Starting phenix.real_space_refine on Thu Jul 2 08:59:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pm2_17756/07_2026/8pm2_17756.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pm2_17756/07_2026/8pm2_17756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pm2_17756/07_2026/8pm2_17756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pm2_17756/07_2026/8pm2_17756.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8pm2_17756/07_2026/8pm2_17756.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pm2_17756/07_2026/8pm2_17756.cif" model { file = "/net/cci-nas-00/data/ceres_data/8pm2_17756/07_2026/8pm2_17756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pm2_17756/07_2026/8pm2_17756.cif" } resolution = 2.92 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= 0.013 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 52 5.16 5 C 4999 2.51 5 N 1345 2.21 5 O 1425 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s 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: 7821 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 3, 'ASN:plan1': 4, 'GLU:plan': 6, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 93 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2587 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 420 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2036 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain breaks: 2 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'8IA': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.25, per 1000 atoms: 0.16 Number of scatterers: 7821 At special positions: 0 Unit cell: (74.16, 98.056, 128.544, 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 52 16.00 O 1425 8.00 N 1345 7.00 C 4999 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=2.03 Simple disulfide: pdb=" SG CYS R 120 " - pdb=" SG CYS R 205 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 348.3 milliseconds 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1896 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 43.8% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 4.095A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.739A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.825A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 removed outlier: 3.531A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.533A pdb=" N ASP A 310 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.013A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.573A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.758A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.875A 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: 3.665A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.600A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 50 through 75 removed outlier: 3.552A pdb=" N PHE R 54 " --> pdb=" O LEU R 50 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN R 65 " --> pdb=" O ALA R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 79 Processing helix chain 'R' and resid 80 through 100 removed outlier: 3.609A pdb=" N PHE R 84 " --> pdb=" O SER R 80 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU R 85 " --> pdb=" O PRO R 81 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL R 86 " --> pdb=" O ALA R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 109 removed outlier: 4.319A pdb=" N VAL R 106 " --> pdb=" O PRO R 102 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG R 107 " --> pdb=" O PHE R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 151 Processing helix chain 'R' and resid 154 through 159 Processing helix chain 'R' and resid 160 through 184 removed outlier: 3.984A pdb=" N ILE R 183 " --> pdb=" O GLY R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 250 Proline residue: R 224 - end of helix removed outlier: 4.266A pdb=" N VAL R 227 " --> pdb=" O ILE R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 298 removed outlier: 3.569A pdb=" N ARG R 267 " --> pdb=" O ARG R 263 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS R 270 " --> pdb=" O LYS R 266 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE R 282 " --> pdb=" O ALA R 278 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SER R 285 " --> pdb=" O