Starting phenix.real_space_refine on Thu Jul 2 11:49:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7td4_25823/07_2026/7td4_25823.cif Found real_map, /net/cci-nas-00/data/ceres_data/7td4_25823/07_2026/7td4_25823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7td4_25823/07_2026/7td4_25823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7td4_25823/07_2026/7td4_25823.map" model { file = "/net/cci-nas-00/data/ceres_data/7td4_25823/07_2026/7td4_25823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7td4_25823/07_2026/7td4_25823.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7td4_25823/07_2026/7td4_25823.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7td4_25823/07_2026/7td4_25823.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.981 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2031 atoms to isotropic. 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 51 5.16 5 C 4417 2.51 5 N 1159 2.21 5 O 1263 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6893 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2497 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 325} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1757 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "G" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 368 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2220 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 6, 'TRANS': 283} Chain breaks: 2 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 4, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "R" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'J8C': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.27, per 1000 atoms: 0.18 Number of scatterers: 6893 At special positions: 0 Unit cell: (92.568, 94.696, 129.808, 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 51 16.00 F 3 9.00 O 1263 8.00 N 1159 7.00 C 4417 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 191 " distance=1.81 Simple disulfide: pdb=" SG CYS R 282 " - pdb=" SG CYS R 287 " distance=2.02 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 Links applied NAG-ASN " NAG R 401 " - " ASN R 30 " Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 289.3 milliseconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1694 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 45.4% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'B' and resid 10 through 24 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.604A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.594A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.996A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.709A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'G' and resid 14 through 24 removed outlier: 3.723A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.724A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.926A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'R' and resid 22 through 33 removed outlier: 3.929A pdb=" N VAL R 26 " --> pdb=" O TYR R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 73 removed outlier: 3.845A pdb=" N VAL R 51 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 104 Processing helix chain 'R' and resid 105 through 109 removed outlier: 3.624A pdb=" N THR R 109 " --> pdb=" O GLY R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 149 removed outlier: 3.786A pdb=" N MET R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 177 removed outlier: 3.884A pdb=" N TRP R 168 " --> pdb=" O ILE R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 234 removed outlier: 3.705A pdb=" N ARG R 234 " --> pdb=" O THR R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 282 removed outlier: 3.669A pdb=" N ALA R 253 " --> pdb=" O GLU R 249 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU R 255 " --> pdb=" O SER R 251 " (cutoff:3.500A) Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 288 through 292 Processing helix chain 'R' and resid 293 through 314 removed outlier: 4.038A pdb=" N SER R 304 " --> pdb=" O ALA R 300 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY R 305 " --> pdb=" O VAL R 301 " (cutoff:3.500A) Proline residue: R 308 - end of helix removed outlier: 3.828A pdb=" N THR R 