Starting phenix.real_space_refine on Tue Aug 4 23:40:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w2i_65572/08_2026/9w2i_65572.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w2i_65572/08_2026/9w2i_65572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w2i_65572/08_2026/9w2i_65572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w2i_65572/08_2026/9w2i_65572.map" model { file = "/net/cci-nas-00/data/ceres_data/9w2i_65572/08_2026/9w2i_65572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w2i_65572/08_2026/9w2i_65572.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 4734 2.51 5 N 1258 2.21 5 O 1293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 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: 7338 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1546 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 189} Chain breaks: 3 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'GLN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "G" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 245 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "N" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 851 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2318 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 11, 'TRANS': 286} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2319 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 5, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 7, 'ASP:plan': 13, 'ASN:plan1': 5, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 113 Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'NMTRANS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'MLE:plan-1': 1, 'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.54, per 1000 atoms: 0.21 Number of scatterers: 7338 At special positions: 0 Unit cell: (128.817, 86.6, 85.5175, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1293 8.00 N 1258 7.00 C 4734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 181 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 350.1 milliseconds 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1840 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 11 sheets defined 39.3% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 26 through 39 removed outlier: 3.806A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.591A pdb=" N ILE A 56 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.701A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.802A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.913A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.814A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.788A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'G' and resid 14 through 24 removed outlier: 3.741A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.810A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 29 through 61 removed outlier: 4.389A pdb=" N LEU R 35 " --> pdb=" O TRP R 31 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS R 61 " --> pdb=" O ILE R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 95 removed outlier: 4.505A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN R 86 " --> pdb=" O MET R 82 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE R 89 " --> pdb=" O PHE R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 137 removed outlier: 3.547A pdb=" N ILE R 121 " --> pdb=" O MET R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 169 Proline residue: R 165 - end of helix removed outlier: 3.894A pdb=" N TYR R 169 " --> pdb=" O PRO R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 227 removed outlier: 4.214A pdb=" N TYR R 197 " --> pdb=" O THR R 193 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU R 208 " --> pdb=" O LEU R 204 " (cutoff:3.500A) Proline residue: R 209 - end of helix Processing helix chain 'R' and resid 240 through 270 Proline residue: R 265 - end of helix removed outlier: 4.060A pdb=" N PHE R 270 " --> pdb=" O TYR R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 275 Processing helix chain 'R' and resid 283 through 298 removed outlier: 4.166A pdb=" N GLN R 287 " --> pdb=" O LYS R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 312 removed outlier: 3.979A pdb=" N ILE R 305 " --> pdb=" O MET R 301 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N HIS R 312 " --> pdb=" O CYS R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 321 removed outlier: 4.315A pdb=" N ALA R 321 " --> pdb=" O GLY R 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 29 