Starting phenix.real_space_refine on Thu Aug 6 09:08:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eea_47953/08_2026/9eea_47953.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eea_47953/08_2026/9eea_47953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9eea_47953/08_2026/9eea_47953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eea_47953/08_2026/9eea_47953.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eea_47953/08_2026/9eea_47953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eea_47953/08_2026/9eea_47953.map" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.225 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: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 4819 2.51 5 N 1306 2.21 5 O 1377 1.98 5 H 7098 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14648 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4064 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 4724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 4724 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 6, 'ARG:plan': 7, 'GLU:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 93 Chain: "C" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 594 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 3408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3408 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 7, 'GLU:plan': 7, 'ASP:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 92 Chain: "E" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1839 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'ADN%rna2p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 2.55, per 1000 atoms: 0.17 Number of scatterers: 14648 At special positions: 0 Unit cell: (75.15, 98.53, 128.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 O 1377 8.00 N 1306 7.00 C 4819 6.00 H 7098 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 262 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 521.7 milliseconds 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1902 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 42.1% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 Processing helix chain 'A' and resid 39 through 69 removed outlier: 4.111A pdb=" N PHE A 44 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) Proline residue: A 61 - end of helix removed outlier: 3.886A pdb=" N GLY A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 108 Processing helix chain 'A' and resid 108 through 116 removed outlier: 4.171A pdb=" N ASN A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLY A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 137 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 181 through 186 removed outlier: 3.802A pdb=" N VAL A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 210 Processing helix chain 'A' and resid 224 through 259 removed outlier: 3.557A pdb=" N GLU A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N CYS A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Proline residue: A 248 - end of helix Processing helix chain 'A' and resid 266 through 288 Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 295 through 302 removed outlier: 3.711A pdb=" N ILE A 302 " --> pdb=" O THR A 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 12 through 24 removed outlier: 3.752A pdb=" N GLU C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'D' and resid 12 through 40 removed outlier: 3.619A pdb=" N GLU D 16 " --> pdb=" O GLN D 12 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS D 32 " --> pdb=" O LYS D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 56 Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 252 through 269 removed outlier: 4.130A pdb=" N GLN D 257 " --> pdb=" O TYR D 253 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU D 258 " --> pdb=" O ASN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 273 Processing helix chain 'D' and resid 283 through 294 Processing helix chain 'D' and resid 297 through 302 removed outlier: 4.245A pdb=" N TYR D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 308 removed outlier: 4.046A pdb=" N TYR D 308 " --> pdb=" O PHE D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 342 removed outlier: 4.511A pdb=" N SER D 342 " --> pdb=" O ILE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 381 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.510A pdb=" N ASN E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.881A pdb=" N THR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.661A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.887A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.592A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 148 removed outlier: 3.521A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 148 removed outlier: 