ALA R 281 " (cutoff:3.500A) Proline residue: R 288 - end of helix Processing helix chain 'R' and resid 304 through 317 Processing helix chain 'R' and resid 317 through 327 Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 335 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.775A pdb=" N VAL A 214 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.910A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.846A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.633A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.388A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.954A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.378A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.874A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8 removed outlier: 3.709A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.155A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1119 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: 0.98 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2525 1.34 - 1.46: 1867 1.46 - 1.58: 3530 1.58 - 1.70: 1 1.70 - 1.82: 73 Bond restraints: 7996 Sorted by residual: bond pdb=" C06 8IA R 401 " pdb=" N01 8IA R 401 " ideal model delta sigma weight residual 1.460 1.599 -0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" CAV Y01 R 402 " pdb=" CAZ Y01 R 402 " ideal model delta sigma weight residual 1.507 1.383 0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" CAI Y01 R 402 " pdb=" CAK Y01 R 402 " ideal model delta sigma weight residual 1.492 1.391 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" CBG Y01 R 402 " pdb=" CBI Y01 R 402 " ideal model delta sigma weight residual 1.537 1.442 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C07 8IA R 401 " pdb=" N01 8IA R 401 " ideal model delta sigma weight residual 1.446 1.529 -0.083 2.00e-02 2.50e+03 1.73e+01 ... (remaining 7991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 10729 2.90 - 5.80: 123 5.80 - 8.70: 4 8.70 - 11.60: 2 11.60 - 14.50: 2 Bond angle restraints: 10860 Sorted by residual: angle pdb=" CAM Y01 R 402 " pdb=" CAY Y01 R 402 " pdb=" OAW Y01 R 402 " ideal model delta sigma weight residual 111.19 125.69 -14.50 3.00e+00 1.11e-01 2.34e+01 angle pdb=" OAG Y01 R 402 " pdb=" CAY Y01 R 402 " pdb=" OAW Y01 R 402 " ideal model delta sigma weight residual 123.38 108.99 14.39 3.00e+00 1.11e-01 2.30e+01 angle pdb=" N TYR R 132 " pdb=" CA TYR R 132 " pdb=" C TYR R 132 " ideal model delta sigma weight residual 111.82 107.43 4.39 1.16e+00 7.43e-01 1.43e+01 angle pdb=" CA TYR R 132 " pdb=" C TYR R 132 " pdb=" O TYR R 132 " ideal model delta sigma weight residual 119.97 115.65 4.32 1.15e+00 7.56e-01 1.41e+01 angle pdb=" N TYR B 59 " pdb=" CA TYR B 59 " pdb=" CB TYR B 59 " ideal model delta sigma weight residual 110.88 105.89 4.99 1.38e+00 5.25e-01 1.31e+01 ... (remaining 10855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 4240 16.01 - 32.01: 376 32.01 - 48.02: 62 48.02 - 64.03: 16 64.03 - 80.03: 10 Dihedral angle restraints: 4704 sinusoidal: 1768 harmonic: 2936 Sorted by residual: dihedral pdb=" CB CYS R 120 " pdb=" SG CYS R 120 " pdb=" SG CYS R 205 " pdb=" CB CYS R 205 " ideal model delta sinusoidal sigma weight residual 93.00 168.84 -75.84 1 1.00e+01 1.00e-02 7.25e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -158.49 -21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ASP A 223 " pdb=" C ASP A 223 " pdb=" N VAL A 224 " pdb=" CA VAL A 224 " ideal model delta harmonic sigma weight residual 180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 4701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1165 0.099 - 0.198: 57 0.198 - 0.297: 1 0.297 - 0.395: 1 0.395 - 0.494: 1 Chirality restraints: 1225 Sorted by residual: chirality pdb=" C06 8IA R 401 " pdb=" C01 8IA R 401 " pdb=" C05 8IA R 401 " pdb=" N01 8IA R 401 " both_signs ideal model delta sigma weight residual False -2.29 -2.79 0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" CA ASN A 14 " pdb=" N ASN A 14 " pdb=" C ASN A 14 " pdb=" CB ASN A 14 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CBH Y01 R 402 " pdb=" CAT Y01 R 402 " pdb=" CAZ Y01 R 402 " pdb=" CBF Y01 R 402 " both_signs ideal model delta sigma weight residual False -2.85 -2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1222 not shown) Planarity restraints: 1380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 75 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" CD GLN B 75 " -0.040 2.00e-02 2.50e+03 pdb=" OE1 GLN B 75 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN B 75 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 378 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" CG ASP A 378 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASP A 378 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP A 378 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO B 39 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " 0.024 5.00e-02 4.00e+02 ... (remaining 1377 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 145 2.69 - 3.24: 7754 3.24 - 3.79: 12333 3.79 - 4.35: 16596 4.35 - 4.90: 27920 Nonbonded interactions: 64748 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.132 3.040 nonbonded pdb=" OG1 THR A 364 " pdb=" OD2 ASP A 368 " model vdw 2.159 3.040 nonbonded pdb=" NE2 GLN B 75 " pdb=" O VAL B 100 " model vdw 2.221 3.120 nonbonded pdb=" NH1 ARG A 228 " pdb=" O GLY B 162 " model vdw 2.234 3.120 nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.248 3.040 ... (remaining 64743 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: 3.320 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.670 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:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 0.139 7999 Z= 0.279 Angle : 0.779 14.501 10866 Z= 0.409 Chirality : 0.048 0.494 1225 Planarity : 0.005 0.060 1380 Dihedral : 13.130 80.034 2799 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 0.56 (0.27), residues: 993 helix: 1.66 (0.27), residues: 383 sheet: -0.38 (0.34), residues: 212 loop : -0.37 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 145 TYR 0.018 0.002 TYR R 51 PHE 0.027 0.002 PHE B 234 TRP 0.017 0.002 TRP B 82 HIS 0.010 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.28 ( 7996) covalent geometry : angle 0.77584 / 0.41 (10860) SS BOND : bond 0.00307 / 0.15 ( 3) SS BOND : angle 3.11160 / 1.68 ( 6) hydrogen bonds : bond 0.18526 / 12.83 ( 397) hydrogen bonds : angle 6.77593 / 5.09 ( 1119) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 SER cc_start: 0.8846 (p) cc_final: 0.8402 (t) REVERT: B 247 ASP cc_start: 0.7010 (m-30) cc_final: 0.6735 (m-30) REVERT: R 273 LYS cc_start: 0.7944 (ptmm) cc_final: 0.7742 (pttm) REVERT: R 277 ILE cc_start: 0.8425 (mt) cc_final: 0.8079 (mt) outliers start: 0 outliers final: 1 residues processed: 178 average time/residue: 0.4548 time to fit residues: 85.3369 Evaluate side-chains 127 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 292 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.0020 chunk 61 optimal weight: 0.0570 chunk 45 optimal weight: 0.5980 overall best weight: 0.2864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN N 123 GLN R 217 ASN R 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.110682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.088462 restraints weight = 14054.745| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.51 r_work: 0.3212 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7999 Z= 0.132 Angle : 0.563 6.307 10866 Z= 0.298 Chirality : 0.041 0.137 1225 Planarity : 0.004 0.040 1380 Dihedral : 6.148 56.451 1125 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.24 % Allowed : 9.73 % Favored : 88.03 % 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: 1.09 (0.27), residues: 993 helix: 2.14 (0.26), residues: 384 sheet: 0.28 (0.37), residues: 198 loop : -0.38 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 105 TYR 0.013 0.001 TYR R 132 PHE 0.016 0.001 PHE A 212 TRP 0.018 0.002 TRP B 169 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 7996) covalent geometry : angle 0.56170 / 0.30 (10860) SS BOND : bond 0.00358 / 0.17 ( 3) SS BOND : angle 1.78387 / 0.92 ( 6) hydrogen bonds : bond 0.04338 / 2.94 ( 397) hydrogen bonds : angle 4.97725 / 3.65 ( 1119) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.7626 (m-80) REVERT: B 247 ASP cc_start: 0.7374 (m-30) cc_final: 0.7058 (m-30) REVERT: R 277 ILE cc_start: 0.8672 (mt) cc_final: 