through 34 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.174A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.647A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 173 through 174 removed outlier: 3.540A pdb=" N THR R 173 " --> pdb=" O LYS R 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.359A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.871A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.228A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.197A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.576A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.486A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.584A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1041 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: 1.09 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1135 1.29 - 1.42: 2105 1.42 - 1.55: 4182 1.55 - 1.69: 11 1.69 - 1.82: 75 Bond restraints: 7508 Sorted by residual: bond pdb=" C GLY C 5 " pdb=" N MLE C 6 " ideal model delta sigma weight residual 1.329 1.518 -0.189 1.40e-02 5.10e+03 1.83e+02 bond pdb=" C GLU C 1 " pdb=" N LYS C 2 " ideal model delta sigma weight residual 1.329 1.501 -0.172 1.38e-02 5.25e+03 1.56e+02 bond pdb=" C TYR C 3 " pdb=" N VAL C 4 " ideal model delta sigma weight residual 1.332 1.498 -0.167 1.36e-02 5.41e+03 1.50e+02 bond pdb=" C LYS C 2 " pdb=" N TYR C 3 " ideal model delta sigma weight residual 1.331 1.489 -0.159 1.37e-02 5.33e+03 1.35e+02 bond pdb=" C VAL C 4 " pdb=" N GLY C 5 " ideal model delta sigma weight residual 1.329 1.481 -0.152 1.40e-02 5.10e+03 1.18e+02 ... (remaining 7503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 10182 3.08 - 6.16: 41 6.16 - 9.24: 1 9.24 - 12.32: 1 12.32 - 15.40: 1 Bond angle restraints: 10226 Sorted by residual: angle pdb=" C ARG N 98 " pdb=" N CYS N 99 " pdb=" CA CYS N 99 " ideal model delta sigma weight residual 121.98 106.58 15.40 3.11e+00 1.03e-01 2.45e+01 angle pdb=" N CYS R 106 " pdb=" CA CYS R 106 " pdb=" C CYS R 106 " ideal model delta sigma weight residual 113.20 108.92 4.28 1.36e+00 5.41e-01 9.88e+00 angle pdb=" C ALA R 159 " pdb=" N LEU R 160 " pdb=" CA LEU R 160 " ideal model delta sigma weight residual 121.58 115.61 5.97 1.95e+00 2.63e-01 9.39e+00 angle pdb=" CA LEU R 160 " pdb=" CB LEU R 160 " pdb=" CG LEU R 160 " ideal model delta sigma weight residual 116.30 127.01 -10.71 3.50e+00 8.16e-02 9.36e+00 angle pdb=" CA LYS C 2 " pdb=" C LYS C 2 " pdb=" N TYR C 3 " ideal model delta sigma weight residual 115.60 120.02 -4.42 1.48e+00 4.57e-01 8.93e+00 ... (remaining 10221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 3843 17.11 - 34.23: 356 34.23 - 51.34: 115 51.34 - 68.45: 25 68.45 - 85.57: 9 Dihedral angle restraints: 4348 sinusoidal: 1505 harmonic: 2843 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 64.19 28.81 1 1.00e+01 1.00e-02 1.19e+01 dihedral pdb=" CA CYS N 107 " pdb=" C CYS N 107 " pdb=" N PHE N 108 " pdb=" CA PHE N 108 " ideal model delta harmonic sigma weight residual 180.00 163.64 16.36 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB GLU B 138 " pdb=" CG GLU B 138 " pdb=" CD GLU B 138 " pdb=" OE1 GLU B 138 " ideal model delta sinusoidal sigma weight residual 0.00 85.57 -85.57 1 3.00e+01 1.11e-03 9.84e+00 ... (remaining 4345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 786 0.035 - 0.069: 287 0.069 - 0.104: 70 0.104 - 0.139: 38 0.139 - 0.173: 1 Chirality restraints: 1182 Sorted by residual: chirality pdb=" CA TYR C 3 " pdb=" N TYR C 3 " pdb=" C TYR C 3 " pdb=" CB TYR C 3 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" CA TYR A 339 " pdb=" N TYR A 339 " pdb=" C TYR A 339 " pdb=" CB TYR A 339 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.41e-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 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 1179 not shown) Planarity restraints: 1279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP R 130 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.27e+00 pdb=" CG ASP R 130 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP R 130 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP R 130 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO N 88 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 203 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.73e+00 pdb=" C ALA R 203 " 0.029 2.00e-02 2.50e+03 pdb=" O ALA R 203 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU R 204 " -0.010 2.00e-02 2.50e+03 ... (remaining 1276 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1319 2.77 - 3.30: 6647 3.30 - 3.83: 12330 3.83 - 4.37: 14376 4.37 - 4.90: 25629 Nonbonded interactions: 60301 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.235 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR R 24 " pdb=" OE2 GLU C 1 " model vdw 2.259 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.279 3.040 nonbonded pdb=" N ASN N 84 " pdb=" OD1 ASN N 84 " model vdw 2.312 3.120 ... (remaining 60296 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.970 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:8.