Starting phenix.real_space_refine on Tue Mar 3 22:19:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dfl_30665/03_2026/7dfl_30665_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dfl_30665/03_2026/7dfl_30665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dfl_30665/03_2026/7dfl_30665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dfl_30665/03_2026/7dfl_30665.map" model { file = "/net/cci-nas-00/data/ceres_data/7dfl_30665/03_2026/7dfl_30665_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dfl_30665/03_2026/7dfl_30665_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.078 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 66 5.16 5 C 5729 2.51 5 N 1535 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8987 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2273 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 9, 'TRANS': 265} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "A" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1847 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain breaks: 2 Chain: "C" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1808 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.08, per 1000 atoms: 0.23 Number of scatterers: 8987 At special positions: 0 Unit cell: (90.72, 119.88, 126.36, 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 66 16.00 O 1657 8.00 N 1535 7.00 C 5729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 180 " distance=2.04 Simple disulfide: pdb=" SG CYS R 441 " - pdb=" SG CYS R 444 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 229 " distance=1.95 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: 0.61 Conformation dependent library (CDL) restraints added in 334.4 milliseconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 12 sheets defined 38.4% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'R' and resid 28 through 53 removed outlier: 3.999A pdb=" N VAL R 32 " --> pdb=" O MET R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 80 removed outlier: 4.084A pdb=" N TYR R 65 " --> pdb=" O VAL R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 90 removed outlier: 3.612A pdb=" N ASN R 84 " --> pdb=" O VAL R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 131 Processing helix chain 'R' and resid 140 through 157 Processing helix chain 'R' and resid 158 through 163 removed outlier: 4.403A pdb=" N ILE R 162 " --> pdb=" O TRP R 158 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU R 163 " --> pdb=" O VAL R 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 158 through 163' Processing helix chain 'R' and resid 168 through 172 removed outlier: 3.642A pdb=" N THR R 172 " --> pdb=" O MET R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 199 Processing helix chain 'R' and resid 199 through 218 Processing helix chain 'R' and resid 408 through 439 Proline residue: R 430 - end of helix removed outlier: 3.735A pdb=" N PHE R 434 " --> pdb=" O PRO R 430 " (cutoff:3.500A) Processing helix chain 'R' and resid 445 through 464 removed outlier: 4.226A pdb=" N LEU R 449 " --> pdb=" O CYS R 445 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN R 460 " --> pdb=" O LEU R 456 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER R 461 " --> pdb=" O GLY R 457 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR R 462 " --> pdb=" O TYR R 458 " (cutoff:3.500A) Processing helix chain 'R' and resid 465 through 467 No H-bonds generated for 'chain 'R' and resid 465 through 467' Processing helix chain 'R' and resid 468 through 472 removed outlier: 3.930A pdb=" N ASN R 472 " --> pdb=" O PRO R 469 " (cutoff:3.500A) Processing helix chain 'R' and resid 475 through 482 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 33 Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'A' and resid 6 through 37 removed outlier: 4.128A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 212 through 221 removed outlier: 3.762A pdb=" N ILE A 217 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N HIS A 218 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS A 219 " --> pdb=" O TRP A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 246 through 260 removed outlier: 4.049A pdb=" N GLU A 250 " --> pdb=" O ASN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.867A pdb=" N GLN A 265 " --> pdb=" O PRO A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 284 Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 301 through 316 removed outlier: 3.920A pdb=" N LEU A 316 " --> pdb=" O MET A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 356 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 53 through 56 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.671A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 224 removed outlier: 3.537A pdb=" N VAL C 224 " --> pdb=" O ALA C 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.630A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.520A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.047A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.513A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.688A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.220A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 276 through 278 Processing sheet with id=AA8, first strand: chain 'A' and resid 190 through 196 removed outlier: 3.691A pdb=" N LEU A 42 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 9.973A pdb=" N SER A 225 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LYS A 41 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N MET A 227 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU A 43 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU A 229 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU A 45 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ALA A 231 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE A 226 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N PHE A 272 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE A 228 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN A 274 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 230 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.446A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'C' and resid 146 through 149 removed outlier: 6.448A pdb=" N VAL C 147 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU C 174 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N