Starting phenix.real_space_refine on Thu Jul 2 12:25:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vuy_32131/07_2026/7vuy_32131.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vuy_32131/07_2026/7vuy_32131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vuy_32131/07_2026/7vuy_32131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vuy_32131/07_2026/7vuy_32131.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7vuy_32131/07_2026/7vuy_32131.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vuy_32131/07_2026/7vuy_32131.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vuy_32131/07_2026/7vuy_32131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vuy_32131/07_2026/7vuy_32131.map" } resolution = 2.84 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= 0.005 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 65 5.16 5 C 5572 2.51 5 N 1458 2.21 5 O 1613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 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: 8708 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2056 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2598 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 427 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1786 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.95, per 1000 atoms: 0.22 Number of scatterers: 8708 At special positions: 0 Unit cell: (116.833, 107.718, 105.232, 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 65 16.00 O 1613 8.00 N 1458 7.00 C 5572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.07 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 0.68 Conformation dependent library (CDL) restraints added in 452.9 milliseconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2068 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 38.1% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'R' and resid 30 through 57 removed outlier: 3.790A pdb=" N VAL R 34 " --> pdb=" O THR R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 94 removed outlier: 3.531A pdb=" N VAL R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 133 removed outlier: 3.521A pdb=" N VAL R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 140 Processing helix chain 'R' and resid 144 through 168 Processing helix chain 'R' and resid 176 through 213 removed outlier: 4.205A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE R 183 " --> pdb=" O TRP R 179 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER R 213 " --> pdb=" O ILE R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 245 removed outlier: 4.601A pdb=" N LEU R 237 " --> pdb=" O LEU R 233 " (cutoff:3.500A) Proline residue: R 238 - end of helix Processing helix chain 'R' and resid 245 through 250 Processing helix chain 'R' and resid 252 through 280 removed outlier: 4.000A pdb=" N LEU R 256 " --> pdb=" O ASP R 252 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N CYS R 258 " --> pdb=" O ASP R 254 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N HIS R 259 " --> pdb=" O VAL R 255 " (cutoff:3.500A) Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 280 through 285 Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 214 removed outlier: 4.552A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.508A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.792A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.184A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.871A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.933A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.147A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.822A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.581A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.606A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.579A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.805A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.564A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.700A 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 151 removed outlier: 3.602A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.479A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.472A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.852A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.618A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.440A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.440A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 129 through 130 