Starting phenix.real_space_refine on Fri Aug 22 21:29:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hj0_33482/08_2025/8hj0_33482.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hj0_33482/08_2025/8hj0_33482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hj0_33482/08_2025/8hj0_33482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hj0_33482/08_2025/8hj0_33482.map" model { file = "/net/cci-nas-00/data/ceres_data/8hj0_33482/08_2025/8hj0_33482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hj0_33482/08_2025/8hj0_33482.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5250 2.51 5 N 1427 2.21 5 O 1531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8260 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1966 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2297 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 2.21, per 1000 atoms: 0.27 Number of scatterers: 8260 At special positions: 0 Unit cell: (88.4, 102.96, 127.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1531 8.00 N 1427 7.00 C 5250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS R 122 " - pdb=" SG CYS R 149 " distance=2.05 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: 0.69 Conformation dependent library (CDL) restraints added in 455.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1966 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 42.5% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 4.105A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 302 removed outlier: 3.905A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 removed outlier: 3.821A pdb=" N ALA A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 306' Processing helix chain 'A' and resid 322 through 342 removed outlier: 3.836A pdb=" N ARG A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 382 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.986A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 removed outlier: 4.887A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.507A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.755A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 26 through 56 removed outlier: 4.382A pdb=" N ILE R 34 " --> pdb=" O LEU R 30 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER R 44 " --> pdb=" O VAL R 40 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY R 45 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASN R 46 " --> pdb=" O ILE R 42 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE R 47 " --> pdb=" O ILE R 43 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE R 48 " --> pdb=" O SER R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 61 Processing helix chain 'R' and resid 62 through 80 removed outlier: 4.079A pdb=" N TYR R 66 " --> pdb=" O HIS R 62 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE R 67 " --> pdb=" O THR R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 91 removed outlier: 4.174A pdb=" N SER R 86 " --> pdb=" O CYS R 82 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS R 91 " --> pdb=" O LEU R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 133 removed outlier: 4.286A pdb=" N ILE R 104 " --> pdb=" O LEU R 100 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL R 111 " --> pdb=" O PHE R 107 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER R 114 " --> pdb=" O SER R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 141 Processing helix chain 'R' and resid 142 through 161 removed outlier: 3.683A pdb=" N PHE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 165 Processing helix chain 'R' and resid 188 through 197 Processing helix chain 'R' and resid 199 through 231 removed outlier: 4.139A pdb=" N ALA R 203 " --> pdb=" O LEU R 199 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA R 204 " --> pdb=" O TYR R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 278 Proline residue: R 267 - end of helix Processing helix chain 'R' and resid 282 through 295 Processing helix chain 'R' and resid 298 through 308 removed outlier: 3.747A pdb=" N VAL R 302 " --> pdb=" O PHE R 298 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE R 303 " --> pdb=" O CYS R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 322 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.791A pdb=" N VAL A 214 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.581A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.517A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.402A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 4.066A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.791A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.004A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.030A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 4.136A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1179 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: 1.36 Time building geometry restraints manager: 0.93 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: 2702 1.35 - 1.48: 2214 1.48 - 1.62: 3457 1.62 - 1.75: 0 1.75 - 1.88: 70 Bond restraints: 8443 Sorted by residual: bond pdb=" CB CYS R 149 " pdb=" SG CYS R 149 " ideal model delta sigma weight residual 1.808 1.877 -0.069 3.30e-02 9.18e+02 4.38e+00 bond pdb=" CA ALA B 328 " pdb=" CB ALA B 328 " ideal model delta sigma weight residual 1.526 1.494 0.032 1.70e-02 3.46e+03 3.61e+00 bond pdb=" C VAL R 84 " pdb=" N PRO R 85 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.46e+00 bond pdb=" C ASN R 300 " pdb=" N PRO R 301 " ideal model delta sigma weight residual 1.335 1.361 -0.025 1.36e-02 5.41e+03 3.43e+00 bond pdb=" CB ASP R 126 " pdb=" CG ASP R 126 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.38e+00 ... (remaining 8438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 10889 2.21 - 4.41: 474 4.41 - 6.62: 59 6.62 - 8.82: 18 8.82 - 11.03: 9 Bond angle restraints: 11449 Sorted by residual: angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 121.54 131.27 -9.73 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C GLU R 97 " pdb=" N GLU R 98 " pdb=" CA GLU R 98 " ideal model delta sigma weight residual 121.54 130.46 -8.92 1.91e+00 2.74e-01 2.18e+01 angle pdb=" CA ASP R 126 " pdb=" CB ASP R 126 " pdb=" CG ASP R 126 " ideal model delta sigma weight residual 112.60 116.75 -4.15 1.00e+00 1.00e+00 1.72e+01 angle pdb=" CB ARG R 256 " pdb=" CG ARG R 256 " pdb=" CD ARG R 256 " ideal model delta sigma weight residual 111.30 119.61 -8.31 2.30e+00 1.89e-01 1.30e+01 angle pdb=" N CYS N 96 " pdb=" CA CYS N 96 " pdb=" C CYS N 96 " ideal model delta sigma weight residual 110.48 105.27 5.21 1.48e+00 4.57e-01 1.24e+01 ... (remaining 11444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4488 17.97 - 35.94: 410 35.94 - 53.91: 80 53.91 - 71.88: 13 71.88 - 89.84: 11 Dihedral angle restraints: 5002 sinusoidal: 1963 harmonic: 3039 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 14.33 78.67 1 1.00e+01 1.00e-02 7.71e+01 dihedral pdb=" CB CYS R 122 " pdb=" SG CYS R 122 " pdb=" SG CYS R 149 " pdb=" CB CYS R 149 " ideal model delta sinusoidal sigma weight residual 93.00 159.02 -66.02 1 1.00e+01 1.00e-02 5.70e+01 dihedral pdb=" CA SER R 307 " pdb=" C SER R 307 " pdb=" N ASP R 308 " pdb=" CA ASP R 308 " ideal model delta harmonic sigma weight residual -180.00 -156.42 -23.58 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 4999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1091 0.078 - 0.155: 171 0.155 - 0.232: 21 0.232 - 0.310: 1 0.310 - 0.387: 3 Chirality restraints: 1287 Sorted by residual: chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CB ILE N 51 " pdb=" CA ILE N 51 " pdb=" CG1 ILE N 51 " pdb=" CG2 ILE N 51 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CB ILE B 269 " pdb=" CA ILE B 269 " pdb=" CG1 ILE B 269 " pdb=" CG2 ILE B 269 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 1284 not shown) Planarity restraints: 1457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN N 13 " -0.077 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO N 14 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO N 14 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO N 14 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 215 " -0.024 2.00e-02 2.50e+03 2.69e-02 1.26e+01 