TYR C 190 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP C 176 " --> pdb=" O LEU C 188 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1185 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: 1.47 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2897 1.35 - 1.47: 2300 1.47 - 1.59: 3884 1.59 - 1.71: 0 1.71 - 1.84: 100 Bond restraints: 9181 Sorted by residual: bond pdb=" C VAL R 80 " pdb=" O VAL R 80 " ideal model delta sigma weight residual 1.233 1.285 -0.052 1.02e-02 9.61e+03 2.60e+01 bond pdb=" N THR C 118 " pdb=" CA THR C 118 " ideal model delta sigma weight residual 1.457 1.509 -0.052 1.23e-02 6.61e+03 1.76e+01 bond pdb=" N PRO C 236 " pdb=" CD PRO C 236 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.56e+01 bond pdb=" N LEU C 187 " pdb=" CA LEU C 187 " ideal model delta sigma weight residual 1.456 1.503 -0.046 1.22e-02 6.72e+03 1.44e+01 bond pdb=" N VAL R 80 " pdb=" CA VAL R 80 " ideal model delta sigma weight residual 1.454 1.497 -0.043 1.19e-02 7.06e+03 1.30e+01 ... (remaining 9176 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 11990 2.21 - 4.42: 356 4.42 - 6.63: 66 6.63 - 8.84: 12 8.84 - 11.05: 3 Bond angle restraints: 12427 Sorted by residual: angle pdb=" N ARG R 218 " pdb=" CA ARG R 218 " pdb=" C ARG R 218 " ideal model delta sigma weight residual 110.80 121.85 -11.05 2.13e+00 2.20e-01 2.69e+01 angle pdb=" N SER C 136 " pdb=" CA SER C 136 " pdb=" C SER C 136 " ideal model delta sigma weight residual 110.80 100.47 10.33 2.13e+00 2.20e-01 2.35e+01 angle pdb=" N ARG R 134 " pdb=" CA ARG R 134 " pdb=" C ARG R 134 " ideal model delta sigma weight residual 108.58 99.99 8.59 1.82e+00 3.02e-01 2.23e+01 angle pdb=" N HIS R 406 " pdb=" CA HIS R 406 " pdb=" C HIS R 406 " ideal model delta sigma weight residual 108.02 116.30 -8.28 1.78e+00 3.16e-01 2.16e+01 angle pdb=" N CYS R 445 " pdb=" CA CYS R 445 " pdb=" C CYS R 445 " ideal model delta sigma weight residual 110.80 101.30 9.50 2.13e+00 2.20e-01 1.99e+01 ... (remaining 12422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 5048 16.82 - 33.65: 340 33.65 - 50.47: 54 50.47 - 67.29: 9 67.29 - 84.12: 6 Dihedral angle restraints: 5457 sinusoidal: 2162 harmonic: 3295 Sorted by residual: dihedral pdb=" C SER C 136 " pdb=" N SER C 136 " pdb=" CA SER C 136 " pdb=" CB SER C 136 " ideal model delta harmonic sigma weight residual -122.60 -110.84 -11.76 0 2.50e+00 1.60e-01 2.21e+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 180.00 160.04 19.96 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ARG R 134 " pdb=" C ARG R 134 " pdb=" N TYR R 135 " pdb=" CA TYR R 135 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 5454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1233 0.085 - 0.169: 142 0.169 - 0.254: 14 0.254 - 0.339: 2 0.339 - 0.423: 2 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA SER C 136 " pdb=" N SER C 136 " pdb=" C SER C 136 " pdb=" CB SER C 136 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CA SER B 67 " pdb=" N SER B 67 " pdb=" C SER B 67 " pdb=" CB SER B 67 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA ARG R 218 " pdb=" N ARG R 218 " pdb=" C ARG R 218 " pdb=" CB ARG R 218 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 1390 not shown) Planarity restraints: 1568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 235 " 0.061 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO C 236 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 435 " -0.029 2.00e-02 2.50e+03 2.46e-02 1.06e+01 pdb=" CG PHE R 435 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE R 435 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE R 435 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE R 435 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE R 435 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE R 435 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 234 " -0.025 2.00e-02 2.50e+03 2.02e-02 7.15e+00 pdb=" CG PHE B 234 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B 234 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 234 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 234 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 234 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 234 " -0.004 2.00e-02 2.50e+03 ... (remaining 1565 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 34 2.51 - 3.11: 7003 3.11 - 3.70: 13351 3.70 - 4.30: 19365 4.30 - 4.90: 32412 Nonbonded interactions: 72165 Sorted by model distance: nonbonded pdb=" SD MET A 203 " pdb=" CE MET A 227 " model vdw 1.910 3.820 nonbonded pdb=" O ILE B 43 " pdb=" NH2 ARG B 304 " model vdw 2.129 3.120 nonbonded pdb=" O ILE R 37 " pdb=" OG1 THR R 41 " model vdw 2.165 3.040 nonbonded pdb=" OG SER B 227 " pdb=" OD1 ASP B 247 " model vdw 2.186 3.040 nonbonded pdb=" OD2 ASP B 212 " pdb=" N GLU B 215 " model vdw 2.297 3.120 ... (remaining 72160 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 0.020 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.330 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 9185 Z= 0.408 Angle : 0.958 12.172 12435 Z= 0.560 Chirality : 0.057 0.423 1393 Planarity : 0.006 0.089 1568 Dihedral : 11.969 84.118 3319 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.24), residues: 1115 helix: 0.54 (0.27), residues: 363 sheet: -0.92 (0.32), residues: 252 loop : -1.31 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 306 TYR 0.025 0.003 TYR R 138 PHE 0.057 0.003 PHE R 435 TRP 0.024 0.002 TRP A 216 HIS 0.013 0.002 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00789 ( 9181) covalent geometry : angle 0.95120 (12427) SS BOND : bond 0.04020 ( 4) SS BOND : angle 4.71112 ( 8) hydrogen bonds : bond 0.16244 ( 429) hydrogen bonds : angle 7.29297 ( 1185) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 37 ILE cc_start: 0.8031 (mt) cc_final: 0.7708 (mt) REVERT: R 179 LYS cc_start: 0.5155 (pttm) cc_final: 0.4651 (mttp) REVERT: R 436 MET cc_start: 0.7342 (mtp) cc_final: 0.7061 (mmp) REVERT: B 32 GLN cc_start: 0.7585 (tt0) cc_final: 0.7350 (tm-30) REVERT: B 118 ASP cc_start: 0.7397 (p0) cc_final: 0.7161 (p0) REVERT: B 255 LEU cc_start: 0.8060 (mt) cc_final: 0.7798 (mt) REVERT: A 311 LYS cc_start: 0.8097 (tptm) cc_final: 0.7812 (tptm) REVERT: C 80 PHE cc_start: 0.6826 (m-10) cc_final: 0.6553 (m-10) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.1054 time to fit residues: 47.7527 