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 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 : 0.006 0.189 7512 Z= 0.389 Angle : 0.538 15.398 10232 Z= 0.285 Chirality : 0.041 0.173 1182 Planarity : 0.003 0.045 1279 Dihedral : 15.785 85.569 2499 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.65 % Allowed : 19.97 % Favored : 77.37 % 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: 0.96 (0.28), residues: 948 helix: 2.40 (0.29), residues: 316 sheet: 0.66 (0.36), residues: 220 loop : -0.80 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 19 TYR 0.012 0.001 TYR R 70 PHE 0.020 0.001 PHE R 91 TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.38 ( 7508) covalent geometry : angle 0.53714 / 0.28 (10226) SS BOND : bond 0.00346 / 0.19 ( 3) SS BOND : angle 1.17747 / 0.75 ( 6) hydrogen bonds : bond 0.17102 / 11.55 ( 369) hydrogen bonds : angle 6.42265 / 4.50 ( 1041) Misc. bond : bond 0.05462 / 3.41 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.276 Fit side-chains outliers start: 19 outliers final: 16 residues processed: 129 average time/residue: 0.3487 time to fit residues: 48.2573 Evaluate side-chains 122 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.0770 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS R 90 ASN R 198 HIS ** R 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.164904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.131255 restraints weight = 8803.577| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.36 r_work: 0.3393 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7512 Z= 0.119 Angle : 0.503 7.664 10232 Z= 0.271 Chirality : 0.041 0.131 1182 Planarity : 0.004 0.045 1279 Dihedral : 5.213 42.126 1071 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 5.59 % Allowed : 15.92 % Favored : 78.49 % 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: 1.04 (0.29), residues: 948 helix: 2.34 (0.29), residues: 322 sheet: 0.61 (0.36), residues: 217 loop : -0.61 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 67 TYR 0.010 0.001 TYR N 95 PHE 0.009 0.001 PHE B 199 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 7508) covalent geometry : angle 0.50275 / 0.27 (10226) SS BOND : bond 0.00347 / 0.19 ( 3) SS BOND : angle 1.18646 / 0.77 ( 6) hydrogen bonds : bond 0.03978 / 2.70 ( 369) hydrogen bonds : angle 4.76003 / 3.35 ( 1041) Misc. bond : bond 0.00063 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 114 time to evaluate : 0.205 Fit side-chains REVERT: A 34 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7934 (tppp) REVERT: A 230 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7916 (mm-30) REVERT: A 333 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7976 (ptm-80) REVERT: R 252 MET cc_start: 0.7269 (mpm) cc_final: 0.6963 (mpm) REVERT: R 288 VAL cc_start: 0.8446 (p) cc_final: 0.8097 (m) REVERT: B 59 TYR cc_start: 0.8991 (OUTLIER) cc_final: 0.7168 (t80) REVERT: B 78 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8036 (mptt) REVERT: B 325 MET cc_start: 0.8812 (mmt) cc_final: 0.8609 (mmm) outliers start: 40 outliers final: 15 residues processed: 139 average time/residue: 0.3843 time to fit residues: 57.0432 Evaluate side-chains 123 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 301 MET Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 65 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 51 optimal weight: 0.0170 chunk 90 optimal weight: 4.9990 overall best weight: 1.