314 " --> pdb=" O ILE R 310 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 323 removed outlier: 3.619A pdb=" N ILE R 323 " --> pdb=" O ARG R 319 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.627A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.631A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.936A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.893A 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 153 removed outlier: 3.662A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.003A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.449A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.843A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.409A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 1062 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: 0.89 Time building geometry restraints manager: 0.51 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: 1108 1.29 - 1.42: 1837 1.42 - 1.56: 4011 1.56 - 1.69: 0 1.69 - 1.82: 72 Bond restraints: 7028 Sorted by residual: bond pdb=" C THR R 193 " pdb=" O THR R 193 " ideal model delta sigma weight residual 1.237 1.160 0.076 1.19e-02 7.06e+03 4.12e+01 bond pdb=" C SER R 192 " pdb=" O SER R 192 " ideal model delta sigma weight residual 1.234 1.159 0.075 1.27e-02 6.20e+03 3.49e+01 bond pdb=" C LEU R 163 " pdb=" O LEU R 163 " ideal model delta sigma weight residual 1.237 1.170 0.067 1.16e-02 7.43e+03 3.30e+01 bond pdb=" C MET R 146 " pdb=" O MET R 146 " ideal model delta sigma weight residual 1.236 1.172 0.064 1.35e-02 5.49e+03 2.23e+01 bond pdb=" C ARG R 27 " pdb=" O ARG R 27 " ideal model delta sigma weight residual 1.237 1.186 0.050 1.17e-02 7.31e+03 1.84e+01 ... (remaining 7023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 9273 1.97 - 3.94: 214 3.94 - 5.91: 49 5.91 - 7.88: 6 7.88 - 9.85: 4 Bond angle restraints: 9546 Sorted by residual: angle pdb=" C GLU R 141 " pdb=" CA GLU R 141 " pdb=" CB GLU R 141 " ideal model delta sigma weight residual 110.88 101.03 9.85 1.57e+00 4.06e-01 3.94e+01 angle pdb=" C HIS R 152 " pdb=" N ASN R 153 " pdb=" CA ASN R 153 " ideal model delta sigma weight residual 122.77 115.03 7.74 1.33e+00 5.65e-01 3.38e+01 angle pdb=" CA THR R 193 " pdb=" CB THR R 193 " pdb=" OG1 THR R 193 " ideal model delta sigma weight residual 109.60 101.33 8.27 1.50e+00 4.44e-01 3.04e+01 angle pdb=" CA VAL R 194 " pdb=" C VAL R 194 " pdb=" O VAL R 194 " ideal model delta sigma weight residual 121.29 115.41 5.88 1.07e+00 8.73e-01 3.02e+01 angle pdb=" CA LYS R 150 " pdb=" C LYS R 150 " pdb=" O LYS R 150 " ideal model delta sigma weight residual 120.70 115.02 5.68 1.08e+00 8.57e-01 2.76e+01 ... (remaining 9541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.82: 4053 25.82 - 51.64: 93 51.64 - 77.46: 16 77.46 - 103.28: 2 103.28 - 129.10: 2 Dihedral angle restraints: 4166 sinusoidal: 1555 harmonic: 2611 Sorted by residual: dihedral pdb=" C GLU R 141 " pdb=" N GLU R 141 " pdb=" CA GLU R 141 " pdb=" CB GLU R 141 " ideal model delta harmonic sigma weight residual -122.60 -110.37 -12.23 0 2.50e+00 1.60e-01 2.39e+01 dihedral pdb=" CA ASP A 350 " pdb=" C ASP A 350 " pdb=" N CYS A 351 " pdb=" CA CYS A 351 " ideal model delta harmonic sigma weight residual 180.00 156.17 23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" C30 J8C R 402 " pdb=" C34 J8C R 402 " pdb=" N31 J8C R 402 " pdb=" C33 J8C R 402 " ideal model delta sinusoidal sigma weight residual 141.61 -89.29 -129.10 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 4163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 972 0.064 - 0.128: 134 0.128 - 0.192: 15 0.192 - 0.256: 4 0.256 - 0.320: 3 Chirality restraints: 1128 Sorted by residual: chirality pdb=" CA TYR R 81 " pdb=" N TYR R 81 " pdb=" C TYR R 81 " pdb=" CB TYR R 81 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA GLU R 141 " pdb=" N GLU R 141 " pdb=" C GLU R 141 " pdb=" CB GLU R 141 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA HIS R 77 " pdb=" N HIS R 77 " pdb=" C HIS R 77 " pdb=" CB HIS R 77 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1125 not shown) Planarity restraints: 1189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 J8C R 402 " 0.092 2.00e-02 2.50e+03 5.30e-02 