pdb=" CG PHE R 215 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE R 215 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE R 215 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE R 215 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE R 215 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE R 215 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 124 " -0.014 2.00e-02 2.50e+03 2.90e-02 8.40e+00 pdb=" C SER R 124 " 0.050 2.00e-02 2.50e+03 pdb=" O SER R 124 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE R 125 " -0.017 2.00e-02 2.50e+03 ... (remaining 1454 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1882 2.78 - 3.31: 7840 3.31 - 3.84: 14430 3.84 - 4.37: 17211 4.37 - 4.90: 28894 Nonbonded interactions: 70257 Sorted by model distance: nonbonded pdb=" O VAL R 83 " pdb=" OG SER R 86 " model vdw 2.254 3.040 nonbonded pdb=" OG SER B 275 " pdb=" O SER B 316 " model vdw 2.256 3.040 nonbonded pdb=" O CYS B 204 " pdb=" OH TYR N 117 " model vdw 2.259 3.040 nonbonded pdb=" O TRP R 180 " pdb=" OG SER R 184 " model vdw 2.259 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.266 3.040 ... (remaining 70252 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.750 Find NCS groups from input model: 0.030 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 8447 Z= 0.265 Angle : 1.074 11.028 11457 Z= 0.600 Chirality : 0.058 0.387 1287 Planarity : 0.008 0.117 1457 Dihedral : 14.888 89.844 3024 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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 aren not related in a simple way. whole: -1.89 (0.24), residues: 1029 helix: -0.90 (0.24), residues: 401 sheet: -0.79 (0.33), residues: 214 loop : -1.73 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG B 52 TYR 0.021 0.003 TYR A 348 PHE 0.063 0.004 PHE R 215 TRP 0.018 0.003 TRP R 180 HIS 0.015 0.002 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00564 ( 8443) covalent geometry : angle 1.07011 (11449) SS BOND : bond 0.01139 ( 4) SS BOND : angle 3.59672 ( 8) hydrogen bonds : bond 0.15475 ( 412) hydrogen bonds : angle 7.19070 ( 1179) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: B 111 TYR cc_start: 0.6383 (m-80) cc_final: 0.6142 (m-80) REVERT: G 21 MET cc_start: 0.4214 (mmm) cc_final: 0.2584 (mtm) REVERT: R 31 GLU cc_start: 0.5584 (mm-30) cc_final: 0.4817 (mm-30) REVERT: R 152 LEU cc_start: 0.6932 (mt) cc_final: 0.6605 (mp) REVERT: R 287 PHE cc_start: 0.5795 (t80) cc_final: 0.5311 (t80) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1170 time to fit residues: 30.8727 Evaluate side-chains 154 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.1980 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 35 ASN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.234165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.200924 restraints weight = 8724.700| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 1.77 r_work: 0.4153 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4019 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8447 Z= 0.131 Angle : 0.592 5.822 11457 Z= 0.318 Chirality : 0.043 0.149 1287 Planarity : 0.005 0.084 1457 Dihedral : 5.305 21.365 1136 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.44 % Allowed : 8.75 % Favored : 89.81 % 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 aren not related in a simple way. whole: -0.99 (0.25), residues: 1029 helix: 0.29 (0.25), residues: 410 sheet: -0.68 (0.33), residues: 217 loop : -1.55 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 67 TYR 0.010 0.001 TYR B 264 PHE 0.018 0.002 PHE R 272 TRP 0.016 0.002 TRP B 169 HIS 0.009 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8443) covalent geometry : angle 0.59008 (11449) SS BOND : bond 0.00799 ( 4) SS BOND : angle 1.90523 ( 8) hydrogen bonds : bond 0.04269 ( 412) hydrogen bonds : angle 5.10094 ( 1179) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.324 Fit side-chains REVERT: A 60 MET cc_start: 0.6928 (mpp) cc_final: 0.6441 (mpp) REVERT: A 360 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6383 (mp0) REVERT: B 42 ARG cc_start: 0.6363 (mtp180) cc_final: 0.5904 (tpt-90) REVERT: B 111 TYR cc_start: 0.7078 (m-80) cc_final: 0.6825 (m-80) REVERT: B 118 ASP cc_start: 0.6290 (t70) cc_final: 0.5801 (t0) REVERT: B 325 MET cc_start: 0.7393 (mmt) cc_final: 0.6901 (mmp) REVERT: G 21 MET cc_start: 0.4022 (mmm) cc_final: 0.2472 (mtt) REVERT: R 152 LEU cc_start: 0.7173 (mt) cc_final: 0.6693 (mp) REVERT: R 194 PHE cc_start: 0.6644 (m-80) cc_final: 0.6420 (m-80) outliers start: 13 outliers final: 8 residues processed: 183 average time/residue: 0.1226 time to fit residues: 29.1138 Evaluate side-chains 161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 153 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 123 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 361 ASN B 17 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 295 ASN R 69 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.226199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.192167 restraints weight = 8756.006| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 1.80 r_work: 0.4080 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3945 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8447 Z= 0.186 Angle : 0.621 6.347 11457 Z= 0.334 Chirality : 0.045 0.197 1287 Planarity : 0.005 0.072 1457 Dihedral : 5.253 21.992 1136 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.99 % Allowed : 12.96 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.25), residues: 1029 helix: 0.53 (0.25), residues: 408 sheet: -0.79 (0.32), residues: 219 loop : -1.38 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 52 TYR 0.015 0.002 TYR B 264 PHE 0.015 0.002 PHE R 272 TRP 0.015 0.002 TRP B 169 HIS 0.007 0.002 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 8443) covalent geometry : angle 0.61881 (11449) SS BOND : bond 0.01044 ( 4) SS BOND : angle 2.25874 ( 8) hydrogen bonds : bond 0.04301 ( 412) hydrogen bonds : angle 4.97830 ( 1179) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.335 Fit side-chains REVERT: A 20 ARG cc_start: 0.6376 (mmt90) cc_final: 0.6131 (mtm-85) REVERT: A 60 MET cc_start: 0.6832 (OUTLIER) cc_final: 0.6367 (mpp) REVERT: A 256 LEU cc_start: 0.8295 (mt) cc_final: 0.8065 (mt) REVERT: A 360 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6418 (mp0) REVERT: B 118 ASP cc_start: 0.6563 (t70) cc_final: 0.5995 (t70) REVERT: B 247 ASP cc_start: 0.7746 (p0) cc_final: 0.7337 (p0) REVERT: B 254 ASP cc_start: 0.6957 (t70) cc_final: 0.6726 (t0) REVERT: B 290 ASP cc_start: 0.7641 (m-30) cc_final: 0.7439 (m-30) REVERT: R 152 LEU cc_start: 0.7334 (mt) cc_final: 0.6796 (mp) outliers start: 27 outliers final: 19 residues processed: 185 average time/residue: 0.1150 time to fit residues: 28.0710 Evaluate side-chains 172 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 36 optimal weight: 0.4980 chunk 90 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.228251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.194224 restraints weight = 8845.516| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 1.81 r_work: 0.4066 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3932 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8447 Z= 0.150 Angle : 0.585 5.819 11457 Z= 0.313 Chirality : 0.044 0.237 1287 Planarity : 0.004 0.066 1457 Dihedral : 4.999 21.806 1136 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.99 % Allowed : 14.84 % Favored : 82.17 % 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 aren not related in a simple way. whole: -0.58 (0.25), residues: 1029 helix: 0.85 (0.25), residues: 407 sheet: -0.77 (0.33), residues: 221 loop : -1.36 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 52 TYR 0.014 0.002 TYR B 264 PHE 0.016 0.002 PHE R 272 TRP 0.013 0.001 TRP B 169 HIS 0.008 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8443) covalent geometry : angle 0.58283 (11449) SS BOND : bond 0.00870 ( 4) SS BOND : angle 2.01295 ( 8) hydrogen bonds : bond 0.03971 ( 412) hydrogen bonds : angle 4.79948 ( 1179) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.6894 (OUTLIER) cc_final: 0.6438 (mpp) REVERT: A 256 LEU cc_start: 0.8283 (mt) cc_final: 0.8032 (mt) REVERT: A 