Starting phenix.real_space_refine on Sun Apr 5 02:29:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p84_71364/04_2026/9p84_71364.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p84_71364/04_2026/9p84_71364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9p84_71364/04_2026/9p84_71364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p84_71364/04_2026/9p84_71364.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p84_71364/04_2026/9p84_71364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p84_71364/04_2026/9p84_71364.map" } resolution = 2.7 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= 0.031 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 44 5.16 5 C 4669 2.51 5 N 1268 2.21 5 O 1311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7296 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2357 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 4, 'TRANS': 336} Chain breaks: 1 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 307 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 21, 'ASP:plan': 16, 'ARG:plan': 8, 'GLN:plan1': 7, 'PHE:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 226 Chain: "R" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2047 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 280} Chain breaks: 3 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 5, 'ASN:plan1': 5, 'TYR:plan': 1, 'ARG:plan': 9, 'GLN:plan1': 2, 'HIS:plan': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 129 Chain: "L" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "B" Number of atoms: 2439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2439 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 10, 'GLN:plan1': 4, 'ARG:plan': 4, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 362 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.62, per 1000 atoms: 0.22 Number of scatterers: 7296 At special positions: 0 Unit cell: (100.672, 95.68, 126.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 3 15.00 Mg 1 11.99 O 1311 8.00 N 1268 7.00 C 4669 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " 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: 0.71 Conformation dependent library (CDL) restraints added in 320.8 milliseconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1946 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 9 sheets defined 52.1% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.903A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 62 through 91 removed outlier: 4.166A pdb=" N ALA A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 111 removed outlier: 3.582A pdb=" N ALA A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 133 Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 158 through 164 removed outlier: 3.519A pdb=" N GLN A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.956A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.270A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.155A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.611A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 328 through 350 Processing helix chain 'R' and resid 51 through 55 removed outlier: 3.577A pdb=" N LEU R 54 " --> pdb=" O SER R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 91 Processing helix chain 'R' and resid 98 through 127 removed outlier: 4.361A pdb=" N MET R 120 " --> pdb=" O LEU R 116 " (cutoff:3.500A) Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 137 through 172 Processing helix chain 'R' and resid 172 through 180 Processing helix chain 'R' and resid 181 through 201 Processing helix chain 'R' and resid 202 through 205 Processing helix chain 'R' and resid 229 through 245 Processing helix chain 'R' and resid 245 through 268 Processing helix chain 'R' and resid 292 through 327 Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 335 through 369 removed outlier: 4.179A pdb=" N MET R 347 " --> pdb=" O HIS R 343 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER R 357 " --> pdb=" O PHE R 353 " (cutoff:3.500A) Proline residue: R 361 - end of helix removed outlier: 4.272A pdb=" N VAL R 367 " --> pdb=" O LEU R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 369 through 375 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.528A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.790A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 207 through 210 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.699A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.926A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.933A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.653A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.111A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.668A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.635A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1341 