6.33e+01 pdb=" C13 J8C R 402 " -0.017 2.00e-02 2.50e+03 pdb=" C14 J8C R 402 " -0.022 2.00e-02 2.50e+03 pdb=" C15 J8C R 402 " -0.019 2.00e-02 2.50e+03 pdb=" C16 J8C R 402 " -0.017 2.00e-02 2.50e+03 pdb=" C17 J8C R 402 " -0.051 2.00e-02 2.50e+03 pdb=" C18 J8C R 402 " -0.045 2.00e-02 2.50e+03 pdb=" C19 J8C R 402 " 0.102 2.00e-02 2.50e+03 pdb=" C25 J8C R 402 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 J8C R 402 " -0.042 2.00e-02 2.50e+03 3.22e-02 2.33e+01 pdb=" C03 J8C R 402 " 0.037 2.00e-02 2.50e+03 pdb=" C04 J8C R 402 " 0.023 2.00e-02 2.50e+03 pdb=" C05 J8C R 402 " 0.006 2.00e-02 2.50e+03 pdb=" C06 J8C R 402 " -0.009 2.00e-02 2.50e+03 pdb=" C07 J8C R 402 " 0.012 2.00e-02 2.50e+03 pdb=" C08 J8C R 402 " 0.049 2.00e-02 2.50e+03 pdb=" C09 J8C R 402 " -0.046 2.00e-02 2.50e+03 pdb=" C30 J8C R 402 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 151 " -0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" C LEU R 151 " 0.073 2.00e-02 2.50e+03 pdb=" O LEU R 151 " -0.027 2.00e-02 2.50e+03 pdb=" N HIS R 152 " -0.025 2.00e-02 2.50e+03 ... (remaining 1186 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 187 2.70 - 3.25: 6918 3.25 - 3.80: 10991 3.80 - 4.35: 14690 4.35 - 4.90: 24420 Nonbonded interactions: 57206 Sorted by model distance: nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.149 3.040 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.200 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.255 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.340 3.040 nonbonded pdb=" O LEU R 177 " pdb=" O GLY R 181 " model vdw 2.371 3.040 ... (remaining 57201 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.380 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:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 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 : 0.008 0.218 7031 Z= 0.421 Angle : 0.791 13.648 9553 Z= 0.503 Chirality : 0.050 0.320 1128 Planarity : 0.005 0.053 1188 Dihedral : 12.459 129.104 2466 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.84 % Allowed : 5.87 % Favored : 93.30 % Cbeta Deviations : 0.35 % 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: 0.11 (0.28), residues: 880 helix: 1.26 (0.27), residues: 367 sheet: 0.27 (0.41), residues: 178 loop : -1.37 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 48 TYR 0.027 0.002 TYR R 82 PHE 0.020 0.002 PHE R 83 TRP 0.014 0.002 TRP B 99 HIS 0.012 0.001 HIS R 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.40 ( 7028) covalent geometry : angle 0.76736 / 0.50 ( 9546) SS BOND : bond 0.15417 / 8.11 ( 2) SS BOND : angle 8.97025 / 4.83 ( 4) hydrogen bonds : bond 0.14689 / 9.80 ( 371) hydrogen bonds : angle 5.84355 / 4.22 ( 1062) link_NAG-ASN : bond 0.00287 / 0.15 ( 1) link_NAG-ASN : angle 3.45013 / 1.75 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 155 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: B 239 ASN cc_start: 0.8677 (m-40) cc_final: 0.8442 (m-40) REVERT: A 22 ASN cc_start: 0.8394 (m-40) cc_final: 0.8192 (m110) REVERT: A 24 ARG cc_start: 0.7428 (ttm110) cc_final: 0.7115 (ttm110) REVERT: R 48 THR cc_start: 0.7502 (p) cc_final: 0.7259 (m) REVERT: R 146 MET cc_start: 0.8835 (mmm) cc_final: 0.8579 (tpp) REVERT: R 229 ARG cc_start: 0.7538 (ttp-170) cc_final: 0.6948 (ttt90) outliers start: 6 outliers final: 3 residues processed: 160 average time/residue: 0.4588 time to fit residues: 77.4523 Evaluate side-chains 137 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 134 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 164 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN B 175 GLN R 199 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.152528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.121143 restraints weight = 8029.725| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.89 r_work: 0.3092 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7031 Z= 0.135 Angle : 0.519 7.061 9553 Z= 0.280 Chirality : 0.041 0.150 1128 Planarity : 0.004 0.050 1188 Dihedral : 8.099 118.549 1004 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.51 % Allowed : 10.89 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.28), residues: 880 helix: 1.90 (0.27), residues: 370 sheet: 0.35 (0.39), residues: 175 loop : -1.29 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 48 TYR 0.016 0.001 TYR R 98 PHE 0.022 0.002 PHE R 273 TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 7028) covalent geometry : angle 0.51702 / 0.28 ( 9546) SS BOND : bond 0.00136 / 0.07 ( 2) SS BOND : angle 0.84413 / 0.45 ( 4) hydrogen bonds : bond 0.04538 / 3.06 ( 371) hydrogen bonds : angle 4.41410 / 3.18 ( 1062) link_NAG-ASN : bond 0.00087 / 0.05 ( 1) link_NAG-ASN : angle 2.24915 / 1.