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS R 74 ASN R 198 HIS ** R 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.160846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.130143 restraints weight = 8783.203| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.44 r_work: 0.3314 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7512 Z= 0.192 Angle : 0.567 9.141 10232 Z= 0.301 Chirality : 0.043 0.144 1182 Planarity : 0.004 0.046 1279 Dihedral : 4.909 37.429 1055 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.03 % Allowed : 17.60 % Favored : 77.37 % 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: 0.84 (0.28), residues: 948 helix: 2.15 (0.29), residues: 322 sheet: 0.50 (0.36), residues: 216 loop : -0.69 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 142 TYR 0.013 0.002 TYR N 95 PHE 0.012 0.002 PHE B 151 TRP 0.012 0.002 TRP A 281 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 ( 7508) covalent geometry : angle 0.56518 / 0.30 (10226) SS BOND : bond 0.00448 / 0.25 ( 3) SS BOND : angle 1.89085 / 1.18 ( 6) hydrogen bonds : bond 0.04445 / 2.99 ( 369) hydrogen bonds : angle 4.78634 / 3.36 ( 1041) Misc. bond : bond 0.00025 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 0.178 Fit side-chains REVERT: A 34 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7934 (tppp) REVERT: A 230 GLU cc_start: 0.8252 (mm-30) cc_final: 0.8016 (mm-30) REVERT: A 293 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8478 (mttm) REVERT: A 333 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7981 (ptm160) REVERT: R 252 MET cc_start: 0.7353 (mpm) cc_final: 0.7076 (mpm) REVERT: B 59 TYR cc_start: 0.9059 (OUTLIER) cc_final: 0.7347 (t80) REVERT: B 78 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.7961 (mptt) REVERT: B 325 MET cc_start: 0.8889 (mmt) cc_final: 0.8641 (mmm) outliers start: 36 outliers final: 20 residues processed: 137 average time/residue: 0.4331 time to fit residues: 63.4854 Evaluate side-chains 130 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 30 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 GLN R 74 ASN R 198 HIS ** R 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.162219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.131010 restraints weight = 8899.210| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.48 r_work: 0.3331 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7512 Z= 0.140 Angle : 0.515 7.349 10232 Z= 0.275 Chirality : 0.042 0.139 1182 Planarity : 0.004 0.046 1279 Dihedral : 4.608 33.693 1053 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 5.87 % Allowed : 17.60 % Favored : 76.54 % 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: 0.87 (0.28), residues: 948 helix: 2.21 (0.29), residues: 322 sheet: 0.42 (0.36), residues: 217 loop : -0.66 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 226 TYR 0.011 0.001 TYR N 95 PHE 0.010 0.001 PHE R 318 TRP 0.012 0.001 TRP N 47 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 7508) covalent geometry : angle 0.51341 / 0.27 (10226) SS BOND : bond 0.00387 / 0.21 ( 3) SS BOND : angle 1.51407 / 0.97 ( 6) hydrogen bonds : bond 0.03929 / 2.65 ( 369) hydrogen bonds : angle 4.58166 / 3.22 ( 1041) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 0.277 Fit side-chains REVERT: A 34 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7916 (tppp) REVERT: A 230 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7954 (mm-30) REVERT: A 333 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7881 (ptm160) REVERT: R 257 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8200 (tt) REVERT: B 59 TYR cc_start: 0.9050 (OUTLIER) cc_final: 0.7358 (t80) REVERT: B 78 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.7955 (mptt) REVERT: B 325 MET cc_start: 0.8884 (mmt) cc_final: 0.8648 (mmm) outliers start: 42 outliers final: 24 residues processed: 135 average time/residue: 0.4249 time to fit residues: 61.4856 Evaluate side-chains 133 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 182 VAL Chi-restraints excluded: chain R residue 232 HIS Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 295 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 80 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 74 ASN ** R 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.162653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.131546 restraints weight = 8787.209| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.45 r_work: 0.3335 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7512 Z= 0.130 Angle : 0.507 8.187 10232 Z= 0.271 Chirality : 0.041 0.136 1182 Planarity : 0.004 0.046 1279 Dihedral : 4.450 30.452 1053 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 5.03 % Allowed : 18.99 % Favored : 75.98 % 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 (0.28), residues: 948 helix: 2.28 (0.29), residues: 320 sheet: 0.26 (0.36), residues: 221 loop : -0.69 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 226 TYR 0.011 0.001 TYR N 95 PHE 0.009 0.001 PHE R 108 TRP 0.012 0.001 TRP N 47 