3.521A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.840A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.720A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 Processing sheet with id=AA9, first strand: chain 'D' and resid 208 through 213 removed outlier: 7.164A pdb=" N ARG D 42 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE D 245 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU D 44 " --> pdb=" O ILE D 245 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL D 247 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU D 46 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N ASP D 249 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ILE D 244 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N PHE D 280 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N PHE D 246 " --> pdb=" O PHE D 280 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASN D 282 " --> pdb=" O PHE D 246 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL D 248 " --> pdb=" O ASN D 282 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 8 removed outlier: 3.927A pdb=" N GLN E 5 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.296A pdb=" N GLY E 10 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL E 124 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA E 92 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL E 93 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET E 34 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG E 38 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP E 50 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER E 59 " --> pdb=" O ASP E 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 68 through 69 removed outlier: 3.530A pdb=" N THR E 69 " --> pdb=" O GLN E 82 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.92 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 7074 1.04 - 1.24: 1038 1.24 - 1.44: 2364 1.44 - 1.64: 4268 1.64 - 1.84: 66 Bond restraints: 14810 Sorted by residual: bond pdb=" CB PRO A 266 " pdb=" CG PRO A 266 " ideal model delta sigma weight residual 1.492 1.601 -0.109 5.00e-02 4.00e+02 4.78e+00 bond pdb=" N GLN C 11 " pdb=" CA GLN C 11 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N GLN E 1 " pdb=" CA GLN E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" N ASP B 5 " pdb=" CA ASP B 5 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" N GLU D 10 " pdb=" CA GLU D 10 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.75e+00 ... (remaining 14805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.31: 26541 11.31 - 22.63: 3 22.63 - 33.94: 3 33.94 - 45.26: 1 45.26 - 56.57: 4 Bond angle restraints: 26552 Sorted by residual: angle pdb=" CA GLY A 76 " pdb=" N GLY A 76 " pdb=" H GLY A 76 " ideal model delta sigma weight residual 114.88 58.31 56.57 3.00e+00 1.11e-01 3.56e+02 angle pdb=" C HIS A 75 " pdb=" N GLY A 76 " pdb=" H GLY A 76 " ideal model delta sigma weight residual 125.18 68.77 56.41 3.00e+00 1.11e-01 3.54e+02 angle pdb=" C ILE A 287 " pdb=" N TYR A 288 " pdb=" H TYR A 288 " ideal model delta sigma weight residual 124.06 73.01 51.05 3.00e+00 1.11e-01 2.90e+02 angle pdb=" CA TYR A 288 " pdb=" N TYR A 288 " pdb=" H TYR A 288 " ideal model delta sigma weight residual 113.76 63.10 50.67 3.00e+00 1.11e-01 2.85e+02 angle pdb=" HG2 PRO A 266 " pdb=" CG PRO A 266 " pdb=" HG3 PRO A 266 " ideal model delta sigma weight residual 110.00 74.67 35.33 3.00e+00 1.11e-01 1.39e+02 ... (remaining 26547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6282 17.88 - 35.76: 566 35.76 - 53.64: 199 53.64 - 71.52: 35 71.52 - 89.39: 18 Dihedral angle restraints: 7100 sinusoidal: 3615 harmonic: 3485 Sorted by residual: dihedral pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " pdb=" SG CYS E 107 " pdb=" CB CYS E 107 " ideal model delta sinusoidal sigma weight residual -86.00 -42.69 -43.31 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CA CYS E 99 " pdb=" C CYS E 99 " pdb=" N PRO E 100 " pdb=" CA PRO E 100 " ideal model delta harmonic sigma weight residual -180.00 -154.99 -25.01 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA ALA A 184 " pdb=" C ALA A 184 " pdb=" N CYS A 185 " pdb=" CA CYS A 185 " ideal model delta harmonic sigma weight residual 180.00 -159.02 -20.98 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 7097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 765 0.028 - 0.057: 305 0.057 - 0.085: 87 0.085 - 0.113: 54 0.113 - 0.141: 20 Chirality restraints: 1231 Sorted by residual: chirality pdb=" CA ILE A 53 " pdb=" N ILE A 53 " pdb=" C ILE A 53 " pdb=" CB ILE A 53 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE E 58 " pdb=" N ILE E 58 " pdb=" C ILE E 58 " pdb=" CB ILE E 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 1228 not shown) Planarity restraints: 2313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 