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.7820 (t80) REVERT: B 239 ASN cc_start: 0.8806 (m-40) cc_final: 0.8527 (m-40) REVERT: B 256 ARG cc_start: 0.8660 (mtm180) cc_final: 0.8455 (mtm-85) REVERT: A 14 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7588 (mt-10) REVERT: A 18 MET cc_start: 0.8043 (tpp) cc_final: 0.7777 (tpp) REVERT: A 24 ARG cc_start: 0.7792 (ttm110) cc_final: 0.7235 (ttm110) REVERT: A 207 GLU cc_start: 0.7831 (tp30) cc_final: 0.7572 (tp30) REVERT: R 48 THR cc_start: 0.7448 (p) cc_final: 0.7175 (m) REVERT: R 146 MET cc_start: 0.8958 (mmm) cc_final: 0.8689 (tpp) REVERT: R 229 ARG cc_start: 0.7639 (ttp-170) cc_final: 0.6766 (ttt90) outliers start: 18 outliers final: 9 residues processed: 162 average time/residue: 0.4704 time to fit residues: 80.3715 Evaluate side-chains 153 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain R residue 191 CYS Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 42 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.151078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.119509 restraints weight = 7989.989| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.90 r_work: 0.3068 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7031 Z= 0.187 Angle : 0.552 6.945 9553 Z= 0.294 Chirality : 0.043 0.144 1128 Planarity : 0.004 0.052 1188 Dihedral : 8.240 123.326 1000 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.49 % Allowed : 12.29 % Favored : 84.22 % 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: 0.65 (0.28), residues: 880 helix: 1.86 (0.26), residues: 375 sheet: 0.37 (0.38), residues: 175 loop : -1.23 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.014 0.002 TYR R 98 PHE 0.020 0.002 PHE R 273 TRP 0.014 0.002 TRP B 99 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 ( 7028) covalent geometry : angle 0.55024 / 0.29 ( 9546) SS BOND : bond 0.00482 / 0.25 ( 2) SS BOND : angle 0.97455 / 0.55 ( 4) hydrogen bonds : bond 0.04894 / 3.31 ( 371) hydrogen bonds : angle 4.43230 / 3.17 ( 1062) link_NAG-ASN : bond 0.00209 / 0.11 ( 1) link_NAG-ASN : angle 2.38788 / 1.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.9302 (OUTLIER) cc_final: 0.7824 (t80) REVERT: B 239 ASN cc_start: 0.8830 (m-40) cc_final: 0.8561 (m-40) REVERT: A 18 MET cc_start: 0.8023 (tpp) cc_final: 0.7797 (tpp) REVERT: A 24 ARG cc_start: 0.7764 (ttm110) cc_final: 0.7187 (ttm110) REVERT: A 207 GLU cc_start: 0.7848 (tp30) cc_final: 0.7567 (tp30) REVERT: A 308 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8240 (mt-10) REVERT: R 27 ARG cc_start: 0.7654 (ttm110) cc_final: 0.7340 (ttm-80) REVERT: R 48 THR cc_start: 0.7417 (p) cc_final: 0.7121 (m) REVERT: R 150 LYS cc_start: 0.8641 (pttt) cc_final: 0.8106 (ptpt) REVERT: R 229 ARG cc_start: 0.7677 (ttp-170) cc_final: 0.6744 (ttt90) REVERT: R 318 MET cc_start: 0.8101 (mmt) cc_final: 0.7735 (mmt) outliers start: 25 outliers final: 15 residues processed: 157 average time/residue: 0.4877 time to fit residues: 80.5481 Evaluate side-chains 153 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 103 LEU Chi-restraints excluded: chain R residue 148 LYS Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 191 CYS Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 78 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 46 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.153186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.121476 restraints weight = 8068.639| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.93 r_work: 0.3096 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7031 Z= 0.135 Angle : 0.499 6.981 9553 Z= 0.266 Chirality : 0.041 0.145 1128 Planarity : 0.004 0.051 1188 Dihedral : 8.008 121.771 1000 