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 7508) covalent geometry : angle 0.50625 / 0.27 (10226) SS BOND : bond 0.00343 / 0.19 ( 3) SS BOND : angle 1.38036 / 0.88 ( 6) hydrogen bonds : bond 0.03823 / 2.57 ( 369) hydrogen bonds : angle 4.48616 / 3.16 ( 1041) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.258 Fit side-chains REVERT: A 34 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7931 (tppp) REVERT: A 293 LYS cc_start: 0.8649 (mmtp) cc_final: 0.8309 (mttp) REVERT: A 333 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7874 (ptm160) REVERT: R 252 MET cc_start: 0.7257 (mpm) cc_final: 0.6944 (mpm) REVERT: R 257 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8180 (tt) REVERT: B 59 TYR cc_start: 0.9030 (OUTLIER) cc_final: 0.7362 (t80) REVERT: B 78 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.7951 (mptt) REVERT: B 325 MET cc_start: 0.8885 (mmt) cc_final: 0.8640 (mmm) outliers start: 36 outliers final: 24 residues processed: 131 average time/residue: 0.4419 time to fit residues: 61.9334 Evaluate side-chains 133 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 182 VAL Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 85 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 39 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 8 optimal weight: 0.1980 chunk 81 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 74 ASN R 97 ASN R 198 HIS R 267 HIS ** R 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.162934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.129137 restraints weight = 8929.160| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.71 r_work: 0.3383 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7512 Z= 0.181 Angle : 0.556 8.671 10232 Z= 0.296 Chirality : 0.043 0.144 1182 Planarity : 0.004 0.047 1279 Dihedral : 4.575 30.537 1052 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 5.59 % Allowed : 20.39 % Favored : 74.02 % 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: 0.75 (0.28), residues: 948 helix: 2.16 (0.29), residues: 321 sheet: 0.21 (0.36), residues: 222 loop : -0.67 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 226 TYR 0.013 0.001 TYR N 95 PHE 0.010 0.002 PHE B 292 TRP 0.012 0.002 TRP N 47 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 ( 7508) covalent geometry : angle 0.55433 / 0.30 (10226) SS BOND : bond 0.00423 / 0.23 ( 3) SS BOND : angle 1.74383 / 1.09 ( 6) hydrogen bonds : bond 0.04177 / 2.81 ( 369) hydrogen bonds : angle 4.62100 / 3.24 ( 1041) Misc. bond : bond 0.00009 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 0.332 Fit side-chains REVERT: A 34 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7748 (tppp) REVERT: A 333 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7961 (ptm160) REVERT: R 82 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7537 (ttm) REVERT: R 97 ASN cc_start: 0.5575 (OUTLIER) cc_final: 0.5201 (t0) REVERT: R 257 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7933 (tt) REVERT: B 59 TYR cc_start: 0.9095 (OUTLIER) cc_final: 0.7079 (t80) REVERT: B 78 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.7565 (mptt) REVERT: B 325 MET cc_start: 0.8827 (mmt) cc_final: 0.8521 (mmm) outliers start: 40 outliers final: 24 residues processed: 132 average time/residue: 0.4249 time to fit residues: 60.2585 Evaluate side-chains 135 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 97 ASN Chi-restraints excluded: chain R residue 182 VAL Chi-restraints excluded: chain R residue 232 HIS Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 55 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 74 ASN R 198 HIS ** R 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** 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 = 0.3873 r_free = 0.3873 target = 0.163252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.129069 restraints weight = 8933.582| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.71 r_work: 0.3368 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7512 Z= 0.189 Angle : 0.573 8.371 10232 Z= 0.302 Chirality : 0.043 0.146 1182 Planarity : 0.004 0.047 1279 Dihedral : 4.634 30.822 1052 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 5.59 % Allowed : 21.09 % Favored : 73.32 % 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: 0.64 (0.28), residues: 948 helix: 1.98 (0.29), residues: 327 sheet: 0.19 (0.36), residues: 222 loop : -0.72 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 226 TYR 0.013 0.002 TYR N 95 PHE 0.012 0.002 PHE R 89 TRP 0.013 0.002 TRP N 47 