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.457A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR S 231 " --> pdb=" O TYR S 215 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR S 215 " --> pdb=" O THR S 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'S' and resid 182 through 183 removed outlier: 5.499A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2778 1.34 - 1.47: 2334 1.47 - 1.61: 3696 1.61 - 1.74: 1 1.74 - 1.87: 90 Bond restraints: 8899 Sorted by residual: bond pdb=" C HIS R 261 " pdb=" N PRO R 262 " ideal model delta sigma weight residual 1.334 1.537 -0.203 2.34e-02 1.83e+03 7.52e+01 bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.647 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" C GLN R 242 " pdb=" N TRP R 243 " ideal model delta sigma weight residual 1.334 1.396 -0.062 1.41e-02 5.03e+03 1.93e+01 bond pdb=" N ILE R 260 " pdb=" CA ILE R 260 " ideal model delta sigma weight residual 1.460 1.498 -0.039 1.21e-02 6.83e+03 1.02e+01 bond pdb=" N ILE R 249 " pdb=" CA ILE R 249 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.28e+00 ... (remaining 8894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 11574 2.54 - 5.09: 406 5.09 - 7.63: 61 7.63 - 10.17: 18 10.17 - 12.72: 4 Bond angle restraints: 12063 Sorted by residual: angle pdb=" CA HIS R 261 " pdb=" C HIS R 261 " pdb=" N PRO R 262 " ideal model delta sigma weight residual 120.93 129.44 -8.51 1.06e+00 8.90e-01 6.45e+01 angle pdb=" O HIS R 261 " pdb=" C HIS R 261 " pdb=" N PRO R 262 " ideal model delta sigma weight residual 120.71 113.17 7.54 9.40e-01 1.13e+00 6.44e+01 angle pdb=" CA CYS B 149 " pdb=" CB CYS B 149 " pdb=" SG CYS B 149 " ideal model delta sigma weight residual 114.40 127.12 -12.72 2.30e+00 1.89e-01 3.06e+01 angle pdb=" N LEU R 245 " pdb=" CA LEU R 245 " pdb=" C LEU R 245 " ideal model delta sigma weight residual 113.43 120.34 -6.91 1.26e+00 6.30e-01 3.01e+01 angle pdb=" O GLN R 242 " pdb=" C GLN R 242 " pdb=" N TRP R 243 " ideal model delta sigma weight residual 122.15 116.44 5.71 1.14e+00 7.69e-01 2.51e+01 ... (remaining 12058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 4702 17.09 - 34.18: 445 34.18 - 51.27: 69 51.27 - 68.36: 11 68.36 - 85.45: 9 Dihedral angle restraints: 5236 sinusoidal: 2028 harmonic: 3208 Sorted by residual: dihedral pdb=" CA GLY B 185 " pdb=" C GLY B 185 " pdb=" N ASP B 186 " pdb=" CA ASP B 186 " ideal model delta harmonic sigma weight residual 180.00 153.00 27.00 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA PHE R 172 " pdb=" C PHE R 172 " pdb=" N SER R 173 " pdb=" CA SER R 173 " ideal model delta harmonic sigma weight residual 180.00 156.75 23.25 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 157.10 22.90 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 5233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1119 0.082 - 0.163: 220 0.163 - 0.245: 25 0.245 - 0.327: 4 0.327 - 0.408: 4 Chirality restraints: 1372 Sorted by residual: chirality pdb=" CG LEU S 166 " pdb=" CB LEU S 166 " pdb=" CD1 LEU S 166 " pdb=" CD2 LEU S 166 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CA LEU R 245 " pdb=" N LEU R 245 " pdb=" C LEU R 245 " pdb=" CB LEU R 245 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CG LEU S 162 " pdb=" CB LEU S 162 " pdb=" CD1 LEU S 162 " pdb=" CD2 LEU S 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 1369 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS R 261 " -0.045 5.00e-02 4.00e+02 7.27e-02 8.45e+00 pdb=" N PRO R 262 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO R 262 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO R 262 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA S 40 " 0.046 5.00e-02 4.00e+02 7.00e-02 7.85e+00 pdb=" N PRO S 41 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO S 41 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO S 41 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.64e+00 pdb=" N PRO G 55 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.038 5.00e-02 4.00e+02 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.42: 30 2.42 - 3.04: 4893 3.04 - 3.66: 13333 3.66 - 4.28: 19997 4.28 - 4.90: 34031 Nonbonded interactions: 72284 Sorted by model distance: nonbonded pdb=" OE1 GLN R 181 " pdb=" CD1 TRP R 248 " model vdw 1.806 3.260 nonbonded pdb=" OE1 GLN R 181 " pdb=" NE1 TRP R 248 " model vdw 2.141 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR R 113 " pdb=" O GLY R 236 " model vdw 2.223 