53 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C ILE A 53 " 0.039 2.00e-02 2.50e+03 pdb=" O ILE A 53 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA A 54 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 189 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.50e+00 pdb=" C PRO A 189 " 0.032 2.00e-02 2.50e+03 pdb=" O PRO A 189 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 190 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 172 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.63e+00 pdb=" N PRO A 173 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " 0.023 5.00e-02 4.00e+02 ... (remaining 2310 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 435 2.13 - 2.74: 26003 2.74 - 3.36: 40483 3.36 - 3.98: 49530 3.98 - 4.60: 77796 Nonbonded interactions: 194247 Sorted by model distance: nonbonded pdb=" H TYR A 288 " pdb=" HA TYR A 288 " model vdw 1.507 1.816 nonbonded pdb=" H GLY A 76 " pdb=" HA2 GLY A 76 " model vdw 1.584 1.816 nonbonded pdb=" HG1 THR B 164 " pdb=" O HIS B 183 " model vdw 1.597 2.450 nonbonded pdb=" O ASP B 186 " pdb=" H CYS B 204 " model vdw 1.602 2.450 nonbonded pdb=" H MET B 101 " pdb=" O GLY B 115 " model vdw 1.603 2.450 ... (remaining 194242 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 0.060 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.410 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 7716 Z= 0.141 Angle : 0.583 14.287 10527 Z= 0.325 Chirality : 0.039 0.141 1231 Planarity : 0.003 0.041 1339 Dihedral : 17.636 89.394 2611 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.40 % Allowed : 30.42 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.27), residues: 995 helix: 1.06 (0.28), residues: 379 sheet: -1.12 (0.36), residues: 210 loop : -1.61 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 304 TYR 0.008 0.001 TYR A 288 PHE 0.017 0.001 PHE A 182 TRP 0.015 0.001 TRP A 268 HIS 0.002 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 7712) covalent geometry : angle 0.58107 / 0.32 (10519) SS BOND : bond 0.00430 / 0.21 ( 4) SS BOND : angle 1.84816 / 0.76 ( 8) hydrogen bonds : bond 0.17047 / 11.05 ( 372) hydrogen bonds : angle 6.76103 / 4.91 ( 1047) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 311 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 308 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.8290 (t) cc_final: 0.8033 (t) REVERT: B 215 GLU cc_start: 0.8136 (tt0) cc_final: 0.7757 (tm-30) REVERT: B 308 LEU cc_start: 0.7576 (mp) cc_final: 0.6930 (mp) outliers start: 3 outliers final: 2 residues processed: 309 average time/residue: 0.1739 time to fit residues: 73.1914 Evaluate side-chains 223 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 221 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 80 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS D 257 GLN D 352 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.095028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.084345 restraints weight = 108941.316| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 6.27 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 7716 Z= 0.212 Angle : 0.662 13.952 10527 Z= 0.366 Chirality : 0.040 0.159 1231 Planarity : 0.004 0.043 1339 Dihedral : 9.477 89.708 1110 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.36 % Allowed : 30.15 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.26), residues: 995 helix: 0.81 (0.27), residues: 379 sheet: -1.10 (0.35), residues: 206 loop : -1.94 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 314 TYR 0.018 0.001 TYR B 264 PHE 0.018 0.002 PHE E 103 TRP 0.011 0.002 TRP A 268 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.21 ( 7712) covalent geometry : angle 0.66090 / 0.37 (10519) SS BOND : bond 0.00548 / 0.26 ( 4) SS BOND : angle 1.79521 / 0.78 ( 8) hydrogen bonds : bond 0.04939 / 3.29 ( 372) hydrogen bonds : angle 5.77382 / 4.19 ( 1047) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 249 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 180 PHE cc_start: 0.7534 (m-80) cc_final: 0.7177 (m-10) outliers start: 25 outliers final: 19 residues processed: 237 average time/residue: 0.1686 time to fit residues: 54.4490 Evaluate side-chains 228 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 209 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 358 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 4 optimal weight: 3.9990 chunk 87 optimal weight: 0.1980 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.094962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.083930 restraints weight = 106118.328| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 6.29 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 7716 Z= 0.156 Angle : 0.626 13.931 10527 Z= 0.341 Chirality : 0.040 0.184 1231 Planarity : 0.004 0.046 