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.91 % Allowed : 13.13 % Favored : 82.96 % 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: 0.79 (0.28), residues: 880 helix: 2.03 (0.26), residues: 378 sheet: 0.34 (0.37), residues: 181 loop : -1.23 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.013 0.001 TYR R 98 PHE 0.019 0.001 PHE R 273 TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 7028) covalent geometry : angle 0.49670 / 0.27 ( 9546) SS BOND : bond 0.00266 / 0.14 ( 2) SS BOND : angle 0.95208 / 0.53 ( 4) hydrogen bonds : bond 0.04311 / 2.92 ( 371) hydrogen bonds : angle 4.23687 / 3.03 ( 1062) link_NAG-ASN : bond 0.00186 / 0.10 ( 1) link_NAG-ASN : angle 2.25235 / 1.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 234 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.7806 (t80) REVERT: B 239 ASN cc_start: 0.8779 (m-40) cc_final: 0.8520 (m-40) REVERT: A 14 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7683 (mt-10) REVERT: A 18 MET cc_start: 0.7988 (tpp) cc_final: 0.7674 (tpp) REVERT: A 24 ARG cc_start: 0.7792 (ttm110) cc_final: 0.7180 (ttm110) REVERT: A 207 GLU cc_start: 0.7741 (tp30) cc_final: 0.7410 (tp30) REVERT: A 297 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6015 (mp0) REVERT: R 27 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7289 (ttm-80) REVERT: R 48 THR cc_start: 0.7397 (p) cc_final: 0.7097 (m) REVERT: R 229 ARG cc_start: 0.7649 (ttp-170) cc_final: 0.6716 (ttt90) outliers start: 28 outliers final: 16 residues processed: 160 average time/residue: 0.4616 time to fit residues: 77.9122 Evaluate side-chains 160 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain R residue 27 ARG Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 148 LYS Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 191 CYS Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.2980 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 76 optimal weight: 0.0030 chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.153187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.122974 restraints weight = 8068.596| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.89 r_work: 0.3140 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7031 Z= 0.127 Angle : 0.507 8.446 9553 Z= 0.264 Chirality : 0.041 0.185 1128 Planarity : 0.003 0.050 1188 Dihedral : 7.977 121.834 1000 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.91 % Allowed : 13.41 % Favored : 82.68 % 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: 880 helix: 2.13 (0.26), residues: 378 sheet: 0.36 (0.38), residues: 181 loop : -1.28 (0.30), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.012 0.001 TYR R 98 PHE 0.018 0.001 PHE R 273 TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 7028) covalent geometry : angle 0.50466 / 0.26 ( 9546) SS BOND : bond 0.00140 / 0.07 ( 2) SS BOND : angle 1.70493 / 0.97 ( 4) hydrogen bonds : bond 0.04161 / 2.81 ( 371) hydrogen bonds : angle 4.20129 / 3.00 ( 1062) link_NAG-ASN : bond 0.00188 / 0.10 ( 1) link_NAG-ASN : angle 2.18815 / 1.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8131 (mmtp) REVERT: B 217 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7993 (pmm) REVERT: B 234 PHE cc_start: 0.9312 (OUTLIER) cc_final: 0.7811 (t80) REVERT: B 239 ASN cc_start: 0.8755 (m-40) cc_final: 0.8492 (m-40) REVERT: A 18 MET cc_start: 0.8012 (tpp) cc_final: 0.7777 (tpp) REVERT: A 24 ARG cc_start: 0.7783 (ttm110) cc_final: 0.7163 (ttm110) REVERT: A 207 GLU cc_start: 0.7742 (tp30) cc_final: 0.7404 (tp30) REVERT: A 297 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6091 (mp0) REVERT: R 27 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7296 (ttm-80) REVERT: R 229 ARG cc_start: 0.7661 (ttp-170) cc_final: 0.6740 (ttt90) outliers start: 28 outliers final: 17 residues processed: 157 average time/residue: 0.4689 time to fit residues: 77.5822 Evaluate side-chains 158 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain R residue 27 ARG Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 148 LYS Chi-restraints excluded: chain R residue 164 ILE Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 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 = 0.3732 r_free = 0.3732 target = 0.152096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.120249 restraints weight = 8150.012| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.93 r_work: 0.3083 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7031 Z= 0.150 Angle : 0.530 9.456 9553 Z= 0.276 Chirality : 0.042 0.152 1128 Planarity : 0.004 0.050 1188 Dihedral : 8.080 122.530 1000 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.91 % Allowed : 14.25 % Favored : 81.84 % 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: 0.85 (0.27), residues: 880 helix: 2.12 (0.26), residues: 377 sheet: 0.50 (0.37), residues: 179 loop : -1.32 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.012 0.001 TYR R 31 PHE 0.017 0.002 PHE R 273 TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 7028) covalent geometry : angle 0.52700 / 0.28 ( 9546) SS BOND : bond 0.00154 / 0.08 ( 2) SS BOND : angle 1.80964 / 1.04 ( 4) hydrogen bonds : bond 0.04377 / 2.96 ( 371) hydrogen bonds : angle 4.23032 / 3.02 ( 1062) link_NAG-ASN : bond 0.00251 / 0.13 ( 1) link_NAG-ASN : angle 2.26171 / 1.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LYS cc_start: 0.8615 (mmtt) cc_final: 0.8392 (mmtp) REVERT: B 239 ASN cc_start: 0.8765 (m-40) cc_final: 0.8520 (m-40) REVERT: A 14 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7580 (mt-10) REVERT: A 18 MET cc_start: 0.7932 (tpp) cc_final: 0.7689 (tpp) REVERT: A 24 ARG cc_start: 0.7754 (ttm110) cc_final: 0.7132 (ttm110) REVERT: A 53 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.7021 (ttm) REVERT: A 207 GLU cc_start: 0.7754 (tp30) cc_final: 0.7398 (tp30) REVERT: A 297 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6131 (mp0) REVERT: R 27 ARG cc_start: 0.7591 (ttm110) cc_final: 0.7206 (ttm-80) REVERT: R 124 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8683 (mmm) REVERT: R 150 LYS cc_start: 0.8545 (pttt) cc_final: 0.7993 (ptpt) REVERT: R 229 ARG cc_start: 0.7657 (ttp-170) cc_final: 0.6718 (ttt90) outliers start: 28 outliers final: 19 residues processed: 150 average time/residue: 0.4451 time to fit residues: 70.4628 Evaluate side-chains 157 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 148 LYS Chi-restraints excluded: chain R residue 164 ILE Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 211 THR Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 54 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 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 = 0.3711 r_free = 0.3711 target = 0.149989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.118103 restraints weight = 8022.589| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.91 r_work: 0.3128 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 7031 Z= 0.250 Angle : 0.617 10.134 9553 Z= 0.321 Chirality : 0.045 0.175 1128 Planarity : 0.004 0.051 1188 Dihedral : 8.379 123.963 1000 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.75 % Allowed : 13.55 % Favored : 81.70 % 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: 0.60 (0.27), residues: 880 helix: 1.75 (0.26), residues: 377 sheet: 0.37 (0.37), residues: 185 loop : -1.25 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.013 0.002 TYR R 98 PHE 0.020 0.002 PHE B 151 TRP 0.014 0.002 TRP B 99 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.25 ( 7028) covalent geometry : angle 0.61399 / 0.32 ( 9546) SS BOND : bond 0.00172 / 0.09 ( 2) SS BOND : angle 2.19633 / 1.27 ( 4) hydrogen bonds : bond 0.05250 / 3.56 ( 371) hydrogen bonds : angle 4.46764 / 3.18 ( 1062) link_NAG-ASN : bond 0.00377 / 0.20 ( 1) link_NAG-ASN : angle 2.58968 / 1.31 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8403 (mmtp) REVERT: B 239 ASN cc_start: 0.8923 (m-40) cc_final: 0.8672 (m-40) REVERT: A 18 MET cc_start: 0.8021 (tpp) cc_final: 0.7789 (tpp) REVERT: A 24 ARG cc_start: 0.7871 (ttm110) cc_final: 0.7269 (ttm110) REVERT: A 207 GLU cc_start: 0.7866 (tp30) cc_final: 0.7518 (tp30) REVERT: A 297 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6294 (mp0) REVERT: R 27 ARG cc_start: 0.7874 (ttm110) cc_final: 0.7537 (ttm-80) REVERT: R 29 TYR cc_start: 0.8741 (m-80) cc_final: 0.8460 (m-80) REVERT: R 124 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8806 (mmm) REVERT: R 150 