0.8400 (mt) outliers start: 18 outliers final: 6 residues processed: 143 average time/residue: 0.4530 time to fit residues: 68.7623 Evaluate side-chains 126 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 291 ILE Chi-restraints excluded: chain R residue 292 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 13 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 25 optimal weight: 0.0010 chunk 23 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.108369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.085871 restraints weight = 13841.586| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.48 r_work: 0.3169 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7999 Z= 0.140 Angle : 0.539 6.281 10866 Z= 0.286 Chirality : 0.042 0.147 1225 Planarity : 0.004 0.041 1380 Dihedral : 6.094 59.196 1125 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.74 % Allowed : 13.72 % Favored : 83.54 % 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: 1.35 (0.27), residues: 993 helix: 2.50 (0.26), residues: 376 sheet: 0.28 (0.35), residues: 205 loop : -0.25 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 105 TYR 0.014 0.001 TYR R 132 PHE 0.016 0.001 PHE A 212 TRP 0.014 0.002 TRP B 169 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 7996) covalent geometry : angle 0.53819 / 0.29 (10860) SS BOND : bond 0.00083 / 0.04 ( 3) SS BOND : angle 1.48033 / 0.74 ( 6) hydrogen bonds : bond 0.04063 / 2.76 ( 397) hydrogen bonds : angle 4.62899 / 3.39 ( 1119) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.190 Fit side-chains REVERT: A 310 ASP cc_start: 0.8907 (m-30) cc_final: 0.8636 (t0) REVERT: B 17 GLN cc_start: 0.9348 (tm-30) cc_final: 0.9118 (tm-30) REVERT: B 59 TYR cc_start: 0.8941 (OUTLIER) cc_final: 0.7757 (m-80) REVERT: B 247 ASP cc_start: 0.7745 (m-30) cc_final: 0.7524 (m-30) REVERT: B 340 ASN cc_start: 0.8176 (t160) cc_final: 0.7898 (t0) REVERT: G 42 GLU cc_start: 0.8820 (tp30) cc_final: 0.8189 (tp30) REVERT: R 113 TRP cc_start: 0.6112 (OUTLIER) cc_final: 0.5541 (m-90) REVERT: R 158 ARG cc_start: 0.8567 (tpp80) cc_final: 0.8189 (ttm-80) REVERT: R 180 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.7142 (t80) REVERT: R 277 ILE cc_start: 0.8676 (mt) cc_final: 0.8362 (mt) outliers start: 22 outliers final: 10 residues processed: 144 average time/residue: 0.4549 time to fit residues: 69.4029 Evaluate side-chains 138 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 113 TRP Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 180 PHE Chi-restraints excluded: chain R residue 282 PHE Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 292 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 51 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 85 optimal weight: 0.0970 chunk 21 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 77 ASN N 123 GLN R 245 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.107985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.085405 restraints weight = 14338.982| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.52 r_work: 0.3158 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7999 Z= 0.138 Angle : 0.531 6.876 10866 Z= 0.280 Chirality : 0.042 0.253 1225 Planarity : 0.003 0.043 1380 Dihedral : 5.873 54.346 1125 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.74 % Allowed : 15.34 % Favored : 81.92 % 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: 1.41 (0.27), residues: 993 helix: 2.55 (0.26), residues: 376 sheet: 0.36 (0.35), residues: 203 loop : -0.25 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 145 TYR 0.017 0.001 TYR R 132 PHE 0.015 0.001 PHE A 212 TRP 0.013 0.001 TRP B 169 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 7996) covalent geometry : angle 0.53000 / 0.28 (10860) SS BOND : bond 0.00046 / 0.02 ( 3) SS BOND : angle 1.31263 / 0.65 ( 6) hydrogen bonds : bond 0.03874 / 2.64 ( 397) hydrogen bonds : angle 4.56825 / 3.34 ( 1119) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7212 (pm20) REVERT: A 230 GLU cc_start: 0.9080 (mp0) cc_final: 0.8182 (mp0) REVERT: A 276 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8764 (mp) REVERT: A 310 ASP cc_start: 0.8900 (m-30) cc_final: 0.8677 (t0) REVERT: A 378 ASP cc_start: 0.8144 (m-30) cc_final: 0.7807 (m-30) REVERT: B 17 GLN cc_start: 0.9333 (tm-30) cc_final: 0.9107 (tm-30) REVERT: B 59 TYR cc_start: 0.8997 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: B 340 ASN cc_start: 0.8265 (t160) cc_final: 0.7998 (t0) REVERT: G 42 GLU cc_start: 0.8849 (tp30) cc_final: 0.8225 (tp30) REVERT: R 113 TRP cc_start: 0.6099 (OUTLIER) cc_final: 0.5556 (m-90) REVERT: R 158 ARG cc_start: 0.8553 (tpp80) cc_final: 0.8164 (ttm-80) REVERT: R 180 PHE cc_start: 0.7482 (OUTLIER) cc_final: 0.7102 (t80) REVERT: R 277 ILE cc_start: 0.8729 (mt) cc_final: 0.8473 (mt) REVERT: R 317 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7603 (m-80) outliers start: 22 outliers final: 10 residues processed: 141 average time/residue: 0.4365 time to fit residues: 65.1874 Evaluate side-chains 139 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 113 TRP Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 180 PHE Chi-restraints excluded: chain R residue 282 PHE Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 292 ASP Chi-restraints excluded: chain R residue 317 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN N 35 ASN N 77 ASN R 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.106307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.083553 restraints weight = 14274.176| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.52 r_work: 0.3133 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7999 Z= 0.151 Angle : 0.528 6.178 10866 Z= 0.281 Chirality : 0.042 0.158 1225 Planarity : 0.004 0.044 1380 Dihedral : 5.487 51.417 1125 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.49 % Allowed : 16.46 % Favored : 80.05 % 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: 1.44 (0.27), residues: 993 helix: 2.51 (0.26), residues: 381 sheet: 0.35 (0.35), residues: 203 loop : -0.18 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 145 TYR 0.021 0.001 TYR R 132 PHE 0.016 0.001 PHE A 212 TRP 0.013 0.001 TRP R 172 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 7996) covalent geometry : angle 0.52755 / 0.28 (10860) SS BOND : bond 0.00058 / 0.03 ( 3) SS BOND : angle 1.35022 / 0.67 ( 6) hydrogen bonds : bond 0.03887 / 2.65 ( 397) hydrogen bonds : angle 4.53492 / 3.33 ( 1119) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7258 (pm20) REVERT: A 211 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8720 (mmtt) REVERT: A 230 GLU cc_start: 0.9033 (mp0) cc_final: 0.8004 (mp0) REVERT: A 378 ASP cc_start: 0.8152 (m-30) cc_final: 0.7739 (m-30) REVERT: B 17 GLN cc_start: 0.9341 (tm-30) cc_final: 0.9106 (tm-30) REVERT: B 59 TYR cc_start: 0.9032 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: G 42 GLU cc_start: 0.8862 (tp30) cc_final: 0.8231 (tp30) REVERT: R 113 TRP cc_start: 0.6238 (OUTLIER) cc_final: 0.5628 (m-90) REVERT: R 158 ARG cc_start: 0.8494 (tpp80) cc_final: 0.8133 (ttm-80) REVERT: R 180 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.7187 (t80) REVERT: R 267 ARG cc_start: 0.7778 (mtp85) cc_final: 0.7516 (ptp90) REVERT: R 317 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.7603 (m-80) outliers start: 28 outliers final: 13 residues processed: 145 average time/residue: 0.4780 time to fit residues: 73.1649 Evaluate side-chains 140 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 113 TRP Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 180 PHE Chi-restraints excluded: chain R residue 282 PHE Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 292 ASP Chi-restraints excluded: chain R residue 317 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 77 ASN R 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.106300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.083662 restraints weight = 14330.666| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.51 r_work: 0.3126 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7999 Z= 0.158 Angle : 0.549 7.113 10866 Z= 0.288 Chirality : 0.042 0.174 1225 Planarity : 0.004 0.052 1380 Dihedral : 5.416 51.136 1125 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.37 % Allowed : 17.46 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.27), residues: 993 helix: 2.61 (0.27), residues: 375 sheet: 0.27 (0.34), residues: 211 loop : -0.29 