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.273 3.040 ... (remaining 72279 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: 0.570 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.260 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 : 0.010 0.203 8903 Z= 0.422 Angle : 1.122 12.716 12071 Z= 0.609 Chirality : 0.068 0.408 1372 Planarity : 0.007 0.073 1514 Dihedral : 13.765 85.451 3156 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.42 % Allowed : 0.95 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.74 (0.23), residues: 1098 helix: -0.35 (0.24), residues: 367 sheet: -1.40 (0.29), residues: 285 loop : -1.50 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG R 220 TYR 0.027 0.003 TYR R 113 PHE 0.027 0.003 PHE R 183 TRP 0.015 0.002 TRP B 332 HIS 0.017 0.002 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00961 / 0.42 ( 8899) covalent geometry : angle 1.11900 / 0.61 (12063) SS BOND : bond 0.01831 / 0.87 ( 4) SS BOND : angle 3.52826 / 1.80 ( 8) hydrogen bonds : bond 0.16318 / 10.48 ( 426) hydrogen bonds : angle 7.64678 / 5.63 ( 1248) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 174 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7986 (mpp) cc_final: 0.7597 (mmt) REVERT: A 305 CYS cc_start: 0.7550 (m) cc_final: 0.7300 (m) REVERT: B 6 GLN cc_start: 0.7374 (pp30) cc_final: 0.7009 (pp30) REVERT: B 15 LYS cc_start: 0.8127 (mmpt) cc_final: 0.7922 (mmmt) REVERT: B 290 ASP cc_start: 0.7987 (m-30) cc_final: 0.7762 (m-30) outliers start: 4 outliers final: 2 residues processed: 177 average time/residue: 0.6292 time to fit residues: 117.8437 Evaluate side-chains 129 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 331 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 261 HIS A 52 GLN A 188 HIS A 306 GLN A 322 HIS A 331 ASN B 110 ASN S 174 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.175912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.136745 restraints weight = 11029.730| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.50 r_work: 0.3663 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8903 Z= 0.185 Angle : 0.659 7.652 12071 Z= 0.345 Chirality : 0.044 0.254 1372 Planarity : 0.004 0.050 1514 Dihedral : 6.152 77.001 1211 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.11 % Allowed : 13.49 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.92 (0.25), residues: 1098 helix: 0.84 (0.26), residues: 371 sheet: -1.33 (0.30), residues: 273 loop : -1.28 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 256 TYR 0.017 0.002 TYR R 113 PHE 0.017 0.001 PHE R 183 TRP 0.020 0.002 TRP B 82 HIS 0.009 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 ( 8899) covalent geometry : angle 0.65767 / 0.34 (12063) SS BOND : bond 0.00952 / 0.45 ( 4) SS BOND : angle 1.87746 / 0.95 ( 8) hydrogen bonds : bond 0.04676 / 3.09 ( 426) hydrogen bonds : angle 5.57608 / 4.10 ( 1248) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: R 34 VAL cc_start: 0.7979 (OUTLIER) cc_final: 0.7765 (p) REVERT: R 220 ARG cc_start: 0.7547 (ttm170) cc_final: 0.7186 (ttt-90) REVERT: R 257 PHE cc_start: 0.5254 (OUTLIER) cc_final: 0.4639 (t80) REVERT: A 51 LYS cc_start: 0.7843 (mtmt) cc_final: 0.7493 (mmtt) REVERT: A 240 MET cc_start: 0.6261 (tpt) cc_final: 0.6024 (mmt) REVERT: A 305 CYS cc_start: 0.7875 (m) cc_final: 0.7520 (m) REVERT: B 6 GLN cc_start: 0.7190 (pp30) cc_final: 0.6790 (pp30) REVERT: B 290 ASP cc_start: 0.8412 (m-30) cc_final: 0.8141 (m-30) REVERT: S 62 ASP cc_start: 0.8295 (m-30) cc_final: 0.8068 (m-30) outliers start: 20 outliers final: 8 residues processed: 156 average time/residue: 0.5035 time to fit residues: 84.2157 Evaluate side-chains 136 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 76 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 275 ASN A 188 HIS B 75 GLN S 13 GLN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.176515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.137606 restraints weight = 10912.049| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.48 r_work: 0.3684 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8903 Z= 0.152 Angle : 0.611 8.671 12071 Z= 0.313 Chirality : 0.043 0.251 1372 Planarity : 0.004 0.043 1514 Dihedral : 5.674 78.509 1207 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.95 % Allowed : 16.23 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.54 (0.25), residues: 1098 helix: 1.30 (0.26), residues: 375 sheet: -1.23 (0.30), residues: 267 loop : -1.15 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 67 TYR 0.019 0.001 TYR R 113 PHE 0.024 0.001 PHE R 94 TRP 0.019 0.001 TRP B 82 HIS 0.009 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 8899) covalent geometry : angle 0.60984 / 0.31 (12063) SS BOND : bond 0.00822 / 0.39 ( 4) SS BOND : angle 1.64240 / 0.83 ( 8) hydrogen bonds : bond 0.04224 / 2.78 ( 426) hydrogen bonds : angle 5.18709 / 3.81 ( 1248) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.380 Fit side-chains REVERT: R 230 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7608 (mp) REVERT: R 257 PHE cc_start: 0.5351 (OUTLIER) cc_final: 0.4707 (t80) REVERT: A 51 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7538 (mmtt) REVERT: A 193 ASP cc_start: 0.8005 (m-30) cc_final: 0.7265 (t0) REVERT: A 305 CYS cc_start: 0.7835 (m) cc_final: 0.7482 (m) REVERT: A 349 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8067 (tmmt) REVERT: B 6 GLN cc_start: 0.7211 (pp30) cc_final: 0.6802 (pp30) REVERT: B 35 ASN cc_start: 0.8362 (t0) cc_final: 0.7776 (p0) REVERT: B 246 ASP cc_start: 0.8550 (m-30) cc_final: 0.8329 (m-30) REVERT: B 290 ASP cc_start: 0.8448 (m-30) cc_final: 0.8202 (m-30) REVERT: G 21 MET cc_start: 0.6471 (tmt) cc_final: 0.6241 (tmt) outliers start: 28 outliers final: 9 residues processed: 173 average time/residue: 0.5429 time to fit residues: 100.2611 Evaluate side-chains 154 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 183 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 2 optimal weight: 2.9990 chunk 100 optimal weight: 0.0870 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 255 ASN B 44 GLN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.176495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.137422 restraints weight = 11142.991| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.50 r_work: 0.3669 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8903 Z= 0.168 Angle : 0.616 9.249 12071 Z= 0.315 Chirality : 0.043 0.248 1372 Planarity : 0.003 0.040 1514 Dihedral : 5.591 79.090 1207 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.21 % Allowed : 17.39 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.25), residues: 1098 helix: 1.56 (0.27), residues: 375 sheet: -1.21 (0.30), residues: 267 loop : -1.07 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 256 TYR 0.019 0.002 TYR R 113 PHE 0.018 0.001 PHE R 94 TRP 0.016 0.001 TRP B 82 HIS 0.009 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 8899) covalent geometry : angle 0.61455 / 0.31 (12063) SS BOND : bond 0.00876 / 0.42 ( 4) SS BOND : angle 1.76921 / 0.90 ( 8) hydrogen bonds : bond 0.04187 / 2.77 ( 426) hydrogen bonds : angle 5.06186 / 3.70 ( 1248) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.349 Fit side-chains REVERT: R 226 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7717 (mm) REVERT: R 257 PHE cc_start: 0.5317 (OUTLIER) cc_final: 0.4640 (t80) REVERT: A 51 LYS cc_start: 0.7918 (mtmt) cc_final: 0.7574 (mmtt) REVERT: A 193 ASP cc_start: 0.8052 (m-30) cc_final: 0.7210 (t0) REVERT: A 305 CYS cc_start: 0.7850 (m) cc_final: 0.7489 (m) REVERT: A 349 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8111 (tmmt) REVERT: B 6 GLN cc_start: 0.7177 (pp30) cc_final: 0.6766 (pp30) REVERT: B 35 ASN cc_start: 0.8349 (t0) cc_final: 0.7802 (p0) REVERT: B 290 ASP cc_start: 0.8447 (m-30) cc_final: 0.8212 (m-30) REVERT: S 95 TYR cc_start: 0.7671 (m-80) cc_final: 0.7471 (m-80) outliers start: 40 outliers final: 16 residues processed: 176 average time/residue: 0.5092 time to fit residues: 96.2197 Evaluate side-chains 155 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 183 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 7.9990 chunk 103 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS B 13 GLN B 44 GLN B 340 ASN S 13 GLN S 159 ASN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.176299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.137521 restraints weight = 11027.873| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.48 r_work: 0.3666 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8903 Z= 0.162 Angle : 0.624 9.666 12071 Z= 0.316 Chirality : 0.043 0.247 1372 Planarity : 0.004 0.041 1514 Dihedral : 5.529 79.810 1207 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.90 % Allowed : 18.76 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.26 (0.26), residues: 1098 helix: 1.69 (0.27), residues: 375 sheet: -1.28 (0.30), residues: 274 