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: 1.18 Time building geometry restraints manager: 0.91 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: 2382 1.34 - 1.46: 1787 1.46 - 1.58: 3213 1.58 - 1.70: 5 1.70 - 1.82: 61 Bond restraints: 7448 Sorted by residual: bond pdb=" CA GLN B 75 " pdb=" C GLN B 75 " ideal model delta sigma weight residual 1.522 1.498 0.024 1.38e-02 5.25e+03 3.08e+00 bond pdb=" C VAL R 201 " pdb=" N PRO R 202 " ideal model delta sigma weight residual 1.333 1.357 -0.024 1.44e-02 4.82e+03 2.82e+00 bond pdb=" N ARG L 9 " pdb=" CA ARG L 9 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.60e-02 3.91e+03 2.62e+00 bond pdb=" N ARG L 8 " pdb=" CA ARG L 8 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.29e+00 bond pdb=" CA VAL R 201 " pdb=" C VAL R 201 " ideal model delta sigma weight residual 1.520 1.530 -0.010 8.80e-03 1.29e+04 1.39e+00 ... (remaining 7443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 9934 1.65 - 3.30: 220 3.30 - 4.95: 35 4.95 - 6.60: 8 6.60 - 8.24: 6 Bond angle restraints: 10203 Sorted by residual: angle pdb=" C ARG L 9 " pdb=" N PRO L 10 " pdb=" CA PRO L 10 " ideal model delta sigma weight residual 119.78 123.82 -4.04 1.03e+00 9.43e-01 1.54e+01 angle pdb=" N PHE R 345 " pdb=" CA PHE R 345 " pdb=" C PHE R 345 " ideal model delta sigma weight residual 111.75 107.53 4.22 1.28e+00 6.10e-01 1.09e+01 angle pdb=" C ILE R 359 " pdb=" N ASN R 360 " pdb=" CA ASN R 360 " ideal model delta sigma weight residual 120.26 116.01 4.25 1.34e+00 5.57e-01 1.01e+01 angle pdb=" C TYR R 344 " pdb=" N PHE R 345 " pdb=" CA PHE R 345 " ideal model delta sigma weight residual 120.38 124.95 -4.57 1.46e+00 4.69e-01 9.79e+00 angle pdb=" CA PRO R 202 " pdb=" N PRO R 202 " pdb=" CD PRO R 202 " ideal model delta sigma weight residual 112.00 107.99 4.01 1.40e+00 5.10e-01 8.20e+00 ... (remaining 10198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.95: 4152 31.95 - 63.90: 144 63.90 - 95.85: 6 95.85 - 127.80: 0 127.80 - 159.76: 2 Dihedral angle restraints: 4304 sinusoidal: 1304 harmonic: 3000 Sorted by residual: dihedral pdb=" CB CYS R 141 " pdb=" SG CYS R 141 " pdb=" SG CYS R 224 " pdb=" CB CYS R 224 " ideal model delta sinusoidal sigma weight residual -86.00 -168.62 82.62 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -55.16 159.76 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -144.03 -146.70 1 2.00e+01 2.50e-03 4.41e+01 ... (remaining 4301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 812 0.035 - 0.071: 303 0.071 - 0.106: 77 0.106 - 0.142: 29 0.142 - 0.177: 4 Chirality restraints: 1225 Sorted by residual: chirality pdb=" CB ILE R 359 " pdb=" CA ILE R 359 " pdb=" CG1 ILE R 359 " pdb=" CG2 ILE R 359 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA ILE B 81 " pdb=" N ILE B 81 " pdb=" C ILE B 81 " pdb=" CB ILE B 81 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA ILE A 319 " pdb=" N ILE A 319 " pdb=" C ILE A 319 " pdb=" CB ILE A 319 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 1222 not shown) Planarity restraints: 1294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 9 " 0.337 9.50e-02 1.11e+02 1.51e-01 1.40e+01 pdb=" NE ARG L 9 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG L 9 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG L 9 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG L 9 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 201 " 0.056 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO R 202 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO R 202 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO R 202 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 354 " -0.023 2.00e-02 2.50e+03 2.07e-02 8.57e+00 pdb=" CG TYR R 354 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR R 354 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR R 354 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR R 354 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR R 354 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR R 354 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR R 354 " -0.001 2.00e-02 2.50e+03 ... (remaining 1291 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 211 2.71 - 3.26: 7342 3.26 - 3.81: 12283 3.81 - 4.35: 14731 4.35 - 4.90: 25415 Nonbonded interactions: 59982 Sorted by model distance: nonbonded pdb=" O2G GTP A 401 " pdb="MG MG A 402 " model vdw 2.164 2.170 nonbonded pdb=" O TYR R 