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 283 TYR 0.022 0.001 TYR R 132 PHE 0.016 0.001 PHE A 212 TRP 0.012 0.001 TRP R 172 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 7996) covalent geometry : angle 0.54779 / 0.29 (10860) SS BOND : bond 0.00048 / 0.02 ( 3) SS BOND : angle 1.37855 / 0.66 ( 6) hydrogen bonds : bond 0.03850 / 2.61 ( 397) hydrogen bonds : angle 4.51728 / 3.31 ( 1119) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7288 (pm20) REVERT: A 211 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8816 (mmtt) REVERT: A 378 ASP cc_start: 0.8165 (m-30) cc_final: 0.7738 (m-30) REVERT: B 17 GLN cc_start: 0.9346 (tm-30) cc_final: 0.9107 (tm-30) REVERT: B 59 TYR cc_start: 0.9066 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: G 42 GLU cc_start: 0.8842 (tp30) cc_final: 0.8181 (tp30) REVERT: R 113 TRP cc_start: 0.6321 (OUTLIER) cc_final: 0.5857 (m-90) REVERT: R 158 ARG cc_start: 0.8482 (ttp80) cc_final: 0.8116 (ttm-80) REVERT: R 180 PHE cc_start: 0.7477 (OUTLIER) cc_final: 0.7141 (t80) REVERT: R 267 ARG cc_start: 0.7809 (mtp85) cc_final: 0.7319 (ptp90) outliers start: 27 outliers final: 13 residues processed: 138 average time/residue: 0.4737 time to fit residues: 69.1207 Evaluate side-chains 136 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 113 TRP Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 180 PHE Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 292 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 5 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 77 ASN R 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.108980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.086434 restraints weight = 14207.439| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.51 r_work: 0.3141 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7999 Z= 0.131 Angle : 0.546 8.583 10866 Z= 0.282 Chirality : 0.041 0.228 1225 Planarity : 0.004 0.052 1380 Dihedral : 5.345 51.646 1125 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.24 % Allowed : 17.83 % Favored : 78.93 % 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: 1.44 (0.27), residues: 993 helix: 2.67 (0.27), residues: 374 sheet: 0.33 (0.35), residues: 203 loop : -0.31 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 283 TYR 0.022 0.001 TYR R 132 PHE 0.016 0.001 PHE A 212 TRP 0.013 0.001 TRP R 172 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 7996) covalent geometry : angle 0.54479 / 0.28 (10860) SS BOND : bond 0.00146 / 0.07 ( 3) SS BOND : angle 1.38919 / 0.66 ( 6) hydrogen bonds : bond 0.03680 / 2.50 ( 397) hydrogen bonds : angle 4.49824 / 3.29 ( 1119) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7243 (pm20) REVERT: A 230 GLU cc_start: 0.8982 (mp0) cc_final: 0.7959 (mp0) REVERT: A 378 ASP cc_start: 0.8191 (m-30) cc_final: 0.7717 (m-30) REVERT: B 17 GLN cc_start: 0.9351 (tm-30) cc_final: 0.9119 (tm-30) REVERT: B 59 TYR cc_start: 0.9057 (OUTLIER) cc_final: 0.7816 (m-80) REVERT: B 72 SER cc_start: 0.9157 (t) cc_final: 0.8951 (t) REVERT: G 42 GLU cc_start: 0.8831 (tp30) cc_final: 0.8145 (tp30) REVERT: R 113 TRP cc_start: 0.6282 (OUTLIER) cc_final: 0.5728 (m-90) REVERT: R 158 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8102 (ttm-80) REVERT: R 180 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.7092 (t80) REVERT: R 267 ARG cc_start: 0.7800 (mtp85) cc_final: 0.7367 (ptp90) REVERT: R 317 TYR cc_start: 0.7859 (OUTLIER) cc_final: 0.7658 (t80) outliers start: 26 outliers final: 13 residues processed: 143 average time/residue: 0.4817 time to fit residues: 72.9072 Evaluate side-chains 138 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 51 TYR Chi-restraints excluded: chain R residue 113 TRP Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 180 PHE Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 292 ASP Chi-restraints excluded: chain R residue 317 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 66 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 71 optimal weight: 0.0970 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.108796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.086289 restraints weight = 14276.751| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.52 