1339 Dihedral : 9.525 89.781 1110 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.36 % Allowed : 29.88 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.27), residues: 995 helix: 0.93 (0.27), residues: 380 sheet: -0.79 (0.36), residues: 206 loop : -1.83 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 375 TYR 0.014 0.001 TYR A 288 PHE 0.019 0.001 PHE B 199 TRP 0.011 0.001 TRP B 63 HIS 0.044 0.002 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 ( 7712) covalent geometry : angle 0.62460 / 0.34 (10519) SS BOND : bond 0.00416 / 0.20 ( 4) SS BOND : angle 1.51549 / 0.68 ( 8) hydrogen bonds : bond 0.04691 / 3.13 ( 372) hydrogen bonds : angle 5.46087 / 3.96 ( 1047) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 246 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 PHE cc_start: 0.7700 (m-80) cc_final: 0.7407 (m-10) REVERT: B 314 ARG cc_start: 0.7671 (mmm-85) cc_final: 0.7248 (mmm-85) outliers start: 25 outliers final: 18 residues processed: 233 average time/residue: 0.1717 time to fit residues: 54.9943 Evaluate side-chains 228 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 292 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 64 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 26 optimal weight: 30.0000 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN C 44 HIS ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.092451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.082010 restraints weight = 109646.898| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 6.11 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 7716 Z= 0.194 Angle : 0.642 13.847 10527 Z= 0.351 Chirality : 0.040 0.147 1231 Planarity : 0.004 0.045 1339 Dihedral : 9.442 88.294 1110 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.98 % Allowed : 29.88 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.27), residues: 995 helix: 0.81 (0.27), residues: 382 sheet: -0.85 (0.35), residues: 214 loop : -1.89 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 102 TYR 0.014 0.001 TYR A 288 PHE 0.018 0.002 PHE B 199 TRP 0.009 0.002 TRP B 63 HIS 0.011 0.002 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 ( 7712) covalent geometry : angle 0.64111 / 0.35 (10519) SS BOND : bond 0.00171 / 0.08 ( 4) SS BOND : angle 1.63343 / 0.71 ( 8) hydrogen bonds : bond 0.04624 / 3.10 ( 372) hydrogen bonds : angle 5.49656 / 3.99 ( 1047) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 211 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 PHE cc_start: 0.7793 (m-80) cc_final: 0.7497 (m-10) REVERT: D 29 GLN cc_start: 0.8892 (mm110) cc_final: 0.8554 (mp10) outliers start: 37 outliers final: 34 residues processed: 228 average time/residue: 0.1722 time to fit residues: 54.3504 Evaluate side-chains 236 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 254 ASN Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 35 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 52 optimal weight: 0.0270 chunk 45 optimal weight: 0.0470 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.094600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.083764 restraints weight = 106042.010| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 6.26 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 7716 Z= 0.129 Angle : 0.618 14.068 10527 Z= 0.328 Chirality : 0.040 0.150 1231 Planarity : 0.004 0.043 1339 Dihedral : 9.320 89.166 1110 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.50 % Allowed : 31.22 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.28), residues: 995 helix: 1.18 (0.28), residues: 381 sheet: -0.67 (0.35), residues: 212 loop : -1.57 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 67 TYR 0.013 0.001 TYR A 288 PHE 0.022 0.001 PHE B 199 TRP 0.014 0.001 TRP B 63 HIS 0.007 0.001 HIS D 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 7712) covalent geometry : angle 0.61728 / 0.33 (10519) SS BOND : bond 0.00361 / 0.18 ( 4) SS BOND : angle 1.40389 / 0.65 ( 8) hydrogen bonds : bond 0.04464 / 2.99 ( 372) hydrogen bonds : angle 5.13332 / 3.73 ( 1047) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 243 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8751 (tt) REVERT: B 180 PHE cc_start: 0.7767 (m-80) cc_final: 0.7527 (m-10) REVERT: D 29 GLN cc_start: 0.8902 (mm110) cc_final: 0.8537 (mp10) outliers start: 26 outliers final: 23 residues processed: 228 average time/residue: 0.1614 time to fit residues: 50.5757 Evaluate side-chains 229 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 254 ASN Chi-restraints excluded: chain D residue 292 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 87 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN E 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.092912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.082357 restraints weight = 107175.501| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 6.15 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 7716 Z= 0.140 Angle : 0.609 13.815 10527 Z= 0.327 Chirality : 0.039 0.144 1231 Planarity : 0.004 0.044 1339 Dihedral : 9.245 88.737 1110 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 4.04 % Allowed : 30.82 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.27), residues: 995 helix: 1.15 (0.27), residues: 387 sheet: -0.65 (0.35), residues: 211 loop : -1.58 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 256 TYR 0.012 0.001 TYR A 288 PHE 0.022 0.001 PHE B 199 TRP 0.011 0.001 TRP B 63 HIS 0.005 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 7712) covalent geometry : angle 0.60821 / 0.33 (10519) SS BOND : bond 0.00323 / 0.16 ( 4) SS BOND : angle 1.30493 / 0.61 ( 8) hydrogen bonds : bond 0.04385 / 2.92 ( 372) hydrogen bonds : angle 5.16937 / 3.75 ( 1047) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8788 (tt) REVERT: B 180 PHE cc_start: 0.7685 (m-80) cc_final: 0.7445 (m-10) REVERT: B 314 ARG cc_start: 0.7497 (mmm-85) cc_final: 0.6995 (mmm-85) REVERT: D 29 GLN cc_start: 0.8836 (mm110) cc_final: 0.8518 (mp10) REVERT: D 252 ASP cc_start: 0.8130 (t0) cc_final: 0.7903 (t0) REVERT: D 380 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8814 (tm-30) outliers start: 30 outliers final: 27 residues processed: 223 average time/residue: 0.1722 time to fit residues: 53.6307 Evaluate side-chains 234 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 249 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 76 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.093943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.083297 restraints weight = 106230.753| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 6.18 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 7716 Z= 0.116 Angle : 0.598 13.839 10527 Z= 0.319 Chirality : 0.039 0.142 1231 Planarity : 0.004 0.041 1339 Dihedral : 9.125 88.831 1110 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.31 % Allowed : 30.15 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.28), residues: 995 helix: 1.29 (0.28), residues: 386 sheet: -0.64 (0.35), residues: 214 loop : -1.43 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 256 TYR 0.011 0.001 TYR A 288 PHE 0.022 0.001 PHE B 199 TRP 0.016 0.001 TRP B 63 HIS 0.005 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 7712) covalent geometry : angle 0.59739 / 0.32 (10519) SS BOND : bond 0.00384 / 0.18 ( 4) SS BOND : angle 1.36064 / 0.62 ( 8) hydrogen bonds : bond 0.04295 / 2.90 ( 372) hydrogen bonds : angle 4.98956 / 3.62 ( 1047) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 247 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8790 (tt) REVERT: B 314 ARG cc_start: 0.7441 (mmm-85) cc_final: 0.6944 (mmm-85) REVERT: D 29 GLN cc_start: 0.8831 (mm110) cc_final: 0.8521 (mp10) REVERT: D 219 PHE cc_start: 0.8553 (m-80) cc_final: 0.8323 (m-80) REVERT: D 252 ASP cc_start: 0.8045 (t0) cc_final: 0.7809 (t0) REVERT: D 380 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8724 (tm-30) outliers start: 32 outliers final: 26 residues processed: 230 average time/residue: 0.1739 time to fit residues: 56.1105 Evaluate side-chains 229 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 254 ASN Chi-restraints excluded: chain E residue 124 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 14 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 97 optimal weight: 0.0770 chunk 54 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.093243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.082699 restraints weight = 108650.113| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 6.21 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 7716 Z= 0.128 Angle : 0.603 13.914 10527 Z= 0.322 Chirality : 0.039 0.140 1231 Planarity : 0.004 0.044 1339 Dihedral : 9.026 86.979 1110 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.58 % Allowed : 29.21 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.27), residues: 995 helix: 1.23 (0.27), residues: 387 sheet: -0.71 (0.34), residues: 215 loop : -1.43 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 256 TYR 0.011 0.001 TYR A 288 PHE 0.023 0.001 PHE B 199 TRP 0.016 0.001 TRP B 63 HIS 0.004 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 7712) covalent geometry : angle 0.60202 / 0.32 (10519) SS BOND : bond 0.00342 / 0.16 ( 4) SS BOND : angle 1.34715 / 0.61 ( 8) hydrogen bonds : bond 0.04245 / 2.87 ( 372) hydrogen bonds : angle 5.03187 / 3.65 ( 1047) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8794 (tt) REVERT: D 29 GLN cc_start: 0.8815 (mm110) cc_final: 0.8521 (mp10) REVERT: D 219 PHE cc_start: 0.8581 (m-80) cc_final: 0.8363 (m-80) REVERT: D 252 ASP cc_start: 0.8043 (t0) cc_final: 0.7816 (t0) outliers