Starting phenix.real_space_refine on Tue Mar 3 21:21:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wyb_32890/03_2026/7wyb_32890_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wyb_32890/03_2026/7wyb_32890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wyb_32890/03_2026/7wyb_32890_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wyb_32890/03_2026/7wyb_32890_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wyb_32890/03_2026/7wyb_32890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wyb_32890/03_2026/7wyb_32890.map" } resolution = 2.97 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= 0.019 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 5587 2.51 5 N 1476 2.21 5 O 1628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8757 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1812 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Chain: "C" 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: "D" 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: "E" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "R" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2123 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 3, 'TRANS': 258} Chain breaks: 1 Time building chain proxies: 1.85, per 1000 atoms: 0.21 Number of scatterers: 8757 At special positions: 0 Unit cell: (92.4, 122.1, 130.9, 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 1628 8.00 N 1476 7.00 C 5587 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 231 " distance=2.04 Simple disulfide: pdb=" SG CYS R1008 " - pdb=" SG CYS R1080 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 250.7 milliseconds 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 35.3% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'B' and resid 8 through 30 removed outlier: 3.551A pdb=" N ALA B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 207 through 212 removed outlier: 4.407A pdb=" N TRP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE B 212 " --> pdb=" O ARG B 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 207 through 212' Processing helix chain 'B' and resid 213 through 216 removed outlier: 3.736A pdb=" N GLU B 216 " --> pdb=" O HIS B 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 213 through 216' Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.842A pdb=" N ALA B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 260 removed outlier: 3.777A pdb=" N PHE B 259 " --> pdb=" O ASN B 256 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 260' Processing helix chain 'B' and resid 271 through 279 Processing helix chain 'B' and resid 295 through 309 removed outlier: 3.654A pdb=" N ALA B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 332 through 348 Processing helix chain 'C' and resid 3 through 26 removed outlier: 3.774A pdb=" N ALA C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 33 Processing helix chain 'D' and resid 6 through 24 Processing helix chain 'D' and resid 29 through 43 Processing helix chain 'D' and resid 44 through 48 removed outlier: 3.521A pdb=" N GLU D 47 " --> pdb=" O HIS D 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.957A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.034A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 924 through 929 Processing helix chain 'R' and resid 940 through 956 Processing helix chain 'R' and resid 958 through 970 removed outlier: 3.821A pdb=" N ILE R 962 " --> pdb=" O VAL R 958 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE R 970 " --> pdb=" O THR R 966 " (cutoff:3.500A) Processing helix chain 'R' and resid 971 through 974 removed outlier: 3.656A pdb=" N GLN R 974 " --> pdb=" O ARG R 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 971 through 974' Processing helix chain 'R' and resid 975 through 999 removed outlier: 3.597A pdb=" N ILE R 999 " --> pdb=" O PHE R 995 " (cutoff:3.500A) Processing helix chain 'R' and resid 1007 through 1038 removed outlier: 3.930A pdb=" N PHE R1011 " --> pdb=" O ALA R1007 " (cutoff:3.500A) Processing helix chain 'R' and resid 1047 through 1070 removed outlier: 3.762A pdb=" N PHE R1051 " --> pdb=" O ARG R1047 " (cutoff:3.500A) Proline residue: R1059 - end of helix Processing helix chain 'R' and resid 1088 through 1091 Processing helix chain 'R' and resid 1092 through 1099 removed outlier: 3.658A pdb=" N ALA R1096 " --> pdb=" O PHE R1092 " (cutoff:3.500A) Processing helix chain 'R' and resid 1099 through 1117 removed outlier: 4.131A pdb=" N ILE R1105 " --> pdb=" O MET R1101 " (cutoff:3.500A) Processing helix chain 'R' and resid 1144 through 1154 removed outlier: 3.652A pdb=" N CYS R1152 " --> pdb=" O ILE R1148 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU R1153 " --> pdb=" O ALA R1149 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU R1154 " --> pdb=" O LEU R1150 " (cutoff:3.500A) Processing helix chain 'R' and resid 1155 through 1162 Processing helix chain 'R' and resid 1169 through 1181 removed outlier: 3.801A pdb=" N ALA R1173 " --> pdb=" O THR R1169 " (cutoff:3.500A) Processing helix chain 'R' and resid 1182 through 1193 removed outlier: 4.024A pdb=" N VAL R1193 " --> pdb=" O ILE R1189 " (cutoff:3.500A) Processing helix chain 'R' and resid 1195 through 1206 Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191 removed outlier: 6.355A pdb=" N VAL B 34 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE B 199 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU B 36 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 7.155A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.808A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.284A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153 removed outlier: 3.807A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER C 161 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 191 removed outlier: 6.829A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 277 