360 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6450 (mp0) REVERT: B 43 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7621 (mp) REVERT: B 118 ASP cc_start: 0.6546 (t70) cc_final: 0.6078 (t70) REVERT: B 254 ASP cc_start: 0.6951 (t70) cc_final: 0.6684 (t0) REVERT: B 275 SER cc_start: 0.8322 (t) cc_final: 0.7610 (m) REVERT: N 120 GLN cc_start: 0.6241 (mm-40) cc_final: 0.5978 (mm-40) REVERT: R 231 ARG cc_start: 0.6771 (tpm170) cc_final: 0.6416 (tpt-90) outliers start: 27 outliers final: 21 residues processed: 178 average time/residue: 0.1165 time to fit residues: 27.3024 Evaluate side-chains 180 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 159 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 86 optimal weight: 0.9980 chunk 49 optimal weight: 0.0370 chunk 70 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.230013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.195980 restraints weight = 8872.046| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 1.84 r_work: 0.4069 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3932 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8447 Z= 0.132 Angle : 0.560 7.597 11457 Z= 0.299 Chirality : 0.043 0.239 1287 Planarity : 0.004 0.053 1457 Dihedral : 4.765 21.898 1136 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.21 % Allowed : 16.39 % Favored : 80.40 % 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 aren not related in a simple way. whole: -0.35 (0.26), residues: 1029 helix: 1.06 (0.25), residues: 409 sheet: -0.67 (0.33), residues: 220 loop : -1.28 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 52 TYR 0.013 0.001 TYR B 264 PHE 0.018 0.002 PHE R 194 TRP 0.019 0.001 TRP A 271 HIS 0.007 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8443) covalent geometry : angle 0.55834 (11449) SS BOND : bond 0.00766 ( 4) SS BOND : angle 1.82943 ( 8) hydrogen bonds : bond 0.03727 ( 412) hydrogen bonds : angle 4.60950 ( 1179) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6354 (mt0) cc_final: 0.6031 (mp10) REVERT: A 239 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7751 (t0) REVERT: A 256 LEU cc_start: 0.8283 (mt) cc_final: 0.8021 (mt) REVERT: A 270 ARG cc_start: 0.7642 (tmt-80) cc_final: 0.7442 (tmt-80) REVERT: A 360 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6417 (mp0) REVERT: B 43 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7589 (mp) REVERT: B 118 ASP cc_start: 0.6490 (t70) cc_final: 0.6052 (t70) REVERT: B 247 ASP cc_start: 0.7738 (p0) cc_final: 0.7295 (p0) REVERT: B 275 SER cc_start: 0.8192 (t) cc_final: 0.7502 (m) REVERT: G 21 MET cc_start: 0.3890 (mmm) cc_final: 0.3640 (mmm) REVERT: N 120 GLN cc_start: 0.6174 (mm-40) cc_final: 0.5933 (mm-40) REVERT: R 178 PHE cc_start: 0.4951 (t80) cc_final: 0.4675 (t80) REVERT: R 231 ARG cc_start: 0.6630 (tpm170) cc_final: 0.6407 (tpt-90) outliers start: 29 outliers final: 20 residues processed: 188 average time/residue: 0.1111 time to fit residues: 27.6694 Evaluate side-chains 185 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 177 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 63 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.230409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.196571 restraints weight = 8731.204| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 1.82 r_work: 0.4121 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3987 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8447 Z= 0.128 Angle : 0.560 7.074 11457 Z= 0.298 Chirality : 0.043 0.236 1287 Planarity : 0.004 0.050 1457 Dihedral : 4.654 21.796 1136 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.54 % Allowed : 17.28 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.26), residues: 1029 helix: 1.19 (0.25), residues: 415 sheet: -0.62 (0.33), residues: 220 loop : -1.25 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 67 TYR 0.011 0.001 TYR B 264 PHE 0.026 0.002 PHE R 287 TRP 0.015 0.001 TRP A 271 HIS 0.007 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8443) covalent geometry : angle 0.55829 (11449) SS BOND : bond 0.00730 ( 4) SS BOND : angle 1.78414 ( 