346 " pdb=" ND2 ASN R 350 " model vdw 2.231 3.120 nonbonded pdb=" NH1 ARG R 148 " pdb=" OH TYR R 319 " model vdw 2.250 3.120 nonbonded pdb=" N GLY B 185 " pdb=" OD1 ASP B 205 " model vdw 2.271 3.120 nonbonded pdb=" OH TYR A 230 " pdb=" O SER A 281 " model vdw 2.280 3.040 ... (remaining 59977 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.190 Find NCS groups from input model: 0.050 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:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7449 Z= 0.163 Angle : 0.631 8.245 10205 Z= 0.355 Chirality : 0.042 0.177 1225 Planarity : 0.006 0.151 1294 Dihedral : 15.608 159.756 2355 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.13 % Allowed : 21.22 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.68 (0.27), residues: 1006 helix: 2.56 (0.23), residues: 491 sheet: 0.61 (0.41), residues: 155 loop : -0.73 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 137 TYR 0.050 0.002 TYR R 354 PHE 0.027 0.002 PHE R 341 TRP 0.013 0.002 TRP B 339 HIS 0.004 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 7448) covalent geometry : angle 0.63106 (10203) SS BOND : bond 0.00447 ( 1) SS BOND : angle 0.67367 ( 2) hydrogen bonds : bond 0.13310 ( 465) hydrogen bonds : angle 5.20785 ( 1341) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.258 Fit side-chains REVERT: R 120 MET cc_start: 0.4711 (ttm) cc_final: 0.3991 (ttm) REVERT: B 163 ASP cc_start: 0.7111 (p0) cc_final: 0.6887 (p0) outliers start: 7 outliers final: 5 residues processed: 113 average time/residue: 0.4525 time to fit residues: 54.6441 Evaluate side-chains 99 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 54 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN R 81 ASN B 125 ASN B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.223514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.164088 restraints weight = 8143.696| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.66 r_work: 0.3812 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7449 Z= 0.193 Angle : 0.608 7.761 10205 Z= 0.324 Chirality : 0.044 0.158 1225 Planarity : 0.005 0.064 1294 Dihedral : 9.587 164.720 1114 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.14 % Allowed : 18.33 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.66 (0.27), residues: 1006 helix: 2.60 (0.23), residues: 487 sheet: 0.66 (0.42), residues: 162 loop : -0.87 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 178 TYR 0.017 0.002 TYR R 354 PHE 0.019 0.002 PHE B 151 TRP 0.014 0.002 TRP B 339 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 7448) covalent geometry : angle 0.60770 (10203) SS BOND : bond 0.00342 ( 1) SS BOND : angle 0.47317 ( 2) hydrogen bonds : bond 0.04843 ( 465) hydrogen bonds : angle 4.59026 ( 1341) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.267 Fit side-chains REVERT: A 33 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6601 (mm-30) REVERT: A 157 ASN cc_start: 0.8058 (m110) cc_final: 0.7695 (m110) REVERT: A 178 ARG cc_start: 0.7376 (tpt170) cc_final: 0.6814 (tpt170) REVERT: R 162 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6924 (mp) REVERT: B 44 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7955 (mt0) REVERT: B 101 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.6932 (mmt) REVERT: B 205 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6518 (m-30) REVERT: B 322 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.7113 (t0) outliers start: 32 outliers final: 11 residues processed: 116 average time/residue: 0.4942 time to fit residues: 60.9440 Evaluate side-chains 107 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 31 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.224329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.165620 restraints weight = 8120.319| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 1.65 r_work: 0.3829 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7449 Z= 0.148 Angle : 0.552 7.135 10205 Z= 0.291 Chirality : 0.042 0.145 1225 Planarity : 0.004 0.060 1294 Dihedral : 9.295 163.095 1112 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.14 % Allowed : 19.13 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.75 (0.27), residues: 1006 helix: 2.72 (0.23), residues: 487 sheet: 0.57 (0.42), residues: 167 loop : -0.84 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 24 TYR 0.015 0.001 TYR R 354 PHE 0.013 0.002 PHE B 151 TRP 0.014 0.002 TRP B 339 HIS 0.003 0.001 HIS R 320 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 7448) covalent geometry : angle 0.55238 (10203) SS BOND : bond 0.00358 ( 1) SS BOND : angle 0.51618 ( 2) hydrogen bonds : bond 0.04335 ( 465) hydrogen bonds : angle 4.37923 ( 1341) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.265 Fit side-chains REVERT: A 144 ARG cc_start: 0.7670 (ptm-80) cc_final: 0.7001 (ptm-80) REVERT: A 178 ARG cc_start: 0.7361 (tpt170) cc_final: 0.6801 (tpt170) REVERT: A 324 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8258 (p) REVERT: R 162 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6889 (mp) REVERT: B 44 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7909 (mt0) REVERT: B 57 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.7877 (mtmt) REVERT: B 101 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.6900 (mmm) REVERT: B 192 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8018 (mp) REVERT: B 205 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6514 (m-30) REVERT: B 336 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7433 (mm) REVERT: C 27 ARG cc_start: 0.6073 (OUTLIER) cc_final: 0.4817 (mtt90) outliers start: 32 outliers final: 13 residues processed: 116 average time/residue: 0.5063 time to fit residues: 62.3837 Evaluate side-chains 113 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 54 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 70 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 17 optimal weight: 0.2980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN R 172 HIS B 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.225116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.167282 restraints weight = 8307.426| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 1.97 r_work: 0.3796 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7449 Z= 0.130 Angle : 0.529 7.218 10205 Z= 0.279 Chirality : 0.041 0.143 1225 Planarity : 0.004 0.057 1294 Dihedral : 9.140 161.152 1112 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.14 % Allowed : 19.13 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.80 (0.27), residues: 1006 helix: 2.78 (0.23), residues: 486 sheet: 0.58 (0.42), residues: 167 loop : -0.83 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 24 TYR 0.016 0.001 TYR R 354 PHE 0.012 0.001 PHE A 334 TRP 0.013 0.001 TRP B 339 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7448) covalent geometry : angle 0.52893 (10203) SS BOND : bond 0.00296 ( 1) SS BOND : angle 0.48837 ( 2) hydrogen bonds : bond 0.04040 ( 465) hydrogen bonds : angle 4.27897 ( 1341) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.287 Fit side-chains REVERT: A 33 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6959 (tp30) REVERT: A 157 ASN cc_start: 0.7869 (m110) cc_final: 0.7585 (m110) REVERT: A 178 ARG cc_start: 0.7364 (tpt170) cc_final: 0.6797 (tpt170) REVERT: A 208 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.5003 (ttt90) REVERT: A 310 LEU cc_start: 0.8374 (mp) cc_final: 0.8171 (mt) REVERT: R 105 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6862 (mp) REVERT: R 162 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6953 (mp) REVERT: B 44 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7889 (mt0) REVERT: B 57 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7862 (mtmt) REVERT: B 101 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.6945 (mmm) REVERT: B 192 LEU cc_start: 0.8234 (mt) cc_final: 0.7968 (mp) REVERT: B 205 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6565 (m-30) REVERT: B 336 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7422 (mm) REVERT: C 27 ARG cc_start: 0.6037 (OUTLIER) cc_final: 0.4723 (mtt90) outliers start: 32 outliers final: 14 residues processed: 116 average time/residue: 0.5012 time to fit residues: 61.8085 Evaluate side-chains 115 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 54 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 40.0000 chunk 91 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 chunk 79 optimal weight: 0.5980 chunk 58 optimal weight: 8.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 171 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.221301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.162128 restraints weight = 8182.203| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.98 r_work: 0.3765 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7449 Z= 0.214 Angle : 0.631 8.608 10205 Z= 0.332 Chirality : 0.044 0.172 1225 Planarity : 0.004 0.055 1294 Dihedral : 9.740 167.952 1112 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 6.27 % Allowed : 18.33 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.58 (0.27), residues: 1006 helix: 2.58 (0.23), residues: 486 sheet: 0.47 (0.42), residues: 166 loop : -0.90 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 