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 ( 7508) covalent geometry : angle 0.57138 / 0.30 (10226) SS BOND : bond 0.00447 / 0.25 ( 3) SS BOND : angle 1.83362 / 1.14 ( 6) hydrogen bonds : bond 0.04233 / 2.85 ( 369) hydrogen bonds : angle 4.64906 / 3.26 ( 1041) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 104 time to evaluate : 0.269 Fit side-chains REVERT: A 34 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7688 (tppp) REVERT: A 333 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7973 (ptm160) REVERT: R 82 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7553 (ttm) REVERT: R 252 MET cc_start: 0.7352 (mpm) cc_final: 0.6945 (mpm) REVERT: R 257 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7920 (tt) REVERT: B 59 TYR cc_start: 0.9089 (OUTLIER) cc_final: 0.7111 (t80) REVERT: B 78 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.7534 (mptt) REVERT: B 175 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.6856 (mp10) REVERT: B 325 MET cc_start: 0.8815 (mmt) cc_final: 0.8503 (mmm) outliers start: 40 outliers final: 25 residues processed: 132 average time/residue: 0.4046 time to fit residues: 57.1019 Evaluate side-chains 137 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 182 VAL Chi-restraints excluded: chain R residue 232 HIS Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 GLN R 97 ASN ** R 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.161537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127695 restraints weight = 8920.312| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.37 r_work: 0.3364 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7512 Z= 0.133 Angle : 0.533 8.972 10232 Z= 0.282 Chirality : 0.042 0.145 1182 Planarity : 0.004 0.046 1279 Dihedral : 4.413 30.684 1052 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.17 % Allowed : 22.07 % Favored : 72.77 % 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: 0.75 (0.28), residues: 948 helix: 2.25 (0.29), residues: 320 sheet: 0.19 (0.36), residues: 221 loop : -0.74 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 226 TYR 0.011 0.001 TYR N 95 PHE 0.011 0.001 PHE B 292 TRP 0.014 0.001 TRP N 47 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 7508) covalent geometry : angle 0.53156 / 0.28 (10226) SS BOND : bond 0.00362 / 0.20 ( 3) SS BOND : angle 1.46250 / 0.92 ( 6) hydrogen bonds : bond 0.03796 / 2.56 ( 369) hydrogen bonds : angle 4.49401 / 3.16 ( 1041) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.171 Fit side-chains REVERT: A 34 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7977 (tppp) REVERT: A 333 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7844 (ptm160) REVERT: R 97 ASN cc_start: 0.5726 (OUTLIER) cc_final: 0.5361 (t0) REVERT: R 248 PHE cc_start: 0.7586 (t80) cc_final: 0.7340 (t80) REVERT: R 252 MET cc_start: 0.7218 (mpm) cc_final: 0.6932 (mpm) REVERT: R 257 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8202 (tt) REVERT: B 59 TYR cc_start: 0.9024 (OUTLIER) cc_final: 0.7324 (t80) REVERT: B 78 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.7948 (mptt) REVERT: B 325 MET cc_start: 0.8834 (mmt) cc_final: 0.8601 (mmm) outliers start: 37 outliers final: 25 residues processed: 135 average time/residue: 0.3883 time to fit residues: 56.2068 Evaluate side-chains 134 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 97 ASN Chi-restraints excluded: chain R residue 182 VAL Chi-restraints excluded: chain R residue 232 HIS Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 74 ASN R 198 HIS ** R 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** 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 = 0.3807 r_free = 0.3807 target = 0.160377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.129619 restraints weight = 8770.816| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.44 r_work: 0.3318 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7512 Z= 0.169 Angle : 0.563 8.712 10232 Z= 0.297 Chirality : 0.043 0.148 1182 Planarity : 0.004 0.047 1279 Dihedral : 4.554 30.811 1052 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.75 % Allowed : 22.49 % Favored : 72.77 % 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: 0.66 (0.28), residues: 948 helix: 2.04 (0.29), residues: 328 sheet: 0.15 (0.36), residues: 221 loop : -0.74 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 226 TYR 0.014 0.001 TYR R 70 PHE 0.017 0.002 PHE B 292 TRP 0.013 0.001 TRP N 47 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 7508) covalent geometry : angle 0.56218 / 0.30 (10226) SS BOND : bond 0.00398 / 0.22 ( 3) SS BOND : angle 1.67563 / 1.04 ( 6) hydrogen bonds : bond 0.04070 / 2.73 ( 369) hydrogen bonds : angle 4.58143 / 3.22 ( 1041) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.167 Fit side-chains REVERT: A 34 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7941 (tppp) REVERT: A 333 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7868 (ptm160) REVERT: R 248 PHE cc_start: 0.7609 (t80) cc_final: 0.7352 (t80) REVERT: R 252 MET cc_start: 0.7267 (mpm) cc_final: 0.6964 (mpm) REVERT: R 257 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8221 (tt) REVERT: B 59 TYR cc_start: 0.9039 (OUTLIER) cc_final: 0.7357 (t80) REVERT: B 78 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.7888 (mptt) REVERT: B 325 MET cc_start: 0.8870 (mmt) cc_final: 0.8637 (mmm) outliers start: 34 outliers final: 25 residues processed: 127 average time/residue: 0.4132 time to fit residues: 55.9275 Evaluate side-chains 132 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 182 VAL Chi-restraints excluded: chain R residue 232 HIS Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 90 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 97 ASN ** R 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.161484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.131125 restraints weight = 8746.479| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.45 r_work: 0.3347 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7512 Z= 0.138 Angle : 0.545 9.287 10232 Z= 0.289 Chirality : 0.042 0.140 1182 Planarity : 0.004 0.046 1279 Dihedral : 4.432 30.798 1052 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.33 % Allowed : 23.04 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.28), residues: 948 helix: 2.15 (0.29), residues: 326 sheet: 0.15 (0.36), residues: 221 loop : -0.76 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 226 TYR 0.013 0.001 TYR R 70 PHE 0.012 0.001 PHE B 292 TRP 0.014 0.001 TRP N 47 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 7508) covalent geometry : angle 0.54381 / 0.29 (10226) SS BOND : bond 0.00354 / 0.20 ( 3) SS BOND : angle 1.47541 / 0.93 ( 6) hydrogen bonds : bond 0.03813 / 2.56 ( 369) hydrogen bonds : angle 4.49359 / 3.16 ( 1041) Misc. bond : bond 0.00005 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.167 Fit side-chains REVERT: A 34 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7965 (tppp) REVERT: A 333 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7830 (ptm160) REVERT: R 97 ASN cc_start: 0.5764 (OUTLIER) cc_final: 0.5431 (t0) REVERT: R 248 PHE cc_start: 0.7603 (t80) cc_final: 0.7343 (t80) REVERT: R 252 MET cc_start: 0.7252 (mpm) cc_final: 0.6963 (mpm) REVERT: B 59 TYR cc_start: 0.9029 (OUTLIER) cc_final: 0.7324 (t80) REVERT: B 78 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.7893 (mptt) REVERT: B 325 MET cc_start: 0.8848 (mmt) cc_final: 0.8620 (mmm) outliers start: 31 outliers final: 22 residues processed: 126 average time/residue: 0.4094 time to fit residues: 55.1421 Evaluate side-chains 128 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 97 ASN Chi-restraints excluded: chain R residue 232 HIS Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 1 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 GLN R 97 ASN R 198 HIS ** R 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.160641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.129745 restraints weight = 8792.635| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.45 r_work: 0.3320 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7512 Z= 0.166 Angle : 0.567 8.979 10232 Z= 0.300 Chirality : 0.042 0.142 1182 Planarity : 0.004 0.047 1279 Dihedral : 4.511 30.835 1052 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.47 % Allowed : 22.91 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.28), residues: 948 helix: 2.07 (0.29), residues: 326 sheet: 0.21 (0.36), residues: 219 loop : -0.83 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 226 TYR 0.015 0.001 TYR R 70 PHE 0.013 0.001 PHE B 292 TRP 0.013 0.001 TRP N 47 HIS 0.007 0.001 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 7508) covalent geometry : angle 0.56566 / 0.30 (10226) SS BOND : bond 0.00397 / 0.22 ( 3) SS BOND : angle 1.59260 / 1.00 ( 6) hydrogen bonds : bond 0.03992 / 2.69 ( 369) hydrogen bonds : angle 4.57109 / 3.21 ( 1041) Misc. bond : bond 0.00004 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2533.76 seconds wall clock time: 43 minutes 48.56 seconds (2628.56 seconds total)