8) hydrogen bonds : bond 0.03653 ( 412) hydrogen bonds : angle 4.53310 ( 1179) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6303 (mt0) cc_final: 0.5946 (mp10) REVERT: A 239 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7692 (t0) REVERT: A 270 ARG cc_start: 0.7755 (tmt-80) cc_final: 0.7491 (tmt-80) REVERT: A 326 ARG cc_start: 0.7252 (mtp-110) cc_final: 0.7033 (ttt-90) REVERT: A 346 ARG cc_start: 0.7046 (mpp80) cc_final: 0.6768 (mpp-170) REVERT: A 360 GLU cc_start: 0.6826 (mt-10) cc_final: 0.6382 (mp0) REVERT: B 43 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7545 (mp) REVERT: B 52 ARG cc_start: 0.7883 (ptp90) cc_final: 0.7680 (mtt90) REVERT: B 118 ASP cc_start: 0.6409 (t70) cc_final: 0.5956 (t70) REVERT: B 275 SER cc_start: 0.8293 (t) cc_final: 0.7600 (m) REVERT: G 21 MET cc_start: 0.4019 (mmm) cc_final: 0.3719 (mmm) REVERT: N 72 ARG cc_start: 0.7224 (ptm160) cc_final: 0.6866 (ptm160) REVERT: R 178 PHE cc_start: 0.4565 (t80) cc_final: 0.4238 (t80) REVERT: R 296 ASN cc_start: 0.6284 (p0) cc_final: 0.6015 (p0) outliers start: 32 outliers final: 25 residues processed: 181 average time/residue: 0.1104 time to fit residues: 26.4559 Evaluate side-chains 183 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 177 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 36 optimal weight: 8.9990 chunk 71 optimal weight: 0.0570 chunk 7 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.228639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.194468 restraints weight = 8848.709| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 1.83 r_work: 0.4108 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3973 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8447 Z= 0.144 Angle : 0.571 6.809 11457 Z= 0.304 Chirality : 0.044 0.220 1287 Planarity : 0.004 0.049 1457 Dihedral : 4.687 21.931 1136 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.77 % Allowed : 17.50 % Favored : 78.74 % 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 aren not related in a simple way. whole: -0.22 (0.26), residues: 1029 helix: 1.21 (0.25), residues: 415 sheet: -0.68 (0.33), residues: 220 loop : -1.23 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 67 TYR 0.011 0.001 TYR B 264 PHE 0.022 0.002 PHE R 287 TRP 0.014 0.001 TRP A 271 HIS 0.008 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8443) covalent geometry : angle 0.56882 (11449) SS BOND : bond 0.00810 ( 4) SS BOND : angle 1.95791 ( 8) hydrogen bonds : bond 0.03705 ( 412) hydrogen bonds : angle 4.58231 ( 1179) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6209 (mt0) cc_final: 0.5717 (mp10) REVERT: A 239 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.7811 (t0) REVERT: A 256 LEU cc_start: 0.8252 (mt) cc_final: 0.7973 (mt) REVERT: A 270 ARG cc_start: 0.7825 (tmt-80) cc_final: 0.7478 (tmt-80) REVERT: A 326 ARG cc_start: 0.7284 (mtp-110) cc_final: 0.7046 (ttt-90) REVERT: A 346 ARG cc_start: 0.7071 (mpp80) cc_final: 0.6799 (mpp-170) REVERT: A 360 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6340 (mp0) REVERT: B 43 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7595 (mp) REVERT: B 118 ASP cc_start: 0.6470 (t70) cc_final: 0.6019 (t70) REVERT: B 247 ASP cc_start: 0.7795 (p0) cc_final: 0.7358 (p0) REVERT: B 275 SER cc_start: 0.8227 (t) cc_final: 0.7514 (m) REVERT: G 21 MET cc_start: 0.3988 (mmm) cc_final: 0.3766 (mmm) REVERT: N 120 GLN cc_start: 0.6188 (mm-40) cc_final: 0.5924 (mm-40) REVERT: R 178 PHE cc_start: 0.4547 (t80) cc_final: 0.4216 (t80) REVERT: R 296 ASN cc_start: 0.6292 (p0) cc_final: 0.6073 (p0) outliers start: 34 outliers final: 28 residues processed: 186 average time/residue: 0.1085 time to fit residues: 26.6212 Evaluate side-chains 191 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 177 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.229741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.195771 restraints weight = 8761.466| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 1.82 r_work: 0.4108 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3973 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8447 Z= 0.137 