22 TYR 0.026 0.002 TYR R 354 PHE 0.021 0.002 PHE B 151 TRP 0.014 0.002 TRP B 339 HIS 0.005 0.002 HIS R 320 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 7448) covalent geometry : angle 0.63055 (10203) SS BOND : bond 0.00356 ( 1) SS BOND : angle 0.56326 ( 2) hydrogen bonds : bond 0.04907 ( 465) hydrogen bonds : angle 4.52529 ( 1341) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 98 time to evaluate : 0.257 Fit side-chains REVERT: A 33 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.7052 (tp30) REVERT: A 157 ASN cc_start: 0.7844 (m110) cc_final: 0.7514 (m110) REVERT: A 178 ARG cc_start: 0.7444 (tpt170) cc_final: 0.6861 (tpt170) REVERT: A 208 ARG cc_start: 0.6727 (OUTLIER) cc_final: 0.4897 (ttt90) REVERT: A 242 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.6292 (mtm180) REVERT: A 324 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8355 (p) REVERT: R 105 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6767 (mp) REVERT: R 162 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6959 (mp) REVERT: B 44 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7980 (mt0) REVERT: B 57 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8201 (mttt) REVERT: B 336 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7601 (mm) REVERT: C 27 ARG cc_start: 0.6133 (OUTLIER) cc_final: 0.4822 (mtt90) outliers start: 39 outliers final: 18 residues processed: 125 average time/residue: 0.4655 time to fit residues: 62.0812 Evaluate side-chains 123 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 54 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 63 optimal weight: 50.0000 chunk 25 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 125 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.220868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.167322 restraints weight = 8206.137| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.05 r_work: 0.3771 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7449 Z= 0.164 Angle : 0.580 7.533 10205 Z= 0.304 Chirality : 0.042 0.152 1225 Planarity : 0.004 0.054 1294 Dihedral : 9.416 164.694 1112 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.31 % Allowed : 20.58 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.60 (0.27), residues: 1006 helix: 2.62 (0.23), residues: 486 sheet: 0.36 (0.41), residues: 171 loop : -0.86 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 144 TYR 0.019 0.001 TYR R 354 PHE 0.015 0.002 PHE B 151 TRP 0.014 0.002 TRP B 339 HIS 0.004 0.001 HIS R 320 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 7448) covalent geometry : angle 0.58013 (10203) SS BOND : bond 0.00311 ( 1) SS BOND : angle 0.49694 ( 2) hydrogen bonds : bond 0.04422 ( 465) hydrogen bonds : angle 4.38278 ( 1341) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 0.296 Fit side-chains REVERT: A 33 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6911 (tp30) REVERT: A 157 ASN cc_start: 0.7844 (m110) cc_final: 0.7526 (m110) REVERT: A 178 ARG cc_start: 0.7415 (tpt170) cc_final: 0.6838 (tpt170) REVERT: A 208 ARG cc_start: 0.6677 (OUTLIER) cc_final: 0.4898 (ttt90) REVERT: A 242 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6316 (mtm180) REVERT: A 310 LEU cc_start: 0.8405 (mp) cc_final: 0.8198 (mt) REVERT: A 324 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8357 (p) REVERT: R 105 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6858 (mp) REVERT: R 162 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6910 (mp) REVERT: B 44 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7896 (mt0) REVERT: B 57 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7844 (mtmt) REVERT: B 101 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.6989 (mmm) REVERT: B 192 LEU cc_start: 0.8255 (mt) cc_final: 0.7963 (mp) REVERT: B 336 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7408 (mm) REVERT: C 27 ARG cc_start: 0.6163 (OUTLIER) cc_final: 0.4838 (mtt90) outliers start: 33 outliers final: 18 residues processed: 120 average time/residue: 0.4735 time to fit residues: 60.6274 Evaluate side-chains 124 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 54 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 70 optimal weight: 0.1980 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.223604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.172659 restraints weight = 8271.980| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 1.87 r_work: 0.3821 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3718 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7449 Z= 0.116 Angle : 0.518 7.257 10205 Z= 0.272 Chirality : 0.041 0.141 1225 Planarity : 0.004 