Evaluate side-chains 225 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 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 = 0.3943 r_free = 0.3943 target = 0.147882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.110501 restraints weight = 14343.246| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.92 r_work: 0.3338 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9185 Z= 0.155 Angle : 0.692 9.079 12435 Z= 0.358 Chirality : 0.045 0.205 1393 Planarity : 0.005 0.066 1568 Dihedral : 5.449 46.082 1239 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.54 % Allowed : 12.11 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.25), residues: 1115 helix: 1.04 (0.27), residues: 371 sheet: -0.52 (0.33), residues: 246 loop : -0.92 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 481 TYR 0.018 0.002 TYR R 50 PHE 0.031 0.002 PHE R 435 TRP 0.022 0.002 TRP B 297 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9181) covalent geometry : angle 0.69029 (12427) SS BOND : bond 0.01035 ( 4) SS BOND : angle 1.97821 ( 8) hydrogen bonds : bond 0.04252 ( 429) hydrogen bonds : angle 5.21771 ( 1185) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 268 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 28 MET cc_start: 0.8100 (pmm) cc_final: 0.6338 (mpp) REVERT: R 130 GLN cc_start: 0.8166 (tp40) cc_final: 0.7611 (tm-30) REVERT: R 133 LEU cc_start: 0.5905 (mp) cc_final: 0.5378 (tp) REVERT: R 179 LYS cc_start: 0.5276 (pttm) cc_final: 0.4422 (mttp) REVERT: R 436 MET cc_start: 0.8158 (mtp) cc_final: 0.7519 (mmp) REVERT: R 481 ARG cc_start: 0.8746 (mtt90) cc_final: 0.7645 (tpt170) REVERT: B 15 LYS cc_start: 0.9314 (mmtp) cc_final: 0.9043 (mmtp) REVERT: B 29 THR cc_start: 0.7102 (t) cc_final: 0.6900 (t) REVERT: B 32 GLN cc_start: 0.8139 (tt0) cc_final: 0.7432 (tm-30) REVERT: B 57 LYS cc_start: 0.8792 (mtmm) cc_final: 0.8322 (mtpt) REVERT: B 172 GLU cc_start: 0.8630 (tp30) cc_final: 0.8401 (tp30) REVERT: B 197 ARG cc_start: 0.8614 (mmp80) cc_final: 0.8368 (mmp80) REVERT: B 217 MET cc_start: 0.7608 (tmm) cc_final: 0.7170 (tmm) REVERT: B 254 ASP cc_start: 0.7960 (t70) cc_final: 0.7614 (t70) REVERT: B 297 TRP cc_start: 0.7738 (m100) cc_final: 0.7239 (m-10) REVERT: G 13 ARG cc_start: 0.8405 (ttm110) cc_final: 0.8092 (mtm-85) REVERT: G 18 GLN cc_start: 0.7404 (tp40) cc_final: 0.6758 (tp-100) REVERT: G 28 ILE cc_start: 0.8641 (tp) cc_final: 0.8188 (tt) REVERT: G 29 LYS cc_start: 0.7389 (mtmm) cc_final: 0.7145 (mptt) REVERT: A 9 ASP cc_start: 0.8295 (m-30) cc_final: 0.7981 (m-30) REVERT: A 38 ARG cc_start: 0.7280 (ptp90) cc_final: 0.6840 (ptp-170) REVERT: A 57 LYS cc_start: 0.8424 (tttt) cc_final: 0.8169 (mttp) REVERT: A 212 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6525 (tm-30) REVERT: A 234 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7403 (mt-10) REVERT: A 265 GLN cc_start: 0.8148 (mt0) cc_final: 0.7854 (mt0) REVERT: A 287 HIS cc_start: 0.7344 (m90) cc_final: 0.6907 (m-70) REVERT: A 295 TYR cc_start: 0.8231 (t80) cc_final: 0.8014 (t80) REVERT: A 311 LYS cc_start: 0.8308 (tptm) cc_final: 0.8090 (tptm) REVERT: A 346 ASP cc_start: 0.8133 (m-30) cc_final: 0.7428 (t70) REVERT: A 350 GLN cc_start: 0.7454 (tp40) cc_final: 0.6673 (mm110) REVERT: C 113 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8185 (tm-30) REVERT: C 153 GLU cc_start: 0.8799 (tp30) cc_final: 0.8547 (tp30) REVERT: C 218 ARG cc_start: 0.8613 (ttm-80) cc_final: 0.7582 (tpp-160) REVERT: C 219 LEU cc_start: 0.7954 (tt) cc_final: 0.6864 (tt) REVERT: C 220 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7326 (mp0) REVERT: C 223 ASP cc_start: 0.7764 (m-30) cc_final: 0.7279 (p0) REVERT: C 230 MET cc_start: 0.7938 (ttp) cc_final: 0.7577 (ttt) REVERT: C 234 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7860 (pt0) outliers start: 25 outliers final: 14 residues processed: 284 average time/residue: 0.0925 time to fit residues: 35.9223 Evaluate side-chains 240 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 225 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 84 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 HIS A 299 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.146501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.111539 restraints weight = 14212.698| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.74 r_work: 0.3369 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9185 Z= 0.136 Angle : 0.641 10.582 12435 Z= 0.331 Chirality : 0.044 0.161 1393 Planarity : 0.004 0.066 1568 Dihedral : 5.018 43.589 1239 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.15 % Allowed : 14.24 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.25), residues: 1115 helix: 1.04 (0.27), residues: 368 sheet: -0.24 (0.34), residues: 235 loop : -0.73 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 202 TYR 0.016 0.001 TYR A 235 PHE 0.032 0.002 PHE R 435 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9181) covalent geometry : angle 0.64023 (12427) SS BOND : bond 0.00440 ( 4) SS BOND : angle 1.65189 ( 8) hydrogen bonds : bond 0.03796 ( 429) hydrogen bonds : angle 4.80321 ( 1185) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 248 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 28 MET cc_start: 0.7935 (pmm) cc_final: 0.6393 (mpp) REVERT: R 93 TRP cc_start: 0.6167 (t-100) cc_final: 0.5484 (t-100) REVERT: R 130 GLN cc_start: 0.8249 (tp40) cc_final: 0.7827 (tm-30) REVERT: R 133 LEU cc_start: 0.5998 (mp) cc_final: 0.5162 (tp) REVERT: R 179 LYS cc_start: 0.5127 (pttm) cc_final: 0.4275 (mttp) REVERT: R 436 MET cc_start: 0.8099 (mtp) cc_final: 0.7510 (mmp) REVERT: R 450 HIS cc_start: 0.7722 (OUTLIER) cc_final: 0.7344 (m90) REVERT: R 481 ARG cc_start: 0.8813 (mtt90) cc_final: 0.7817 (tpt170) REVERT: B 20 ASP cc_start: 0.8420 (m-30) cc_final: 0.8153 (m-30) REVERT: B 29 THR cc_start: 0.7100 (t) cc_final: 0.6892 (t) REVERT: B 32 GLN cc_start: 0.8101 (tt0) cc_final: 0.7369 (tm-30) REVERT: B 42 ARG cc_start: 0.7655 (tpp80) cc_final: 0.7383 (tpp80) REVERT: B 44 GLN cc_start: 0.7188 (mp10) cc_final: 0.6903 (mp10) REVERT: B 57 LYS cc_start: 0.8678 (mtmm) cc_final: 0.8248 (mtpt) REVERT: B 75 GLN cc_start: 0.8685 (tt0) cc_final: 0.8407 (tt0) REVERT: B 197 ARG cc_start: 0.8652 (mmp80) cc_final: 0.8377 (mmp80) REVERT: B 254 ASP cc_start: 0.8004 (t70) cc_final: 0.7589 (t70) REVERT: B 260 GLU cc_start: 0.8449 (tt0) cc_final: 0.7954 (tt0) REVERT: B 297 TRP cc_start: 0.7534 (m100) cc_final: 0.6909 (m-10) REVERT: B 325 MET cc_start: 0.8611 (tpp) cc_final: 0.8343 (tpt) REVERT: G 13 ARG cc_start: 0.8361 (ttm110) cc_final: 0.8086 (mtm-85) REVERT: G 18 GLN cc_start: 0.7490 (tp40) cc_final: 0.7161 (tp-100) REVERT: G 21 MET cc_start: 0.8124 (ptt) cc_final: 0.7881 (ptt) REVERT: G 28 ILE cc_start: 0.8626 (tp) cc_final: 0.8227 (tt) REVERT: A 9 ASP cc_start: 0.8281 (m-30) cc_final: 0.7921 (m-30) REVERT: A 57 LYS cc_start: 0.8382 (tttt) cc_final: 0.8150 (mttp) REVERT: A 234 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6746 (mt-10) REVERT: A 265 GLN cc_start: 0.8170 (mt0) cc_final: 0.7889 (mt0) REVERT: A 284 MET cc_start: 0.8670 (mtt) cc_final: 0.8459 (mtm) REVERT: A 350 GLN cc_start: 0.7601 (tp40) cc_final: 0.6767 (mm110) REVERT: C 73 ASP cc_start: 0.6867 (t0) cc_final: 0.6309 (t0) REVERT: C 113 GLN cc_start: 0.8679 (tm-30) cc_final: 0.7948 (tm-30) REVERT: C 153 GLU cc_start: 0.8575 (tp30) cc_final: 0.8221 (tp30) REVERT: C 218 ARG cc_start: 0.8552 (ttm-80) cc_final: 0.7952 (ttm-80) REVERT: C 220 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7745 (mp0) REVERT: C 230 MET cc_start: 0.8139 (ttp) cc_final: 0.7769 (ttp) REVERT: C 234 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7860 (pt0) outliers start: 31 outliers final: 21 residues processed: 264 average time/residue: 0.0964 time to fit residues: 34.6573 Evaluate side-chains 235 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 450 HIS Chi-restraints excluded: chain R residue 451 MET Chi-restraints excluded: chain R residue 463 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 106 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 76 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.147771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.110404 restraints weight = 14828.119| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 4.00 r_work: 0.3336 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9185 Z= 0.139 Angle : 0.635 10.216 12435 Z= 0.326 Chirality : 0.044 0.171 1393 Planarity : 0.004 0.065 1568 Dihedral : 4.813 38.716 1239 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.36 % Allowed : 15.77 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.25), residues: 1115 helix: 1.07 (0.27), residues: 367 sheet: -0.25 (0.33), residues: 247 loop : -0.66 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 202 TYR 0.028 0.001 TYR A 295 PHE 0.039 0.002 PHE R 435 TRP 0.013 0.001 TRP C 47 HIS 0.002 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9181) covalent geometry : angle 0.63452 (12427) SS BOND : bond 0.00478 ( 4) SS BOND : angle 1.38688 ( 8) hydrogen bonds : bond 0.03623 ( 429) hydrogen bonds : angle 4.68987 ( 1185) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 236 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 28 MET cc_start: 0.7690 (pmm) cc_final: 0.6440 (mpp) REVERT: R 93 TRP cc_start: 0.5720 (t-100) cc_final: 0.5142 (t-100) REVERT: R 130 GLN cc_start: 0.8182 (tp40) cc_final: 0.7714 (tm-30) REVERT: R 133 LEU cc_start: 0.5976 (mp) cc_final: 0.4901 (tp) REVERT: R 158 TRP cc_start: 0.7799 (OUTLIER) cc_final: 0.5425 (t60) REVERT: R 179 LYS cc_start: 0.5245 (pttm) cc_final: 0.4367 (mttp) REVERT: R 186 ASP cc_start: 0.7313 (p0) cc_final: 0.6822 (t0) REVERT: R 436 MET cc_start: 0.8071 (mtp) cc_final: 0.7437 (mmp) REVERT: R 450 HIS cc_start: 0.7533 (OUTLIER) cc_final: 0.7180 (m90) REVERT: R 481 ARG cc_start: 0.8839 (mtt90) cc_final: 0.7848 (tpt170) REVERT: B 15 LYS cc_start: 0.9379 (mmtp) cc_final: 0.9176 (mmtp) REVERT: B 32 GLN cc_start: 0.8044 (tt0) cc_final: 0.7300 (tm-30) REVERT: B 44 GLN cc_start: 0.7335 (mp10) cc_final: 0.7015 (mp10) REVERT: B 57 LYS cc_start: 0.8510 (mtmm) cc_final: 0.8128 (mtpt) REVERT: B 160 SER cc_start: 0.8881 (m) cc_final: 0.8094 (p) REVERT: B 234 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.8136 (m-10) REVERT: B 247 ASP cc_start: 0.9084 (m-30) cc_final: 0.8812 (m-30) REVERT: B 254 ASP cc_start: 0.7935 (t70) cc_final: 0.7439 (t70) REVERT: B 260 GLU cc_start: 0.8343 (tt0) cc_final: 0.7809 (tt0) REVERT: B 266 HIS cc_start: 0.5373 (t-90) cc_final: 0.5145 (t-90) REVERT: B 297 TRP cc_start: 0.7612 (m100) cc_final: 0.7044 (m-10) REVERT: G 13 ARG cc_start: 0.8385 (ttm110) cc_final: 0.8135 (mtm-85) REVERT: G 18 GLN cc_start: 0.7528 (tp40) cc_final: 0.7317 (tp40) REVERT: G 20 LYS cc_start: 0.9063 (mtmt) cc_final: 0.8764 (mtmm) REVERT: G 46 LYS cc_start: 0.9307 (mptt) cc_final: 0.8756 (tptp) REVERT: A 9 ASP cc_start: 0.8304 (m-30) cc_final: 0.8018 (m-30) REVERT: A 57 LYS cc_start: 0.8346 (tttt) cc_final: 0.8089 (mttp) REVERT: A 234 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6769 (tt0) REVERT: A 265 GLN cc_start: 0.8165 (mt0) cc_final: 0.7821 (mt0) REVERT: A 350 GLN cc_start: 0.7503 (tp40) cc_final: 0.6726 (mm110) REVERT: C 113 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8318 (tp40) REVERT: C 153 GLU cc_start: 0.8613 (tp30) cc_final: 0.8257 (tp30) REVERT: C 160 ARG cc_start: 0.7813 (ttp-110) cc_final: 0.7512 (ttm-80) REVERT: C 192 MET cc_start: 0.8229 (ptm) cc_final: 0.7831 (ptm) REVERT: C 218 ARG cc_start: 0.8510 (ttm-80) cc_final: 0.8220 (mmm160) REVERT: C 230 MET cc_start: 0.8233 (ttp) cc_final: 0.7768 (ttp) outliers start: 33 outliers final: 21 residues processed: 254 average time/residue: 0.1023 time to fit residues: 35.1173 Evaluate side-chains 236 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 437 VAL Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 450 HIS Chi-restraints excluded: chain R residue 451 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 97 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 0.0470 overall best weight: 1.4884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.144596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.108196 restraints weight = 14819.256| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.84 r_work: 0.3325 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9185 Z= 0.186 Angle : 0.659 9.556 12435 Z= 0.339 Chirality : 0.045 0.180 1393 Planarity : 0.004 0.069 1568 Dihedral : 4.852 34.611 1239 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.58 % Allowed : 15.46 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.25), residues: 1115 helix: 1.10 (0.27), residues: 368 sheet: -0.53 (0.32), residues: 253 loop : -0.65 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 