r_work: 0.3139 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7999 Z= 0.144 Angle : 0.574 8.920 10866 Z= 0.299 Chirality : 0.042 0.205 1225 Planarity : 0.004 0.042 1380 Dihedral : 5.331 51.141 1125 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.49 % Allowed : 18.33 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.27), residues: 993 helix: 2.54 (0.27), residues: 380 sheet: 0.21 (0.34), residues: 212 loop : -0.39 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 38 TYR 0.021 0.001 TYR R 132 PHE 0.019 0.001 PHE R 282 TRP 0.014 0.001 TRP R 172 HIS 0.015 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 7996) covalent geometry : angle 0.57305 / 0.30 (10860) SS BOND : bond 0.00046 / 0.02 ( 3) SS BOND : angle 1.37165 / 0.66 ( 6) hydrogen bonds : bond 0.03725 / 2.54 ( 397) hydrogen bonds : angle 4.50539 / 3.30 ( 1119) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7262 (pm20) REVERT: A 230 GLU cc_start: 0.8978 (mp0) cc_final: 0.7957 (mp0) REVERT: A 378 ASP cc_start: 0.8207 (m-30) cc_final: 0.7722 (m-30) REVERT: B 59 TYR cc_start: 0.9050 (OUTLIER) cc_final: 0.7809 (m-80) REVERT: B 72 SER cc_start: 0.9170 (t) cc_final: 0.8966 (t) REVERT: G 42 GLU cc_start: 0.8832 (tp30) cc_final: 0.8201 (tp30) REVERT: R 99 MET cc_start: 0.7881 (mpp) cc_final: 0.7673 (ptp) REVERT: R 113 TRP cc_start: 0.6297 (OUTLIER) cc_final: 0.5697 (m-90) REVERT: R 158 ARG cc_start: 0.8499 (ttp80) cc_final: 0.8113 (ttm-80) REVERT: R 180 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.7090 (t80) REVERT: R 267 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7428 (ptp90) outliers start: 28 outliers final: 15 residues processed: 144 average time/residue: 0.4362 time to fit residues: 66.4826 Evaluate side-chains 140 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 51 TYR Chi-restraints excluded: chain R residue 113 TRP Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 180 PHE Chi-restraints excluded: chain R residue 282 PHE Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 292 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 86 optimal weight: 0.0770 chunk 89 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.110390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.087705 restraints weight = 14095.973| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.51 r_work: 0.3144 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7999 Z= 0.142 Angle : 0.585 9.294 10866 Z= 0.302 Chirality : 0.042 0.185 1225 Planarity : 0.004 0.075 1380 Dihedral : 5.328 50.965 1125 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.99 % Allowed : 19.45 % Favored : 77.56 % 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: 1.27 (0.27), residues: 993 helix: 2.50 (0.27), residues: 380 sheet: 0.20 (0.34), residues: 212 loop : -0.40 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 283 TYR 0.021 0.001 TYR R 132 PHE 0.018 0.001 PHE R 282 TRP 0.016 0.001 TRP R 172 HIS 0.014 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 7996) covalent geometry : angle 0.58418 / 0.30 (10860) SS BOND : bond 0.00055 / 0.03 ( 3) SS BOND : angle 1.36058 / 0.65 ( 6) hydrogen bonds : bond 0.03675 / 2.50 ( 397) hydrogen bonds : angle 4.51769 / 3.31 ( 1119) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7236 (pm20) REVERT: A 230 GLU cc_start: 0.8978 (mp0) cc_final: 0.7947 (mp0) REVERT: A 378 ASP cc_start: 0.8182 (m-30) cc_final: 0.7689 (m-30) REVERT: B 59 TYR cc_start: 0.9046 (OUTLIER) cc_final: 0.7782 (m-80) REVERT: B 72 SER cc_start: 0.9158 (t) cc_final: 0.8930 (t) REVERT: B 98 SER cc_start: 0.8627 (OUTLIER) cc_final: 0.7874 (t) REVERT: G 42 GLU cc_start: 0.8823 (tp30) cc_final: 0.8195 (tp30) REVERT: R 99 MET cc_start: 0.7775 (mpp) cc_final: 0.7538 (ptp) REVERT: R 113 TRP cc_start: 0.6310 (OUTLIER) cc_final: 0.5745 (m-90) REVERT: R 158 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8069 (ttm-80) REVERT: R 180 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.7017 (t80) REVERT: R 267 ARG cc_start: 0.7817 (mtp85) cc_final: 0.7433 (ptp90) outliers start: 24 outliers final: 16 residues processed: 141 average time/residue: 0.4368 time to fit residues: 65.4176 Evaluate side-chains 141 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 