start: 34 outliers final: 31 residues processed: 220 average time/residue: 0.1800 time to fit residues: 55.0221 Evaluate side-chains 227 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 254 ASN Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain E residue 124 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.093354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.082904 restraints weight = 108871.341| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 6.16 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 7716 Z= 0.118 Angle : 0.610 13.935 10527 Z= 0.323 Chirality : 0.039 0.143 1231 Planarity : 0.003 0.040 1339 Dihedral : 8.951 86.193 1110 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.44 % Allowed : 30.15 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.28), residues: 995 helix: 1.23 (0.28), residues: 387 sheet: -0.79 (0.34), residues: 217 loop : -1.31 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 256 TYR 0.010 0.001 TYR A 288 PHE 0.023 0.001 PHE B 199 TRP 0.020 0.001 TRP B 63 HIS 0.004 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 7712) covalent geometry : angle 0.60949 / 0.32 (10519) SS BOND : bond 0.00320 / 0.15 ( 4) SS BOND : angle 1.26404 / 0.60 ( 8) hydrogen bonds : bond 0.04208 / 2.85 ( 372) hydrogen bonds : angle 4.95647 / 3.60 ( 1047) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8822 (tt) REVERT: B 314 ARG cc_start: 0.7453 (mmm-85) cc_final: 0.6930 (mmm-85) REVERT: D 29 GLN cc_start: 0.8797 (mm110) cc_final: 0.8526 (mp10) REVERT: D 219 PHE cc_start: 0.8595 (m-80) cc_final: 0.8380 (m-80) REVERT: D 252 ASP cc_start: 0.8021 (t0) cc_final: 0.7783 (t0) outliers start: 33 outliers final: 32 residues processed: 214 average time/residue: 0.1797 time to fit residues: 53.4937 Evaluate side-chains 225 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 254 ASN Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 380 GLN Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 34 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.093134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.082763 restraints weight = 109162.605| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 6.17 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.183 7716 Z= 0.207 Angle : 0.951 59.180 10527 Z= 0.562 Chirality : 0.040 0.295 1231 Planarity : 0.004 0.040 1339 Dihedral : 8.940 86.062 1110 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 4.71 % Allowed : 30.28 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.28), residues: 995 helix: 1.21 (0.27), residues: 388 sheet: -0.80 (0.34), residues: 217 loop : -1.32 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 256 TYR 0.011 0.001 TYR A 288 PHE 0.022 0.001 PHE B 199 TRP 0.017 0.001 TRP B 63 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.21 ( 7712) covalent geometry : angle 0.95101 / 0.56 (10519) SS BOND : bond 0.00388 / 0.19 ( 4) SS BOND : angle 1.27786 / 0.60 ( 8) hydrogen bonds : bond 0.04240 / 2.88 ( 372) hydrogen bonds : angle 4.97874 / 3.61 ( 1047) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8829 (tt) REVERT: D 29 GLN cc_start: 0.8803 (mm110) cc_final: 0.8530 (mp10) REVERT: D 219 PHE cc_start: 0.8599 (m-80) cc_final: 0.8398 (m-80) REVERT: D 252 ASP cc_start: 0.8038 (t0) cc_final: 0.7808 (t0) outliers start: 35 outliers final: 34 residues processed: 205 average time/residue: 0.1705 time to fit residues: 48.8005 Evaluate side-chains 227 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 380 GLN Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 54 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 85 optimal weight: 0.2980 chunk 25 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.093163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.082834 restraints weight = 109294.626| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 6.16 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.183 7716 Z= 0.207 Angle : 0.951 59.180 10527 Z= 0.562 Chirality : 0.040 0.295 1231 Planarity : 0.004 0.040 1339 Dihedral : 8.940 86.062 1110 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 4.71 % Allowed : 30.28 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.28), residues: 995 helix: 1.21 (0.27), residues: 388 sheet: -0.80 (0.34), residues: 217 loop : -1.32 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 256 TYR 0.011 0.001 TYR A 288 PHE 0.022 0.001 PHE B 199 TRP 0.017 0.001 TRP B 63 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.21 ( 7712) covalent geometry : angle 0.95101 / 0.56 (10519) SS BOND : bond 0.00388 / 0.19 ( 4) SS BOND : angle 1.27786 / 0.60 ( 8) hydrogen bonds : bond 0.04240 / 2.88 ( 372) hydrogen bonds : angle 4.97874 / 3.61 ( 1047) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2892.92 seconds wall clock time: 50 minutes 4.28 seconds (3004.28 seconds total)