202 TYR 0.029 0.002 TYR A 295 PHE 0.038 0.002 PHE R 435 TRP 0.014 0.002 TRP C 47 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 9181) covalent geometry : angle 0.65804 (12427) SS BOND : bond 0.00514 ( 4) SS BOND : angle 1.18994 ( 8) hydrogen bonds : bond 0.03805 ( 429) hydrogen bonds : angle 4.74898 ( 1185) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 223 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 28 MET cc_start: 0.7649 (pmm) cc_final: 0.6371 (mpp) REVERT: R 103 TRP cc_start: 0.7225 (t60) cc_final: 0.6898 (t60) REVERT: R 130 GLN cc_start: 0.8171 (tp40) cc_final: 0.7840 (tm-30) REVERT: R 158 TRP cc_start: 0.7529 (OUTLIER) cc_final: 0.5370 (t60) REVERT: R 179 LYS cc_start: 0.5469 (pttm) cc_final: 0.4044 (mttp) REVERT: R 186 ASP cc_start: 0.7630 (p0) cc_final: 0.6884 (t0) REVERT: R 426 LEU cc_start: 0.8491 (tt) cc_final: 0.7982 (mt) REVERT: R 450 HIS cc_start: 0.7573 (OUTLIER) cc_final: 0.7238 (m90) REVERT: R 481 ARG cc_start: 0.8828 (mtt90) cc_final: 0.7843 (tpt170) REVERT: B 15 LYS cc_start: 0.9388 (mmtp) cc_final: 0.9179 (mmtp) REVERT: B 32 GLN cc_start: 0.8048 (tt0) cc_final: 0.7360 (tm-30) REVERT: B 57 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8300 (mtmt) REVERT: B 217 MET cc_start: 0.7028 (tmm) cc_final: 0.6560 (tmm) REVERT: B 234 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8293 (m-10) REVERT: B 254 ASP cc_start: 0.8089 (t70) cc_final: 0.7597 (t70) REVERT: B 260 GLU cc_start: 0.8339 (tt0) cc_final: 0.7893 (tt0) REVERT: B 266 HIS cc_start: 0.5659 (t-90) cc_final: 0.5459 (t-90) REVERT: B 293 ASN cc_start: 0.7297 (m-40) cc_final: 0.6730 (p0) REVERT: G 13 ARG cc_start: 0.8419 (ttm110) cc_final: 0.8141 (mtm-85) REVERT: A 9 ASP cc_start: 0.8409 (m-30) cc_final: 0.8127 (m-30) REVERT: A 57 LYS cc_start: 0.8379 (tttt) cc_final: 0.8152 (mttp) REVERT: A 212 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6466 (tm-30) REVERT: A 248 MET cc_start: 0.7942 (mtt) cc_final: 0.7594 (mtt) REVERT: A 265 GLN cc_start: 0.8179 (mt0) cc_final: 0.7829 (mt0) REVERT: A 266 ASN cc_start: 0.9185 (t0) cc_final: 0.8940 (t0) REVERT: A 275 LYS cc_start: 0.8346 (tttp) cc_final: 0.7951 (tttp) REVERT: A 315 ASP cc_start: 0.8884 (m-30) cc_final: 0.8356 (m-30) REVERT: A 333 ASP cc_start: 0.3212 (OUTLIER) cc_final: 0.2171 (t70) REVERT: A 350 GLN cc_start: 0.7468 (tp40) cc_final: 0.6673 (mm110) REVERT: C 73 ASP cc_start: 0.6997 (t0) cc_final: 0.6451 (t0) REVERT: C 113 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8355 (tp40) REVERT: C 153 GLU cc_start: 0.8590 (tp30) cc_final: 0.8256 (tp30) REVERT: C 160 ARG cc_start: 0.7917 (ttp-110) cc_final: 0.7612 (ttm-80) REVERT: C 218 ARG cc_start: 0.8432 (ttm-80) cc_final: 0.7515 (mpp80) REVERT: C 220 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: C 230 MET cc_start: 0.8316 (ttp) cc_final: 0.7982 (ttp) outliers start: 45 outliers final: 32 residues processed: 248 average time/residue: 0.0890 time to fit residues: 30.6453 Evaluate side-chains 250 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 437 VAL Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 450 HIS Chi-restraints excluded: chain R residue 451 MET Chi-restraints excluded: chain R residue 462 THR Chi-restraints excluded: chain R residue 463 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain A residue 63 HIS Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 0 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 64 optimal weight: 0.0670 chunk 105 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 0.0040 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 107 optimal weight: 0.0010 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 450 HIS B 6 GLN C 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.147903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.113334 restraints weight = 14332.761| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 3.73 r_work: 0.3401 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9185 Z= 0.116 Angle : 0.620 10.033 12435 Z= 0.317 Chirality : 0.043 0.152 1393 Planarity : 0.004 0.062 1568 Dihedral : 4.501 28.310 1239 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.76 % Allowed : 17.90 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.26), residues: 1115 helix: 1.20 (0.27), residues: 372 sheet: -0.43 (0.31), residues: 272 loop : -0.48 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 202 TYR 0.016 0.001 TYR A 235 PHE 0.032 0.002 PHE R 435 TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9181) covalent geometry : angle 0.61922 (12427) SS BOND : bond 0.00375 ( 4) SS BOND : angle 1.23946 ( 8) hydrogen bonds : bond 0.03483 ( 429) hydrogen bonds : angle 4.50680 ( 1185) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 28 MET cc_start: 0.7720 (pmm) cc_final: 0.6481 (mpp) REVERT: R 130 GLN cc_start: 0.8192 (tp40) cc_final: 0.7937 (tm-30) REVERT: R 158 TRP cc_start: 0.7708 (OUTLIER) cc_final: 0.5590 (t60) REVERT: R 179 LYS cc_start: 0.5427 (pttm) cc_final: 0.4871 (ptmt) REVERT: R 426 LEU cc_start: 0.8326 (tt) cc_final: 0.7833 (mt) REVERT: R 436 MET cc_start: 0.8398 (tpp) cc_final: 0.8167 (mmp) REVERT: R 450 HIS cc_start: 0.7613 (OUTLIER) cc_final: 0.7361 (m-70) REVERT: R 481 ARG cc_start: 0.8782 (mtt90) cc_final: 0.7915 (tpt170) REVERT: B 15 LYS cc_start: 0.9379 (mmtp) cc_final: 0.9176 (mmtp) REVERT: B 32 GLN cc_start: 0.7901 (tt0) cc_final: 0.7202 (tm-30) REVERT: B 57 LYS cc_start: 0.8649 (mtmm) cc_final: 0.8269 (mtpt) REVERT: B 75 GLN cc_start: 0.8646 (tt0) cc_final: 0.8425 (tt0) REVERT: B 137 ARG cc_start: 0.7160 (mmt-90) cc_final: 0.6729 (mmm-85) REVERT: B 160 SER cc_start: 0.8823 (m) cc_final: 0.8097 (p) REVERT: B 234 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.7664 (m-80) REVERT: B 254 ASP cc_start: 0.8025 (t70) cc_final: 0.7603 (t70) REVERT: B 297 TRP cc_start: 0.7671 (m100) cc_final: 0.7044 (m-10) REVERT: G 21 MET cc_start: 0.7727 (ptm) cc_final: 0.7390 (ptm) REVERT: G 46 LYS cc_start: 0.9336 (mptt) cc_final: 0.8808 (tptp) REVERT: A 9 ASP cc_start: 0.8332 (m-30) cc_final: 0.8003 (m-30) REVERT: A 57 LYS cc_start: 0.8390 (tttt) cc_final: 0.8161 (mttp) REVERT: A 234 GLU cc_start: 0.7574 (mt-10) cc_final: 0.6815 (mt-10) REVERT: A 265 GLN cc_start: 0.8182 (mt0) cc_final: 0.7836 (mt0) REVERT: A 266 ASN cc_start: 0.9145 (t0) cc_final: 0.8894 (t0) REVERT: A 275 LYS cc_start: 0.8269 (tttp) cc_final: 0.7891 (tttp) REVERT: A 311 LYS cc_start: 0.8284 (tptm) cc_final: 0.7955 (tptm) REVERT: A 315 ASP cc_start: 0.8882 (m-30) cc_final: 0.8167 (m-30) REVERT: A 316 LEU cc_start: 0.7697 (mt) cc_final: 0.7174 (mp) REVERT: A 346 ASP cc_start: 0.8225 (m-30) cc_final: 0.7496 (t70) REVERT: A 350 GLN cc_start: 0.7380 (tp40) cc_final: 0.6565 (mm110) REVERT: C 73 ASP cc_start: 0.7043 (t0) cc_final: 0.6491 (t0) REVERT: C 113 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8249 (tp40) REVERT: C 153 GLU cc_start: 0.8456 (tp30) cc_final: 0.8148 (tp30) REVERT: C 195 LEU cc_start: 0.7183 (mp) cc_final: 0.6745 (mt) REVERT: C 202 ARG cc_start: 0.7251 (mtm-85) cc_final: 0.6991 (mtp180) REVERT: C 218 ARG cc_start: 0.8411 (ttm-80) cc_final: 0.7708 (mpp80) REVERT: C 230 MET cc_start: 0.8316 (ttp) cc_final: 0.8111 (ttp) REVERT: C 234 GLU cc_start: 0.7617 (pt0) cc_final: 0.7011 (pm20) outliers start: 37 outliers final: 24 residues processed: 255 average time/residue: 0.1074 time to fit residues: 37.0783 Evaluate side-chains 246 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 169 MET Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 429 ILE Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 450 HIS Chi-restraints excluded: chain R residue 451 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain A residue 63 HIS Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 78 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 220 GLN C 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.147986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.111691 restraints weight = 14725.741| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.94 r_work: 0.3372 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9185 Z= 0.134 Angle : 0.658 10.240 12435 Z= 0.334 Chirality : 0.043 0.225 1393 Planarity : 0.004 0.063 1568 Dihedral : 4.495 27.516 1239 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.56 % Allowed : 17.90 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.26), residues: 1115 helix: 1.21 (0.27), residues: 372 sheet: -0.47 (0.31), residues: 272 loop : -0.48 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 202 TYR 0.028 0.002 TYR A 295 PHE 0.032 0.002 PHE R 435 TRP 0.018 0.001 TRP B 211 HIS 0.009 0.001 HIS R 450 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9181) covalent geometry : angle 0.65581 (12427) SS BOND : bond 0.00488 ( 4) SS BOND : angle 2.01631 ( 8) hydrogen bonds : bond 0.03505 ( 429) hydrogen bonds : angle 4.54036 ( 1185) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 37 ILE cc_start: 0.8081 (mt) cc_final: 0.7814 (mt) REVERT: R 103 TRP cc_start: 0.7215 (t60) cc_final: 0.6983 (t60) REVERT: R 130 GLN cc_start: 0.8223 (tp40) cc_final: 0.7962 (tm-30) REVERT: R 158 TRP cc_start: 0.7427 (OUTLIER) cc_final: 0.5338 (t60) REVERT: R 179 LYS cc_start: 0.5708 (pttm) cc_final: 0.4561 (ptmt) REVERT: R 426 LEU cc_start: 0.8312 (tt) cc_final: 0.7879 (mt) REVERT: R 436 MET cc_start: 0.8412 (tpp) cc_final: 0.7945 (mmp) REVERT: R 481 ARG cc_start: 0.8789 (mtt90) cc_final: 0.7915 (tpt170) REVERT: B 32 GLN cc_start: 0.7904 (tt0) cc_final: 0.7225 (tm-30) REVERT: B 75 GLN cc_start: 0.8676 (tt0) cc_final: 0.8457 (tt0) REVERT: B 137 ARG cc_start: 0.7235 (mmt-90) cc_final: 0.6762 (mmm-85) REVERT: B 217 MET cc_start: 0.6917 (tmm) cc_final: 0.6533 (tmm) REVERT: B 219 ARG cc_start: 0.8167 (mmt90) cc_final: 0.7773 (mmt180) REVERT: B 228 ASP cc_start: 0.7675 (m-30) cc_final: 0.7347 (m-30) REVERT: B 234 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.7863 (m-80) REVERT: B 254 ASP cc_start: 0.8101 (t70) cc_final: 0.7647 (t70) REVERT: B 297 TRP cc_start: 0.7640 (m100) cc_final: 0.7069 (m-10) REVERT: G 32 LYS cc_start: 0.8356 (ttmm) cc_final: 0.7970 (ttpp) REVERT: G 46 LYS cc_start: 0.9327 (mptt) cc_final: 0.8860 (tptp) REVERT: A 9 ASP cc_start: 0.8372 (m-30) cc_final: 0.8095 (m-30) REVERT: A 57 LYS cc_start: 0.8366 (tttt) cc_final: 0.8124 (mttp) REVERT: A 234 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6908 (mt-10) REVERT: A 265 GLN cc_start: 0.8177 (mt0) cc_final: 0.7812 (mt0) REVERT: A 266 ASN cc_start: 0.9172 (t0) cc_final: 0.8928 (t0) REVERT: A 275 LYS cc_start: 0.8331 (tttp) cc_final: 0.7937 (tttp) REVERT: A 316 LEU cc_start: 0.7748 (mt) cc_final: 0.7228 (mp) REVERT: A 333 ASP cc_start: 0.2956 (OUTLIER) cc_final: 0.1944 (t0) REVERT: A 350 GLN cc_start: 0.7383 (tp40) cc_final: 0.6594 (mm110) REVERT: C 34 MET cc_start: 0.8288 (mtt) cc_final: 0.7997 (mtp) REVERT: C 73 ASP cc_start: 0.7132 (t0) cc_final: 0.6653 (t0) REVERT: C 113 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8285 (tp40) REVERT: C 153 GLU cc_start: 0.8450 (tp30) cc_final: 0.8109 (tp30) REVERT: C 195 LEU cc_start: 0.7255 (mp) cc_final: 0.6853 (mt) REVERT: C 202 ARG cc_start: 0.7303 (mtm-85) cc_final: 0.6984 (mtp180) REVERT: C 218 ARG cc_start: 0.8414 (ttm-80) cc_final: 0.7729 (mpp80) REVERT: C 234 GLU cc_start: 0.7671 (pt0) cc_final: 0.7082 (pm20) outliers start: 35 outliers final: 26 residues processed: 247 average time/residue: 0.1092 time to fit residues: 36.4816 Evaluate side-chains 246 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 169 MET Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 421 MET Chi-restraints excluded: chain R residue 429 ILE Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 451 MET Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain A residue 63 HIS Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 50 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 48 optimal weight: 0.0170 chunk 35 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.149045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.112836 restraints weight = 14624.274| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.89 r_work: 0.3388 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9185 Z= 0.130 Angle : 0.665 10.902 12435 Z= 0.339 Chirality : 0.043 0.163 1393 Planarity : 0.004 0.061 1568 Dihedral : 4.449 26.944 1239 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.15 % Allowed : 18.92 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.25), residues: 1115 helix: 1.19 (0.27), residues: 372 sheet: -0.52 (0.31), residues: 272 loop : -0.46 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 160 TYR 0.018 0.001 TYR C 228 PHE 0.030 0.001 PHE R 435 TRP 0.021 0.001 TRP B 211 HIS 0.004 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9181) covalent geometry : angle 0.66392 (12427) SS BOND : bond 0.00419 ( 4) SS BOND : angle 1.37579 ( 8) hydrogen bonds : bond 0.03529 ( 429) hydrogen bonds : angle 4.54006 ( 1185) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 37 ILE cc_start: 0.8006 (mt) cc_final: 0.7730 (mt) REVERT: R 103 TRP cc_start: 0.7186 (t60) cc_final: 0.6700 (t60) REVERT: R 130 GLN cc_start: 0.8246 (tp40) cc_final: 0.7946 (tm-30) REVERT: R 179 LYS cc_start: 0.5672 (pttm) cc_final: 0.5176 (ptmt) REVERT: R 426 LEU cc_start: 0.8279 (tt) cc_final: 0.7927 (mp) REVERT: R 436 MET cc_start: 0.8404 (tpp) cc_final: 0.7958 (mmp) REVERT: R 481 ARG cc_start: 0.8775 (mtt90) cc_final: 0.7847 (tpt90) REVERT: B 32 GLN cc_start: 0.7899 (tt0) cc_final: 0.7214 (tm-30) REVERT: B 57 LYS cc_start: 0.8785 (mtmt) cc_final: 0.8267 (mtpt) REVERT: B 137 ARG cc_start: 0.7298 (mmt-90) cc_final: 0.6816 (mmm-85) REVERT: B 215 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7628 (mp0) REVERT: B 219 ARG cc_start: 0.8081 (mmt90) cc_final: 0.7726 (mmt180) REVERT: B 228 ASP cc_start: 0.7603 (m-30) cc_final: 0.7275 (m-30) REVERT: B 234 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: B 254 ASP cc_start: 0.8065 (t70) cc_final: 0.7621 (t70) REVERT: B 297 TRP cc_start: 0.7622 (m100) cc_final: 0.6947 (m-10) REVERT: G 32 LYS cc_start: 0.8362 (ttmm) cc_final: 0.8044 (ttpp) REVERT: G 46 LYS cc_start: 0.9328 (mptt) cc_final: 0.8859 (tptp) REVERT: A 9 ASP cc_start: 0.8351 (m-30) cc_final: 0.8070 (m-30) REVERT: A 57 LYS cc_start: 0.8359 (tttt) cc_final: 0.8118 (mttp) REVERT: A 234 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7022 (mt-10) REVERT: A 265 GLN cc_start: 0.8180 (mt0) cc_final: 0.7804 (mt0) REVERT: A 266 ASN cc_start: 0.9182 (t0) cc_final: 0.8918 (t0) REVERT: A 275 LYS cc_start: 0.8252 (tttp) cc_final: 0.7846 (tttp) REVERT: A 315 ASP cc_start: 0.8821 (m-30) cc_final: 0.8406 (m-30) REVERT: A 316 LEU cc_start: 0.7669 (mt) cc_final: 0.7152 (mp) REVERT: A 337 ILE cc_start: 0.8364 (tt) cc_final: 0.8145 (mm) REVERT: A 346 ASP cc_start: 0.8100 (m-30) cc_final: 0.7496 (t70) REVERT: A 350 GLN cc_start: 0.7321 (tp40) cc_final: 0.6554 (mm110) REVERT: C 3 GLN cc_start: 0.7528 (tp-100) cc_final: 0.6629 (mm-40) REVERT: C 73 ASP cc_start: 0.7168 (t0) cc_final: 0.6573 (t0) REVERT: C 113 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8267 (tp40) REVERT: C 153 GLU cc_start: 0.8471 (tp30) cc_final: 0.8153 (tp30) REVERT: C 195 LEU cc_start: 0.7233 (mp) cc_final: 0.6864 (mt) REVERT: C 202 ARG cc_start: 0.7299 (mtm-85) cc_final: 0.6984 (mtp180) REVERT: C 218 ARG cc_start: 0.8443 (ttm-80) cc_final: 0.7716 (mpp80) REVERT: C 234 GLU cc_start: 0.7591 (pt0) cc_final: 0.7012 (pm20) outliers start: 31 outliers final: 27 residues processed: 247 average time/residue: 0.1005 time to fit residues: 33.7703 Evaluate side-chains 248 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 169 MET Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 429 ILE Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 451 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain A residue 63 HIS Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 95 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 416 GLN B 6 GLN C 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.146517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.111663 restraints weight = 14287.163| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.80 r_work: 0.3376 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9185 Z= 0.150 Angle : 0.703 10.867 12435 Z= 0.356 Chirality : 0.044 0.201 1393 Planarity : 0.004 0.063 1568 Dihedral : 4.462 26.488 1239 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.36 % Allowed : 19.02 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.25), residues: 1115 helix: 1.15 (0.27), residues: 372 sheet: -0.58 (0.31), residues: 272 loop : -0.48 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 160 TYR 0.025 0.002 TYR A 295 PHE 0.032 0.002 PHE R 435 TRP 0.018 0.001 TRP B 211 HIS 0.004 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9181) covalent geometry : angle 0.70226 (12427) SS BOND : bond 0.00467 ( 4) SS BOND : angle 1.35316 ( 8) hydrogen bonds : bond 0.03591 ( 429) hydrogen bonds : angle 4.57266 ( 1185) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 37 ILE cc_start: 0.8069 (mt) cc_final: 0.7785 (mt) REVERT: R 83 MET cc_start: 0.8218 (mmm) cc_final: 0.7960 (mmt) REVERT: R 130 GLN cc_start: 0.8185 (tp40) cc_final: 0.7843 (tm-30) REVERT: R 179 LYS cc_start: 0.5830 (pttm) cc_final: 0.5289 (ptmt) REVERT: R 181 GLU cc_start: 0.5059 (OUTLIER) cc_final: 0.4643 (tp30) REVERT: R 426 LEU cc_start: 0.8307 (tt) cc_final: 0.7968 (mp) REVERT: R 436 MET cc_start: 0.8463 (tpp) cc_final: 0.8043 (mmp) REVERT: R 481 ARG cc_start: 0.8735 (mtt90) cc_final: 0.7830 (tpt90) REVERT: B 6 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8537 (pp30) REVERT: B 32 GLN cc_start: 0.7921 (tt0) cc_final: 0.7235 (tm-30) REVERT: B 57 LYS cc_start: 0.8829 (mtmt) cc_final: 0.8333 (mtpt) REVERT: B 137 ARG cc_start: 0.7326 (mmt-90) cc_final: 0.6817 (mmm-85) REVERT: B 215 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7436 (mp0) REVERT: B 219 ARG cc_start: 0.8140 (mmt90) cc_final: 0.7717 (mmt180) REVERT: B 228 ASP cc_start: 0.7646 (m-30) cc_final: 0.7297 (m-30) REVERT: B 234 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.8088 (m-10) REVERT: B 254 ASP cc_start: 0.8121 (t70) cc_final: 0.7651 (t70) REVERT: B 293 ASN cc_start: 0.7247 (m-40) cc_final: 0.6706 (p0) REVERT: B 297 TRP cc_start: 0.7655 (m100) cc_final: 0.7094 (m100) REVERT: G 20 LYS cc_start: 0.8940 (tppt) cc_final: 0.8691 (tppp) REVERT: G 32 LYS cc_start: 0.8380 (ttmm) cc_final: 0.8064 (ttpp) REVERT: G 46 LYS cc_start: 0.9305 (mptt) cc_final: 0.8854 (tptp) REVERT: A 9 ASP cc_start: 0.8398 (m-30) cc_final: 0.8112 (m-30) REVERT: A 57 LYS cc_start: 0.8390 (tttt) cc_final: 0.8144 (mttp) REVERT: A 234 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7052 (mt-10) REVERT: A 237 GLN cc_start: 0.7110 (tm-30) cc_final: 0.6900 (tm-30) REVERT: A 265 GLN cc_start: 0.8187 (mt0) cc_final: 0.7821 (mt0) REVERT: A 266 ASN cc_start: 0.9186 (t0) cc_final: 0.8925 (t0) REVERT: A 275 LYS cc_start: 0.8357 (tttp) cc_final: 0.7968 (tttp) REVERT: A 311 LYS cc_start: 0.8354 (tptm) cc_final: 0.7986 (tptt) REVERT: A 315 ASP cc_start: 0.8772 (m-30) cc_final: 0.8145 (m-30) REVERT: A 333 ASP cc_start: 0.3063 (OUTLIER) cc_final: 0.1959 (t0) REVERT: A 337 ILE cc_start: 0.8421 (tt) cc_final: 0.8209 (mm) REVERT: A 350 GLN cc_start: 0.7414 (tp40) cc_final: 0.6618 (mm110) REVERT: C 3 GLN cc_start: 0.7484 (tp-100) cc_final: 0.6533 (mm-40) REVERT: C 73 ASP cc_start: 0.7143 (t0) cc_final: 0.6542 (t0) REVERT: C 113 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8301 (tp40) REVERT: C 153 GLU cc_start: 0.8493 (tp30) cc_final: 0.8122 (tp30) REVERT: C 202 ARG cc_start: 0.7344 (mtm-85) cc_final: 0.7007 (mtp180) REVERT: C 218 ARG cc_start: 0.8464 (ttm-80) cc_final: 0.7731 (mpp80) REVERT: C 230 MET cc_start: 0.7965 (ttp) cc_final: 0.7455 (ttp) REVERT: C 234 GLU cc_start: 0.7605 (pt0) cc_final: 0.7106 (pm20) outliers start: 33 outliers final: 28 residues processed: 239 average time/residue: 0.1003 time to fit residues: 32.5533 Evaluate side-chains 250 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 218 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 169 MET Chi-restraints excluded: chain R residue 181 GLU Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 429 ILE Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 451 MET Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain A residue 63 HIS Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 4 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 57 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.147751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.112998 restraints weight = 14384.547| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 3.73 r_work: 0.3398 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9185 Z= 0.136 Angle : 0.699 11.157 12435 Z= 0.352 Chirality : 0.043 0.187 1393 Planarity : 0.004 0.061 1568 Dihedral : 4.436 27.032 1239 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.26 % Allowed : 19.02 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.25), residues: 1115 helix: 1.12 (0.27), residues: 372 sheet: -0.59 (0.30), residues: 272 loop : -0.49 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 160 TYR 0.019 0.001 TYR C 228 PHE 0.034 0.002 PHE R 435 TRP 0.030 0.001 TRP R 103 HIS 0.004 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9181) covalent geometry : angle 0.69811 (12427) SS BOND : bond 0.00398 ( 4) SS BOND : angle 1.20753 ( 8) hydrogen bonds : bond 0.03514 ( 429) hydrogen bonds : angle 4.53777 ( 1185) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 37 ILE cc_start: 0.8097 (mt) cc_final: 0.7810 (mt) REVERT: R 81 MET cc_start: 0.8059 (mtt) cc_final: 0.7650 (ptp) REVERT: R 130 GLN cc_start: 0.8159 (tp40) cc_final: 0.7821 (tm-30) REVERT: R 179 LYS cc_start: 0.5878 (pttm) cc_final: 0.5159 (tttt) REVERT: R 426 LEU cc_start: 0.8280 (tt) cc_final: 0.7956 (mp) REVERT: R 436 MET cc_start: 0.8463 (tpp) cc_final: 0.8060 (mmp) REVERT: R 481 ARG cc_start: 0.8743 (mtt90) cc_final: 0.7837 (tpt90) REVERT: B 6 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8552 (pp30) REVERT: B 32 GLN cc_start: 0.7916 (tt0) cc_final: 0.7226 (tm-30) REVERT: B 215 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7640 (mp0) REVERT: B 219 ARG cc_start: 0.8086 (mmt90) cc_final: 0.7846 (mmt180) REVERT: B 228 ASP cc_start: 0.7587 (m-30) cc_final: 0.7236 (m-30) REVERT: B 234 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.7941 (m-80) REVERT: B 254 ASP cc_start: 0.8067 (t70) cc_final: 0.7611 (t70) REVERT: B 293 ASN cc_start: 0.7252 (m-40) cc_final: 0.6728 (p0) REVERT: B 297 TRP cc_start: 0.7690 (m100) cc_final: 0.7078 (m100) REVERT: G 20 LYS cc_start: 0.8979 (tppt) cc_final: 0.8722 (tppp) REVERT: G 32 LYS cc_start: 0.8339 (ttmm) cc_final: 0.7984 (ttpp) REVERT: G 46 LYS cc_start: 0.9291 (mptt) cc_final: 0.8845 (mmmt) REVERT: A 9 ASP cc_start: 0.8385 (m-30) cc_final: 0.8105 (m-30) REVERT: A 57 LYS cc_start: 0.8382 (tttt) cc_final: 0.8144 (mttp) REVERT: A 234 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7047 (mt-10) REVERT: A 265 GLN cc_start: 0.8180 (mt0) cc_final: 0.7815 (mt0) REVERT: A 266 ASN cc_start: 0.9178 (t0) cc_final: 0.8919 (t0) REVERT: A 275 LYS cc_start: 0.8251 (tttp) cc_final: 0.7852 (tttp) REVERT: A 311 LYS cc_start: 0.8351 (tptm) cc_final: 0.8002 (tptt) REVERT: A 315 ASP cc_start: 0.8766 (m-30) cc_final: 0.8250 (m-30) REVERT: A 350 GLN cc_start: 0.7331 (tp40) cc_final: 0.6521 (mm110) REVERT: C 3 GLN cc_start: 0.7473 (tp-100) cc_final: 0.6544 (mm-40) REVERT: C 73 ASP cc_start: 0.7103 (t0) cc_final: 0.6498 (t0) REVERT: C 113 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8274 (tp40) REVERT: C 153 GLU cc_start: 0.8510 (tp30) cc_final: 0.8155 (tp30) REVERT: C 195 LEU cc_start: 0.7192 (mp) cc_final: 0.6865 (mt) REVERT: C 218 ARG cc_start: 0.8432 (ttm-80) cc_final: 0.8074 (mmm160) REVERT: C 230 MET cc_start: 0.7939 (ttp) cc_final: 0.7433 (ttp) REVERT: C 234 GLU cc_start: 0.7610 (pt0) cc_final: 0.7123 (pm20) outliers start: 32 outliers final: 29 residues processed: 241 average time/residue: 0.0999 time to fit residues: 32.8233 Evaluate side-chains 244 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 169 MET Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 429 ILE Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 451 MET Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain A residue 63 HIS Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.147311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.112056 restraints weight = 14248.596| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 3.81 r_work: 0.3381 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9185 Z= 0.150 Angle : 0.711 11.016 12435 Z= 0.359 Chirality : 0.044 0.190 1393 Planarity : 0.005 0.073 1568 Dihedral : 4.458 26.371 1239 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.36 % Allowed : 18.92 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.25), residues: 1115 helix: 1.12 (0.27), residues: 372 sheet: -0.64 (0.30), residues: 272 loop : -0.49 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 160 TYR 0.020 0.001 TYR C 228 PHE 0.035 0.002 PHE R 435 TRP 0.025 0.001 TRP R 103 HIS 0.003 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9181) covalent geometry : angle 0.71076 (12427) SS BOND : bond 0.00454 ( 4) SS BOND : angle 1.24145 ( 8) hydrogen bonds : bond 0.03465 ( 429) hydrogen bonds : angle 4.52500 ( 1185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2355.86 seconds wall clock time: 41 minutes 6.57 seconds (2466.57 seconds total)