0.054 1294 Dihedral : 9.010 159.167 1112 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.82 % Allowed : 21.86 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.78 (0.27), residues: 1006 helix: 2.81 (0.23), residues: 487 sheet: 0.36 (0.41), residues: 170 loop : -0.82 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 144 TYR 0.013 0.001 TYR R 354 PHE 0.016 0.001 PHE R 136 TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 7448) covalent geometry : angle 0.51843 (10203) SS BOND : bond 0.00244 ( 1) SS BOND : angle 0.43456 ( 2) hydrogen bonds : bond 0.03848 ( 465) hydrogen bonds : angle 4.18447 ( 1341) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.207 Fit side-chains REVERT: A 33 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6891 (tp30) REVERT: A 157 ASN cc_start: 0.7866 (m110) cc_final: 0.7564 (m110) REVERT: A 178 ARG cc_start: 0.7375 (tpt170) cc_final: 0.6851 (tpt170) REVERT: A 208 ARG cc_start: 0.6598 (OUTLIER) cc_final: 0.4838 (ttt90) REVERT: R 105 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6908 (mp) REVERT: R 162 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6887 (mp) REVERT: B 101 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.6972 (mmm) REVERT: B 192 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7973 (mp) REVERT: B 205 ASP cc_start: 0.7032 (OUTLIER) cc_final: 0.6720 (m-30) REVERT: B 336 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7320 (mm) REVERT: C 27 ARG cc_start: 0.6085 (OUTLIER) cc_final: 0.4752 (mtt90) outliers start: 30 outliers final: 14 residues processed: 116 average time/residue: 0.4610 time to fit residues: 57.0691 Evaluate side-chains 114 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 27 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 20 optimal weight: 0.3980 chunk 11 optimal weight: 40.0000 chunk 26 optimal weight: 0.2980 chunk 72 optimal weight: 0.3980 chunk 99 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 54 optimal weight: 0.0970 chunk 8 optimal weight: 20.0000 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.225294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.173729 restraints weight = 8296.965| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 1.89 r_work: 0.3849 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7449 Z= 0.105 Angle : 0.499 7.049 10205 Z= 0.264 Chirality : 0.040 0.142 1225 Planarity : 0.004 0.053 1294 Dihedral : 8.646 152.376 1112 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.34 % Allowed : 22.19 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.87 (0.27), residues: 1006 helix: 2.90 (0.23), residues: 489 sheet: 0.33 (0.40), residues: 172 loop : -0.79 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 137 TYR 0.021 0.001 TYR A 74 PHE 0.012 0.001 PHE A 334 TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 7448) covalent geometry : angle 0.49891 (10203) SS BOND : bond 0.00193 ( 1) SS BOND : angle 0.36935 ( 2) hydrogen bonds : bond 0.03582 ( 465) hydrogen bonds : angle 4.03373 ( 1341) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.269 Fit side-chains REVERT: A 53 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.5945 (mpp) REVERT: A 178 ARG cc_start: 0.7317 (tpt170) cc_final: 0.6806 (tpt170) REVERT: R 162 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6907 (mp) REVERT: B 57 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7743 (mtmt) REVERT: B 192 LEU cc_start: 0.8205 (mt) cc_final: 0.7933 (mp) REVERT: B 336 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7284 (mm) REVERT: C 27 ARG cc_start: 0.6089 (OUTLIER) cc_final: 0.4825 (mtt90) outliers start: 27 outliers final: 13 residues processed: 119 average time/residue: 0.4612 time to fit residues: 58.4442 Evaluate side-chains 111 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 27 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 38 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 0.0010 chunk 98 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 91 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 88 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.224621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.164739 restraints weight = 8225.150| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 1.72 r_work: 0.3838 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7449 Z= 0.115 Angle : 0.518 7.129 10205 Z= 0.271 Chirality : 0.041 0.140 1225 Planarity : 0.004 0.051 1294 Dihedral : 8.506 151.492 1110 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.54 % Allowed : 22.83 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.88 (0.27), residues: 1006 helix: 2.92 (0.23), residues: 