LYS cc_start: 0.8605 (pttt) cc_final: 0.8073 (ptpt) REVERT: R 229 ARG cc_start: 0.7716 (ttp-170) cc_final: 0.6801 (ttt90) outliers start: 34 outliers final: 23 residues processed: 156 average time/residue: 0.4286 time to fit residues: 70.4840 Evaluate side-chains 156 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 148 LYS Chi-restraints excluded: chain R residue 164 ILE Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 211 THR Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 77 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 65 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 75 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 315 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.152085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.120245 restraints weight = 8149.425| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.94 r_work: 0.3095 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7031 Z= 0.142 Angle : 0.529 9.391 9553 Z= 0.276 Chirality : 0.042 0.180 1128 Planarity : 0.004 0.051 1188 Dihedral : 8.098 122.349 1000 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.91 % Allowed : 14.94 % Favored : 81.15 % 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: 0.76 (0.27), residues: 880 helix: 1.98 (0.26), residues: 377 sheet: 0.42 (0.37), residues: 187 loop : -1.30 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.012 0.001 TYR R 98 PHE 0.017 0.001 PHE R 273 TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 7028) covalent geometry : angle 0.52638 / 0.28 ( 9546) SS BOND : bond 0.00128 / 0.07 ( 2) SS BOND : angle 1.68637 / 0.97 ( 4) hydrogen bonds : bond 0.04392 / 2.97 ( 371) hydrogen bonds : angle 4.25877 / 3.05 ( 1062) link_NAG-ASN : bond 0.00327 / 0.17 ( 1) link_NAG-ASN : angle 2.28703 / 1.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LYS cc_start: 0.8584 (mmtt) cc_final: 0.8373 (mmtp) REVERT: B 239 ASN cc_start: 0.8802 (m-40) cc_final: 0.8561 (m-40) REVERT: A 18 MET cc_start: 0.7993 (tpp) cc_final: 0.7683 (tpp) REVERT: A 24 ARG cc_start: 0.7822 (ttm110) cc_final: 0.7206 (ttm110) REVERT: A 207 GLU cc_start: 0.7794 (tp30) cc_final: 0.7460 (tp30) REVERT: A 297 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6132 (mp0) REVERT: R 27 ARG cc_start: 0.7653 (ttm110) cc_final: 0.7280 (ttm-80) REVERT: R 150 LYS cc_start: 0.8536 (pttt) cc_final: 0.8031 (ptpt) REVERT: R 229 ARG cc_start: 0.7731 (ttp-170) cc_final: 0.6801 (ttt90) outliers start: 28 outliers final: 20 residues processed: 154 average time/residue: 0.4260 time to fit residues: 69.1327 Evaluate side-chains 158 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 148 LYS Chi-restraints excluded: chain R residue 164 ILE Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 211 THR Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 175 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.152269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.120437 restraints weight = 8101.101| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.94 r_work: 0.3124 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7031 Z= 0.147 Angle : 0.533 9.236 9553 Z= 0.277 Chirality : 0.042 0.204 1128 Planarity : 0.004 0.051 1188 Dihedral : 8.103 122.679 1000 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.63 % Allowed : 14.94 % Favored : 81.42 % 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: 0.81 (0.28), residues: 880 helix: 2.02 (0.26), residues: 377 sheet: 0.54 (0.38), residues: 185 loop : -1.33 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.013 0.001 TYR R 98 PHE 0.017 0.002 PHE R 273 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS R 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 7028) covalent geometry : angle 0.53057 / 0.28 ( 9546) SS BOND : bond 0.00126 / 0.07 ( 2) SS BOND : angle 1.58650 / 0.91 ( 4) hydrogen bonds : bond 0.04399 / 2.98 ( 371) hydrogen bonds : angle 4.23265 / 3.02 ( 1062) link_NAG-ASN : bond 0.00235 / 0.12 ( 1) link_NAG-ASN : angle 2.10905 / 1.