loop : -0.98 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 46 TYR 0.020 0.002 TYR R 113 PHE 0.015 0.001 PHE R 94 TRP 0.018 0.001 TRP B 82 HIS 0.008 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 8899) covalent geometry : angle 0.62224 / 0.32 (12063) SS BOND : bond 0.00817 / 0.39 ( 4) SS BOND : angle 1.73895 / 0.89 ( 8) hydrogen bonds : bond 0.04082 / 2.70 ( 426) hydrogen bonds : angle 4.95948 / 3.62 ( 1248) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 0.370 Fit side-chains REVERT: R 226 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7721 (mm) REVERT: A 51 LYS cc_start: 0.7906 (mtmt) cc_final: 0.7615 (mmtt) REVERT: A 193 ASP cc_start: 0.8078 (m-30) cc_final: 0.7196 (t0) REVERT: A 242 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7483 (mmt-90) REVERT: A 282 PRO cc_start: 0.7447 (Cg_endo) cc_final: 0.7176 (Cg_exo) REVERT: A 305 CYS cc_start: 0.7867 (m) cc_final: 0.7505 (m) REVERT: A 349 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8136 (tmmt) REVERT: B 6 GLN cc_start: 0.7198 (pp30) cc_final: 0.6774 (pp30) REVERT: B 35 ASN cc_start: 0.8305 (t0) cc_final: 0.7789 (p0) REVERT: B 37 ILE cc_start: 0.7845 (tt) cc_final: 0.7597 (pt) REVERT: B 246 ASP cc_start: 0.8541 (m-30) cc_final: 0.8281 (m-30) REVERT: B 258 ASP cc_start: 0.7811 (t70) cc_final: 0.7525 (t70) REVERT: B 290 ASP cc_start: 0.8442 (m-30) cc_final: 0.8208 (m-30) REVERT: S 206 ARG cc_start: 0.7876 (mpp-170) cc_final: 0.7656 (mpp-170) outliers start: 37 outliers final: 19 residues processed: 184 average time/residue: 0.4936 time to fit residues: 97.6904 Evaluate side-chains 165 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 94 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS B 13 GLN B 44 GLN B 88 ASN B 340 ASN S 174 GLN S 182 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.179943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.141655 restraints weight = 10967.477| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.49 r_work: 0.3736 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8903 Z= 0.113 Angle : 0.589 10.377 12071 Z= 0.295 Chirality : 0.042 0.230 1372 Planarity : 0.003 0.037 1514 Dihedral : 5.281 79.697 1207 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.95 % Allowed : 21.92 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.06 (0.26), residues: 1098 helix: 1.87 (0.27), residues: 376 sheet: -1.11 (0.29), residues: 283 loop : -0.92 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 46 TYR 0.022 0.001 TYR R 113 PHE 0.013 0.001 PHE A 189 TRP 0.021 0.001 TRP B 82 HIS 0.008 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8899) covalent geometry : angle 0.58855 / 0.29 (12063) SS BOND : bond 0.00524 / 0.24 ( 4) SS BOND : angle 1.28345 / 0.65 ( 8) hydrogen bonds : bond 0.03617 / 2.39 ( 426) hydrogen bonds : angle 4.68811 / 3.42 ( 1248) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.298 Fit side-chains REVERT: R 226 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7603 (mm) REVERT: A 193 ASP cc_start: 0.8060 (m-30) cc_final: 0.7153 (t0) REVERT: A 282 PRO cc_start: 0.7423 (Cg_endo) cc_final: 0.7193 (Cg_exo) REVERT: A 305 CYS cc_start: 0.7925 (m) cc_final: 0.7531 (m) REVERT: B 6 GLN cc_start: 0.7124 (pp30) cc_final: 0.6707 (pp30) REVERT: B 35 ASN cc_start: 0.8320 (t0) cc_final: 0.7797 (p0) REVERT: B 246 ASP cc_start: 0.8554 (m-30) cc_final: 0.8180 (m-30) REVERT: B 290 ASP cc_start: 0.8429 (m-30) cc_final: 0.8215 (m-30) outliers start: 28 outliers final: 9 residues processed: 173 average time/residue: 0.4695 time to fit residues: 87.2269 Evaluate side-chains 147 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS B 13 GLN B 44 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.175575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.136737 restraints weight = 11092.956| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.48 r_work: 0.3655 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8903 Z= 0.178 Angle : 0.653 10.346 12071 Z= 0.330 Chirality : 0.044 0.241 1372 Planarity : 0.004 0.038 1514 Dihedral : 5.487 81.030 1207 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.63 % Allowed : 22.97 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.26), residues: 1098 helix: 1.88 (0.26), residues: 375 sheet: -1.13 (0.29), residues: 283 loop : -1.00 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 140 TYR 0.018 0.002 TYR R 113 PHE 0.015 0.001 PHE A 189 TRP 0.014 0.001 TRP B 82 HIS 0.008 