target = 0.134889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.090027 restraints weight = 52002.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.093239 restraints weight = 21322.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.095208 restraints weight = 11905.316| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9974 Z= 0.113 Angle : 0.495 6.433 13591 Z= 0.251 Chirality : 0.036 0.175 1652 Planarity : 0.003 0.056 1758 Dihedral : 6.324 118.726 1511 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.57 % Allowed : 11.57 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.30 (0.23), residues: 1388 helix: 3.79 (0.17), residues: 785 sheet: 1.08 (0.49), residues: 98 loop : -0.29 (0.29), residues: 505 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 0.007 0.000 ARG B 103 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 677) hydrogen bonds : angle 3.48906 ( 2007) covalent geometry : bond 0.00247 ( 9974) covalent geometry : angle 0.49540 (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 129 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 1.542 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: 0.8040 (mt-10) cc_final: 0.7645 (mt-10) REVERT: B 101 MET cc_start: 0.8718 (mmm) cc_final: 0.8433 (mmt) REVERT: C 41 LYS cc_start: 0.8697 (tttt) cc_final: 0.8432 (ttmm) REVERT: C 291 PHE cc_start: 0.7549 (t80) cc_final: 0.6948 (t80) REVERT: D 223 ARG cc_start: 0.7214 (ttm-80) cc_final: 0.6830 (ttp-170) REVERT: D 306 MET cc_start: 0.6527 (tmm) cc_final: 0.6251 (tmm) REVERT: D 326 GLU cc_start: 0.8664 (pp20) cc_final: 0.8279 (pp20) REVERT: E 123 LEU cc_start: 0.8980 (tt) cc_final: 0.8563 (mt) REVERT: E 141 ARG cc_start: 0.8028 (mtp180) cc_final: 0.7640 (tpm170) REVERT: E 170 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8338 (tm-30) outliers start: 13 outliers final: 11 residues processed: 123 average time/residue: 0.5379 time to fit residues: 88.5223 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 : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 51 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 135 optimal weight: 50.0000 chunk 77 optimal weight: 0.9990 chunk 101 optimal weight: 0.2980 chunk 136 optimal weight: 20.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.133028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.087284 restraints weight = 53263.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.090541 restraints weight = 22269.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.092648 restraints weight = 12542.763| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9974 Z= 0.176 Angle : 0.528 6.933 13591 Z= 0.275 Chirality : 0.037 0.171 1652 Planarity : 0.003 0.031 1758 Dihedral : 6.447 121.659 1511 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.69 % Allowed : 11.57 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.12 (0.23), residues: 1388 helix: 3.64 (0.17), residues: 785 sheet: 1.13 (0.49), residues: 96 loop : -0.41 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 298 HIS 0.005 0.001 HIS B 97 PHE 0.012 0.001 PHE A 32 TYR 0.011 0.001 TYR D 252 ARG 0.008 0.000 ARG B 103 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 677) hydrogen bonds : angle 3.62043 ( 2007) covalent geometry : bond 0.00402 ( 9974) covalent geometry : angle 0.52817 (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 129 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.536 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: 0.8092 (mt-10) cc_final: 0.7712 (mt-10) REVERT: B 101 MET cc_start: 0.8777 (mmm) cc_final: 0.8479 (mmt) REVERT: C 41 LYS cc_start: 0.8722 (tttt) cc_final: 0.8458 (ttmm) REVERT: C 291 PHE cc_start: 0.7616 (t80) cc_final: 0.7031 (t80) REVERT: D 223 ARG cc_start: 0.7253 (ttm-80) cc_final: 0.6847 (ttp-170) REVERT: D 306 MET cc_start: 0.6594 (tmm) cc_final: 0.6317 (tmm) REVERT: D 326 GLU cc_start: 0.8686 (pp20) cc_final: 0.8281 (pp20) REVERT: E 119 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8041 (tp) REVERT: E 123 LEU cc_start: 0.8958 (tt) cc_final: 0.8554 (mt) REVERT: E 141 ARG cc_start: 0.8079 (mtp180) cc_final: 0.7641 (tpm170) REVERT: E 170 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8328 (tm-30) outliers start: 14 outliers final: 11 residues processed: 123 average time/residue: 0.5609 time to fit residues: 92.1215 Evaluate side-chains 126 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 1.459 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 51 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 101 optimal weight: 0.0970 chunk 79 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 38 optimal weight: 0.0770 chunk 46 optimal weight: 0.6980 chunk 128 optimal weight: 50.0000 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.134548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.088675 restraints weight = 52982.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.091968 restraints weight = 22136.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.094138 restraints weight = 12458.860| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9974 Z= 0.123 Angle : 0.501 6.661 13591 Z= 0.256 Chirality : 0.036 0.174 1652 Planarity : 0.003 0.031 1758 Dihedral : 6.314 119.535 1511 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.57 % Allowed : 11.81 % 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: 3.27 (0.23), residues: 1388 helix: 3.75 (0.17), residues: 785 sheet: 1.18 (0.49), residues: 96 loop : -0.32 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.004 0.001 HIS B 97 PHE 0.008 0.001 PHE A 32 TYR 0.009 0.001 TYR D 252 ARG 0.011 0.000 ARG B 103 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 677) hydrogen bonds : angle 3.48844 ( 2007) covalent geometry : bond 0.00273 ( 9974) covalent geometry : angle 0.50092 (13591) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6810.47 seconds wall clock time: 117 minutes 57.97 seconds (7077.97 seconds total)