51 TYR Chi-restraints excluded: chain R residue 113 TRP Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 180 PHE Chi-restraints excluded: chain R residue 282 PHE Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 292 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 27 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 97 optimal weight: 0.0170 chunk 64 optimal weight: 0.0370 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 384 GLN R 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.111490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.088847 restraints weight = 13983.350| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.50 r_work: 0.3163 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7999 Z= 0.123 Angle : 0.573 9.821 10866 Z= 0.295 Chirality : 0.041 0.174 1225 Planarity : 0.004 0.073 1380 Dihedral : 5.200 50.458 1125 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.87 % Allowed : 19.83 % Favored : 77.31 % 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: 1.35 (0.27), residues: 993 helix: 2.56 (0.27), residues: 380 sheet: 0.30 (0.34), residues: 210 loop : -0.36 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 283 TYR 0.021 0.001 TYR R 132 PHE 0.027 0.001 PHE R 170 TRP 0.018 0.001 TRP R 172 HIS 0.013 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 7996) covalent geometry : angle 0.57224 / 0.30 (10860) SS BOND : bond 0.00067 / 0.04 ( 3) SS BOND : angle 1.23544 / 0.59 ( 6) hydrogen bonds : bond 0.03518 / 2.39 ( 397) hydrogen bonds : angle 4.45158 / 3.26 ( 1119) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7741 (pm20) cc_final: 0.7193 (pm20) REVERT: A 230 GLU cc_start: 0.8961 (mp0) cc_final: 0.7951 (mp0) REVERT: A 378 ASP cc_start: 0.8169 (m-30) cc_final: 0.7660 (m-30) REVERT: B 59 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: B 72 SER cc_start: 0.9101 (t) cc_final: 0.8791 (p) REVERT: B 98 SER cc_start: 0.8695 (OUTLIER) cc_final: 0.7990 (t) REVERT: G 42 GLU cc_start: 0.8812 (tp30) cc_final: 0.8202 (tp30) REVERT: R 99 MET cc_start: 0.7825 (mpp) cc_final: 0.7565 (ptp) REVERT: R 113 TRP cc_start: 0.6286 (OUTLIER) cc_final: 0.5689 (m-90) REVERT: R 158 ARG cc_start: 0.8478 (ttp80) cc_final: 0.8105 (ttm-80) REVERT: R 180 PHE cc_start: 0.7238 (m-80) cc_final: 0.6951 (t80) REVERT: R 267 ARG cc_start: 0.7767 (mtp85) cc_final: 0.7400 (ptp90) REVERT: R 317 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.7626 (t80) outliers start: 23 outliers final: 13 residues processed: 142 average time/residue: 0.4817 time to fit residues: 72.3434 Evaluate side-chains 135 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 51 TYR Chi-restraints excluded: chain R residue 113 TRP Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 282 PHE Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 292 ASP Chi-restraints excluded: chain R residue 317 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 3 optimal weight: 2.9990 chunk 82 optimal weight: 0.0070 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 77 ASN R 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.110286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.087643 restraints weight = 14070.650| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.51 r_work: 0.3144 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7999 Z= 0.159 Angle : 0.590 9.689 10866 Z= 0.304 Chirality : 0.042 0.179 1225 Planarity : 0.004 0.042 1380 Dihedral : 5.032 40.257 1125 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.49 % Allowed : 20.32 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.27), residues: 993 helix: 2.56 (0.27), residues: 380 sheet: 0.21 (0.34), residues: 212 loop : -0.43 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 27 TYR 0.020 0.001 TYR R 132 PHE 0.027 0.002 PHE R 170 TRP 0.021 0.001 TRP R 172 HIS 0.012 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 7996) covalent geometry : angle 0.58935 / 0.30 (10860) SS BOND : bond 0.00043 / 0.02 ( 3) SS BOND : angle 1.34157 / 0.64 ( 6) hydrogen bonds : bond 0.03674 / 2.49 ( 397) hydrogen bonds : angle 4.49562 / 3.29 ( 1119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2123.32 seconds wall clock time: 36 minutes 59.72 seconds (2219.72 seconds total)