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 ( 8899) covalent geometry : angle 0.65163 / 0.33 (12063) SS BOND : bond 0.00852 / 0.40 ( 4) SS BOND : angle 1.74957 / 0.89 ( 8) hydrogen bonds : bond 0.04074 / 2.70 ( 426) hydrogen bonds : angle 4.87382 / 3.55 ( 1248) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.316 Fit side-chains REVERT: R 226 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7721 (mm) REVERT: A 51 LYS cc_start: 0.7966 (mtmt) cc_final: 0.7555 (mmtt) REVERT: A 193 ASP cc_start: 0.8096 (m-30) cc_final: 0.7191 (t0) REVERT: A 305 CYS cc_start: 0.7943 (m) cc_final: 0.7572 (m) REVERT: A 349 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8153 (tmmt) REVERT: B 6 GLN cc_start: 0.7178 (pp30) cc_final: 0.6724 (pp30) REVERT: B 35 ASN cc_start: 0.8444 (t0) cc_final: 0.7928 (p0) REVERT: B 246 ASP cc_start: 0.8611 (m-30) cc_final: 0.8309 (m-30) outliers start: 25 outliers final: 15 residues processed: 166 average time/residue: 0.4482 time to fit residues: 80.0214 Evaluate side-chains 157 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 11 optimal weight: 0.0060 chunk 104 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 99 optimal weight: 30.0000 chunk 56 optimal weight: 0.1980 chunk 48 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 86 optimal weight: 0.0980 chunk 40 optimal weight: 0.6980 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS B 13 GLN B 35 ASN B 44 GLN B 340 ASN S 13 GLN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.179685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.141627 restraints weight = 10980.926| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.48 r_work: 0.3728 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8903 Z= 0.118 Angle : 0.621 11.047 12071 Z= 0.310 Chirality : 0.042 0.225 1372 Planarity : 0.003 0.037 1514 Dihedral : 5.241 80.107 1207 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.21 % Allowed : 24.03 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.07 (0.26), residues: 1098 helix: 2.02 (0.27), residues: 377 sheet: -0.97 (0.30), residues: 281 loop : -0.96 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 148 TYR 0.023 0.001 TYR R 113 PHE 0.013 0.001 PHE A 189 TRP 0.019 0.001 TRP B 82 HIS 0.008 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 8899) covalent geometry : angle 0.62033 / 0.31 (12063) SS BOND : bond 0.00654 / 0.31 ( 4) SS BOND : angle 1.52987 / 0.77 ( 8) hydrogen bonds : bond 0.03559 / 2.35 ( 426) hydrogen bonds : angle 4.62898 / 3.37 ( 1248) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.229 Fit side-chains REVERT: R 226 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7549 (mm) REVERT: A 51 LYS cc_start: 0.7866 (mtmt) cc_final: 0.7413 (mmtt) REVERT: A 193 ASP cc_start: 0.8072 (m-30) cc_final: 0.7107 (t0) REVERT: A 305 CYS cc_start: 0.7896 (m) cc_final: 0.7479 (m) REVERT: B 6 GLN cc_start: 0.7080 (pp30) cc_final: 0.6639 (pp30) REVERT: B 35 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.7881 (p0) REVERT: B 234 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: B 246 ASP cc_start: 0.8524 (m-30) cc_final: 0.8155 (m-30) outliers start: 21 outliers final: 10 residues processed: 165 average time/residue: 0.4342 time to fit residues: 76.8512 Evaluate side-chains 151 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 3.9990 chunk 99 optimal weight: 30.0000 chunk 24 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 144 HIS A 188 HIS B 13 GLN B 35 ASN B 44 GLN B 88 ASN B 340 ASN S 174 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.171495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.131374 restraints weight = 11139.001| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.53 r_work: 0.3590 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 8903 Z= 0.287 Angle : 0.754 11.292 12071 Z= 0.380 Chirality : 0.048 0.252 1372 Planarity : 0.004 0.041 1514 Dihedral : 5.747 82.185 1207 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.74 % Allowed : 24.24 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.27 (0.26), residues: 1098 helix: 1.70 (0.26), residues: 373 sheet: -1.09 (0.30), residues: 282 loop : -1.13 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 140 TYR 0.024 0.002 TYR R 113 PHE 0.017 0.002 PHE A 189 TRP 0.017 0.002 TRP R 248 HIS 0.010 0.002 HIS R 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00675 / 0.29 ( 8899) covalent geometry : angle 0.75120 / 0.38 (12063) SS BOND : bond 0.01337 / 