Angle : 0.567 6.585 11457 Z= 0.301 Chirality : 0.044 0.226 1287 Planarity : 0.004 0.049 1457 Dihedral : 4.642 22.040 1136 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.99 % Allowed : 17.28 % Favored : 78.74 % 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 aren not related in a simple way. whole: -0.10 (0.26), residues: 1029 helix: 1.34 (0.25), residues: 409 sheet: -0.43 (0.35), residues: 204 loop : -1.28 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 67 TYR 0.011 0.001 TYR N 95 PHE 0.026 0.002 PHE R 194 TRP 0.014 0.001 TRP A 271 HIS 0.008 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8443) covalent geometry : angle 0.56495 (11449) SS BOND : bond 0.00783 ( 4) SS BOND : angle 1.89706 ( 8) hydrogen bonds : bond 0.03644 ( 412) hydrogen bonds : angle 4.56664 ( 1179) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6272 (mt0) cc_final: 0.5805 (mp10) REVERT: A 239 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.7800 (t0) REVERT: A 270 ARG cc_start: 0.7849 (tmt-80) cc_final: 0.7485 (tmt-80) REVERT: A 346 ARG cc_start: 0.7066 (mpp80) cc_final: 0.6787 (mpp-170) REVERT: A 360 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6342 (mp0) REVERT: B 43 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7581 (mp) REVERT: B 52 ARG cc_start: 0.7920 (ptp90) cc_final: 0.7661 (mtt90) REVERT: B 118 ASP cc_start: 0.6411 (t70) cc_final: 0.5982 (t70) REVERT: B 275 SER cc_start: 0.8217 (t) cc_final: 0.7506 (m) REVERT: G 21 MET cc_start: 0.3989 (mmm) cc_final: 0.3711 (mmm) REVERT: N 120 GLN cc_start: 0.6187 (mm-40) cc_final: 0.5920 (mm-40) REVERT: R 178 PHE cc_start: 0.4556 (t80) cc_final: 0.4235 (t80) REVERT: R 296 ASN cc_start: 0.6280 (p0) cc_final: 0.6062 (p0) outliers start: 36 outliers final: 31 residues processed: 186 average time/residue: 0.1059 time to fit residues: 26.2728 Evaluate side-chains 192 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 266 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 0.0170 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.231058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.197275 restraints weight = 8751.804| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 1.81 r_work: 0.4128 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3993 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8447 Z= 0.126 Angle : 0.570 10.828 11457 Z= 0.299 Chirality : 0.043 0.209 1287 Planarity : 0.004 0.052 1457 Dihedral : 4.523 21.891 1136 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.54 % Allowed : 18.05 % Favored : 78.41 % 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 aren not related in a simple way. whole: 0.01 (0.26), residues: 1029 helix: 1.43 (0.25), residues: 410 sheet: -0.37 (0.36), residues: 203 loop : -1.21 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 67 TYR 0.016 0.001 TYR N 117 PHE 0.030 0.002 PHE R 194 TRP 0.013 0.001 TRP A 271 HIS 0.008 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8443) covalent geometry : angle 0.56843 (11449) SS BOND : bond 0.00722 ( 4) SS BOND : angle 1.78362 ( 8) hydrogen bonds : bond 0.03543 ( 412) hydrogen bonds : angle 4.49740 ( 1179) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6046 (mt0) cc_final: 0.5684 (mp10) REVERT: A 239 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7753 (t0) REVERT: A 270 ARG cc_start: 0.7831 (tmt-80) cc_final: 0.7535 (tmt-80) REVERT: A 326 ARG cc_start: 0.7291 (mtp-110) cc_final: 0.7064 (ttt-90) REVERT: A 360 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6340 (mp0) REVERT: B 43 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7608 (mp) REVERT: B 52 ARG cc_start: 0.7900 (ptp90) cc_final: 0.7643 (mtt90) REVERT: B 118 ASP cc_start: 0.6341 (t70) cc_final: 0.5905 (t70) REVERT: B 247 ASP cc_start: 0.7765 (p0) cc_final: 0.7308 (p0) REVERT: B 275 SER cc_start: 0.8181 (t) cc_final: 0.7495 (m) REVERT: G 21 MET cc_start: 0.4094 (mmm) cc_final: 0.3808 (mmm) REVERT: G 28 ILE cc_start: 0.7269 (mm) cc_final: 0.7018 (mp) REVERT: N 120 GLN cc_start: 0.6154 (mm-40) cc_final: 0.5916 (mm-40) REVERT: R 178 PHE cc_start: 0.4550 (t80) cc_final: 0.4169 (t80) REVERT: R 275 