489 sheet: 0.32 (0.40), residues: 170 loop : -0.79 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 137 TYR 0.011 0.001 TYR R 354 PHE 0.017 0.001 PHE R 136 TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 7448) covalent geometry : angle 0.51762 (10203) SS BOND : bond 0.00189 ( 1) SS BOND : angle 0.39823 ( 2) hydrogen bonds : bond 0.03698 ( 465) hydrogen bonds : angle 4.04299 ( 1341) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.262 Fit side-chains REVERT: A 53 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.5861 (mpp) REVERT: A 157 ASN cc_start: 0.7792 (m110) cc_final: 0.7481 (m110) REVERT: A 178 ARG cc_start: 0.7341 (tpt170) cc_final: 0.6854 (tpt170) REVERT: A 208 ARG cc_start: 0.6505 (OUTLIER) cc_final: 0.4703 (ttt90) REVERT: R 162 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6837 (mp) REVERT: B 57 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7805 (mtmt) REVERT: B 192 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7946 (mp) REVERT: B 205 ASP cc_start: 0.6834 (OUTLIER) cc_final: 0.6459 (m-30) REVERT: B 336 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7326 (mm) REVERT: C 27 ARG cc_start: 0.6055 (OUTLIER) cc_final: 0.4787 (mtt90) outliers start: 22 outliers final: 14 residues processed: 114 average time/residue: 0.4417 time to fit residues: 53.9208 Evaluate side-chains 116 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 0.0670 chunk 23 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.221531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.160178 restraints weight = 8189.532| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.73 r_work: 0.3766 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7449 Z= 0.171 Angle : 0.587 7.641 10205 Z= 0.309 Chirality : 0.043 0.148 1225 Planarity : 0.004 0.052 1294 Dihedral : 8.814 157.821 1110 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.34 % Allowed : 22.83 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.71 (0.27), residues: 1006 helix: 2.77 (0.23), residues: 488 sheet: 0.28 (0.40), residues: 173 loop : -0.87 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 137 TYR 0.021 0.002 TYR A 74 PHE 0.018 0.002 PHE B 151 TRP 0.012 0.002 TRP B 339 HIS 0.004 0.001 HIS R 320 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 7448) covalent geometry : angle 0.58661 (10203) SS BOND : bond 0.00237 ( 1) SS BOND : angle 0.57334 ( 2) hydrogen bonds : bond 0.04352 ( 465) hydrogen bonds : angle 4.25729 ( 1341) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.271 Fit side-chains REVERT: A 33 GLU cc_start: 0.7229 (tp30) cc_final: 0.6942 (tp30) REVERT: A 178 ARG cc_start: 0.7295 (tpt170) cc_final: 0.6782 (tpt170) REVERT: A 208 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.4770 (ttt90) REVERT: A 242 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6298 (mtm180) REVERT: R 162 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6885 (mp) REVERT: B 57 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7856 (mtmt) REVERT: B 192 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8008 (mp) REVERT: B 205 ASP cc_start: 0.7028 (OUTLIER) cc_final: 0.6746 (m-30) REVERT: B 336 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7482 (mm) REVERT: C 27 ARG cc_start: 0.6139 (OUTLIER) cc_final: 0.4767 (mtt90) outliers start: 27 outliers final: 14 residues processed: 116 average time/residue: 0.4763 time to fit residues: 58.8908 Evaluate side-chains 114 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 17 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.222511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.162939 restraints weight = 8154.584| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.02 r_work: 0.3780 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7449 Z= 0.146 Angle : 0.562 7.482 10205 Z= 0.294 Chirality : 0.042 0.144 1225 Planarity : 0.004 0.053 1294 Dihedral : 8.725 157.013 1110 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.02 % Allowed : 23.15 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.27), residues: 1006 helix: 2.86 (0.23), residues: 482 sheet: 0.23 (0.40), residues: 175 loop : -0.87 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 137 TYR 0.011 0.001 TYR R 319 PHE 0.017 0.002 PHE R 136 TRP 0.011 0.001 TRP B 339 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7448) covalent geometry : angle 0.56178 (10203) SS BOND : bond 0.00245 ( 1) SS BOND : angle 0.50318 ( 2) hydrogen bonds : bond 0.04135 ( 465) hydrogen bonds : angle 4.21103 ( 1341) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3529.07 seconds wall clock time: 60 minutes 32.33 seconds (3632.33 seconds total)