0.64 ( 4) SS BOND : angle 2.61524 / 1.33 ( 8) hydrogen bonds : bond 0.04709 / 3.12 ( 426) hydrogen bonds : angle 5.13133 / 3.74 ( 1248) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.268 Fit side-chains REVERT: R 226 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7684 (mm) REVERT: A 51 LYS cc_start: 0.7930 (mtmt) cc_final: 0.7591 (mmtt) REVERT: A 193 ASP cc_start: 0.7953 (m-30) cc_final: 0.7562 (m-30) REVERT: A 305 CYS cc_start: 0.7834 (m) cc_final: 0.7451 (m) REVERT: B 6 GLN cc_start: 0.7200 (pp30) cc_final: 0.6744 (pp30) REVERT: B 35 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.8114 (p0) REVERT: B 234 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.7858 (m-80) outliers start: 26 outliers final: 10 residues processed: 158 average time/residue: 0.4600 time to fit residues: 77.8297 Evaluate side-chains 145 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 59 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 144 HIS A 188 HIS B 13 GLN B 35 ASN B 44 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN S 13 GLN S 174 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.178022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.139882 restraints weight = 11009.954| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.48 r_work: 0.3706 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8903 Z= 0.129 Angle : 0.670 11.592 12071 Z= 0.331 Chirality : 0.043 0.236 1372 Planarity : 0.004 0.038 1514 Dihedral : 5.356 80.895 1207 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.37 % Allowed : 26.03 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.03 (0.26), residues: 1098 helix: 1.91 (0.26), residues: 376 sheet: -1.02 (0.30), residues: 287 loop : -0.97 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 148 TYR 0.026 0.001 TYR R 113 PHE 0.013 0.001 PHE A 189 TRP 0.020 0.001 TRP B 82 HIS 0.010 0.001 HIS R 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 8899) covalent geometry : angle 0.66924 / 0.33 (12063) SS BOND : bond 0.00571 / 0.27 ( 4) SS BOND : angle 1.58398 / 0.80 ( 8) hydrogen bonds : bond 0.03704 / 2.44 ( 426) hydrogen bonds : angle 4.72578 / 3.44 ( 1248) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.302 Fit side-chains REVERT: R 62 ASN cc_start: 0.7480 (OUTLIER) cc_final: 0.6973 (m-40) REVERT: R 226 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7611 (mm) REVERT: A 51 LYS cc_start: 0.7857 (mtmt) cc_final: 0.7388 (mmtm) REVERT: A 193 ASP cc_start: 0.8097 (m-30) cc_final: 0.7155 (t0) REVERT: A 297 GLU cc_start: 0.7906 (pm20) cc_final: 0.7533 (mm-30) REVERT: A 305 CYS cc_start: 0.7978 (m) cc_final: 0.7590 (m) REVERT: B 6 GLN cc_start: 0.7095 (pp30) cc_final: 0.6684 (pp30) REVERT: B 46 ARG cc_start: 0.8402 (mmm-85) cc_final: 0.8123 (mmm-85) REVERT: B 234 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.7831 (m-80) REVERT: B 246 ASP cc_start: 0.8522 (m-30) cc_final: 0.8289 (m-30) outliers start: 13 outliers final: 8 residues processed: 151 average time/residue: 0.4579 time to fit residues: 74.1834 Evaluate side-chains 151 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 92 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 97 optimal weight: 0.2980 chunk 36 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS B 44 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.176743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.138241 restraints weight = 11023.656| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.48 r_work: 0.3685 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8903 Z= 0.149 Angle : 0.685 11.605 12071 Z= 0.339 Chirality : 0.043 0.235 1372 Planarity : 0.004 0.039 1514 Dihedral : 5.362 81.214 1207 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.90 % Allowed : 25.71 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.02 (0.26), residues: 1098 helix: 1.94 (0.26), residues: 376 sheet: -0.98 (0.30), residues: 287 loop : -0.94 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 148 TYR 0.026 0.002 TYR R 113 PHE 0.015 0.001 PHE A 189 TRP 0.018 0.001 TRP S 47 HIS 0.008 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 8899) covalent geometry : angle 0.68415 / 0.34 (12063) SS BOND : bond 0.00744 / 0.35 ( 4) SS BOND : angle 1.71324 / 0.87 ( 8) hydrogen bonds : bond 0.03806 / 2.51 ( 426) hydrogen bonds : angle 4.73302 / 3.45 ( 1248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3394.76 seconds wall clock time: 58 minutes 41.87 seconds (3521.87 seconds total)