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LYS cc_start: 0.8554 (mmtt) cc_final: 0.8343 (mmtp) REVERT: B 239 ASN cc_start: 0.8797 (m-40) cc_final: 0.8558 (m-40) REVERT: A 18 MET cc_start: 0.7996 (tpp) cc_final: 0.7756 (tpp) REVERT: A 24 ARG cc_start: 0.7815 (ttm110) cc_final: 0.7199 (ttm110) REVERT: A 207 GLU cc_start: 0.7802 (tp30) cc_final: 0.7439 (tp30) REVERT: A 297 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6179 (mp0) REVERT: R 27 ARG cc_start: 0.7741 (ttm110) cc_final: 0.7348 (ttm-80) REVERT: R 150 LYS cc_start: 0.8545 (pttt) cc_final: 0.8019 (ptpt) REVERT: R 229 ARG cc_start: 0.7738 (ttp-170) cc_final: 0.6798 (ttt90) outliers start: 26 outliers final: 19 residues processed: 153 average time/residue: 0.4407 time to fit residues: 71.0645 Evaluate side-chains 155 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 148 LYS Chi-restraints excluded: chain R residue 164 ILE Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 211 THR Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 84 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 chunk 69 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.152701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121159 restraints weight = 8008.740| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.91 r_work: 0.3142 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7031 Z= 0.142 Angle : 0.525 9.113 9553 Z= 0.275 Chirality : 0.042 0.244 1128 Planarity : 0.004 0.051 1188 Dihedral : 8.058 121.740 1000 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.93 % Allowed : 15.92 % Favored : 81.15 % 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: 880 helix: 2.07 (0.26), residues: 378 sheet: 0.52 (0.38), residues: 185 loop : -1.33 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.013 0.001 TYR R 98 PHE 0.017 0.002 PHE R 273 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 7028) covalent geometry : angle 0.52316 / 0.27 ( 9546) SS BOND : bond 0.00128 / 0.07 ( 2) SS BOND : angle 1.58870 / 0.91 ( 4) hydrogen bonds : bond 0.04319 / 2.93 ( 371) hydrogen bonds : angle 4.22330 / 3.02 ( 1062) link_NAG-ASN : bond 0.00204 / 0.11 ( 1) link_NAG-ASN : angle 1.96996 / 1.02 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8357 (mmtp) REVERT: B 239 ASN cc_start: 0.8833 (m-40) cc_final: 0.8599 (m-40) REVERT: A 18 MET cc_start: 0.7979 (tpp) cc_final: 0.7748 (tpp) REVERT: A 24 ARG cc_start: 0.7811 (ttm110) cc_final: 0.7197 (ttm110) REVERT: A 207 GLU cc_start: 0.7810 (tp30) cc_final: 0.7460 (tp30) REVERT: A 297 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6185 (mp0) REVERT: R 27 ARG cc_start: 0.7742 (ttm110) cc_final: 0.7352 (ttm-80) REVERT: R 150 LYS cc_start: 0.8584 (pttt) cc_final: 0.8058 (ptpt) REVERT: R 229 ARG cc_start: 0.7752 (ttp-170) cc_final: 0.6824 (ttt90) outliers start: 21 outliers final: 19 residues processed: 150 average time/residue: 0.4369 time to fit residues: 69.2465 Evaluate side-chains 155 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 148 LYS Chi-restraints excluded: chain R residue 164 ILE Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 211 THR Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 87 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.152302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.120544 restraints weight = 8034.872| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.92 r_work: 0.3123 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7031 Z= 0.155 Angle : 0.543 9.198 9553 Z= 0.283 Chirality : 0.043 0.245 1128 Planarity : 0.004 0.051 1188 Dihedral : 8.102 121.911 1000 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.93 % Allowed : 16.34 % Favored : 80.73 % 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: 0.79 (0.28), residues: 880 helix: 2.01 (0.26), residues: 379 sheet: 0.52 (0.38), residues: 185 loop : -1.36 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.014 0.001 TYR R 31 PHE 0.016 0.002 PHE R 273 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 7028) covalent geometry : angle 0.54143 / 0.28 ( 9546) SS BOND : bond 0.00124 / 0.06 ( 2) SS BOND : angle 1.62800 / 0.93 ( 4) hydrogen bonds : bond 0.04454 / 3.02 ( 371) hydrogen bonds : angle 4.26845 / 3.04 ( 1062) link_NAG-ASN : bond 0.00264 / 0.14 ( 1) link_NAG-ASN : angle 2.05441 / 1.05 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2677.91 seconds wall clock time: 46 minutes 7.07 seconds (2767.07 seconds total)