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6676 (mt-10) REVERT: R 296 ASN cc_start: 0.6407 (p0) cc_final: 0.6180 (p0) outliers start: 32 outliers final: 27 residues processed: 180 average time/residue: 0.1128 time to fit residues: 26.6587 Evaluate side-chains 186 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 266 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 41 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 15 optimal weight: 0.0370 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.232803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.199288 restraints weight = 8673.735| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 1.81 r_work: 0.4149 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4014 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8447 Z= 0.115 Angle : 0.573 15.139 11457 Z= 0.296 Chirality : 0.043 0.190 1287 Planarity : 0.004 0.052 1457 Dihedral : 4.416 21.567 1136 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.10 % Allowed : 18.94 % Favored : 77.96 % 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 aren not related in a simple way. whole: 0.12 (0.26), residues: 1029 helix: 1.54 (0.26), residues: 410 sheet: -0.31 (0.35), residues: 206 loop : -1.20 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 67 TYR 0.014 0.001 TYR N 117 PHE 0.030 0.002 PHE R 194 TRP 0.013 0.001 TRP A 271 HIS 0.009 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8443) covalent geometry : angle 0.57102 (11449) SS BOND : bond 0.00604 ( 4) SS BOND : angle 1.67030 ( 8) hydrogen bonds : bond 0.03461 ( 412) hydrogen bonds : angle 4.40679 ( 1179) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.6731 (mtt180) cc_final: 0.6362 (mtt90) REVERT: A 59 GLN cc_start: 0.5950 (mt0) cc_final: 0.5572 (mp10) REVERT: A 270 ARG cc_start: 0.7845 (tmt-80) cc_final: 0.7568 (tmt-80) REVERT: A 326 ARG cc_start: 0.7268 (mtp-110) cc_final: 0.6930 (ttt180) REVERT: A 360 GLU cc_start: 0.6847 (mt-10) cc_final: 0.6413 (mp0) REVERT: B 43 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7587 (mp) REVERT: B 118 ASP cc_start: 0.6305 (t70) cc_final: 0.5879 (t70) REVERT: B 252 LEU cc_start: 0.7188 (tp) cc_final: 0.6574 (tp) REVERT: B 275 SER cc_start: 0.8256 (t) cc_final: 0.7570 (m) REVERT: G 21 MET cc_start: 0.4218 (mmm) cc_final: 0.3920 (mmm) REVERT: G 28 ILE cc_start: 0.7298 (mm) cc_final: 0.7051 (mp) REVERT: N 120 GLN cc_start: 0.6130 (mm-40) cc_final: 0.5926 (mm-40) REVERT: R 178 PHE cc_start: 0.4534 (t80) cc_final: 0.4178 (t80) outliers start: 28 outliers final: 26 residues processed: 182 average time/residue: 0.1045 time to fit residues: 24.9737 Evaluate side-chains 180 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 266 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 61 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 0.0170 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.228845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.194651 restraints weight = 8765.201| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 1.82 r_work: 0.4107 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3970 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8447 Z= 0.152 Angle : 0.625 14.179 11457 Z= 0.320 Chirality : 0.045 0.178 1287 Planarity : 0.004 0.052 1457 Dihedral : 4.571 22.636 1136 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.32 % Allowed : 19.27 % Favored : 77.41 % 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 aren not related in a simple way. whole: -0.00 (0.26), residues: 1029 helix: 1.44 (0.25), residues: 409 sheet: -0.45 (0.36), residues: 205 loop : -1.21 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 52 TYR 0.015 0.002 TYR N 117 PHE 0.034 0.002 PHE R 194 TRP 0.013 0.001 TRP B 169 HIS 0.010 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8443) covalent geometry : angle 0.62325 (11449) SS BOND : bond 0.00832 ( 4) SS BOND : angle 2.02968 ( 8) hydrogen bonds : bond 0.03752 ( 412) hydrogen bonds : angle 4.53268 ( 1179) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2503.10 seconds wall clock time: 43 minutes 36.75 seconds (2616.75 seconds total)