removed outlier: 3.691A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 6.545A pdb=" N GLY E 16 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.739A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 142 through 144 Processing sheet with id=AB3, first strand: chain 'E' and resid 149 through 150 removed outlier: 3.898A pdb=" N GLU E 248 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU E 180 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU E 189 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR E 192 " --> pdb=" O ASN E 196 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN E 196 " --> pdb=" O TYR E 192 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1104 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: 1.39 Time building geometry restraints manager: 0.84 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: 2808 1.35 - 1.47: 2259 1.47 - 1.59: 3778 1.59 - 1.71: 0 1.71 - 1.83: 96 Bond restraints: 8941 Sorted by residual: bond pdb=" N THR E 212 " pdb=" CA THR E 212 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.32e-02 5.74e+03 7.61e+00 bond pdb=" N GLU E 236 " pdb=" CA GLU E 236 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.18e-02 7.18e+03 7.46e+00 bond pdb=" CA ALA C 299 " pdb=" C ALA C 299 " ideal model delta sigma weight residual 1.523 1.479 0.044 1.80e-02 3.09e+03 6.01e+00 bond pdb=" N TYR E 237 " pdb=" CA TYR E 237 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.41e-02 5.03e+03 5.99e+00 bond pdb=" C GLN C 44 " pdb=" N MET C 45 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.31e-02 5.83e+03 5.87e+00 ... (remaining 8936 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 11676 1.90 - 3.80: 345 3.80 - 5.70: 64 5.70 - 7.59: 11 7.59 - 9.49: 3 Bond angle restraints: 12099 Sorted by residual: angle pdb=" N SER R1168 " pdb=" CA SER R1168 " pdb=" C SER R1168 " ideal model delta sigma weight residual 113.23 107.67 5.56 1.22e+00 6.72e-01 2.08e+01 angle pdb=" N LYS B 349 " pdb=" CA LYS B 349 " pdb=" C LYS B 349 " ideal model delta sigma weight residual 114.04 108.94 5.10 1.24e+00 6.50e-01 1.69e+01 angle pdb=" C PRO E 14 " pdb=" CA PRO E 14 " pdb=" CB PRO E 14 " ideal model delta sigma weight residual 111.39 116.45 -5.06 1.28e+00 6.10e-01 1.57e+01 angle pdb=" N PHE R 970 " pdb=" CA PHE R 970 " pdb=" C PHE R 970 " ideal model delta sigma weight residual 109.15 114.77 -5.62 1.44e+00 4.82e-01 1.52e+01 angle pdb=" C LEU C 55 " pdb=" CA LEU C 55 " pdb=" CB LEU C 55 " ideal model delta sigma weight residual 109.65 103.09 6.56 1.68e+00 3.54e-01 1.52e+01 ... (remaining 12094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 4853 17.55 - 35.10: 360 35.10 - 52.65: 52 52.65 - 70.20: 3 70.20 - 87.75: 6 Dihedral angle restraints: 5274 sinusoidal: 2047 harmonic: 3227 Sorted by residual: dihedral pdb=" CB CYS E 161 " pdb=" SG CYS E 161 " pdb=" SG CYS E 231 " pdb=" CB CYS E 231 " ideal model delta sinusoidal sigma weight residual 93.00 135.64 -42.64 1 1.00e+01 1.00e-02 2.54e+01 dihedral pdb=" CB CYS R1008 " pdb=" SG CYS R1008 " pdb=" SG CYS R1080 " pdb=" CB CYS R1080 " ideal model delta sinusoidal sigma weight residual -86.00 -47.47 -38.53 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" CA ARG E 193 " pdb=" C ARG E 193 " pdb=" N MET E 194 " pdb=" CA MET E 194 " ideal model delta harmonic sigma weight residual 180.00 160.55 19.45 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 5271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1023 0.051 - 0.102: 282 0.102 - 0.153: 56 0.153 - 0.204: 6 0.204 - 0.255: 2 Chirality restraints: 1369 Sorted by residual: chirality pdb=" CA LEU R 928 " pdb=" N LEU R 928 " pdb=" C LEU R 928 " pdb=" CB LEU R 928 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA GLU B 216 " pdb=" N GLU B 216 " pdb=" C GLU B 216 " pdb=" CB GLU B 216 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ALA C 56 " pdb=" N ALA C 56 " pdb=" C ALA C 56 " pdb=" CB ALA C 56 " both_signs ideal model delta sigma weight residual False 2.48 2.68 -0.20 2.00e-01 2.50e+01 9.81e-01 ... (remaining 1366 not shown) Planarity restraints: 1525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 182 " -0.050 5.00e-02 4.00e+02 7.57e-02 9.18e+00 pdb=" N PRO E 183 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO E 183 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 183 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER E 210 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C SER E 210 " 0.032 2.00e-02 2.50e+03 pdb=" O SER E 210 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY E 211 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 222 " -0.007 2.00e-02 2.50e+03 1.37e-02 3.29e+00 pdb=" CG PHE C 222 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE C 222 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE C 222 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 222 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE C 222 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 222 " 0.002 2.00e-02 2.50e+03 ... (remaining 1522 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 447 2.72 - 3.27: 8475 3.27 - 3.81: 13324 3.81 - 4.36: 16117 4.36 - 4.90: 28133 Nonbonded interactions: 66496 Sorted by model distance: nonbonded pdb=" O GLY E 211 " pdb=" OG1 THR E 212 " model vdw 2.176 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.258 3.040 nonbonded pdb=" O ALA B 41 " pdb=" OG SER B 44 " model vdw 2.259 3.040 nonbonded pdb=" O GLU R1167 " pdb=" OG SER R1168 " model vdw 2.276 3.040 nonbonded pdb=" O ARG C 314 " pdb=" OG SER C 331 " model vdw 2.293 3.040 ... (remaining 66491 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: 0.010 Normalize map: mean=0, sd=1: 1.880 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.560 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5858 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 : 0.005 0.053 8943 Z= 0.252 Angle : 0.803 9.493 12103 Z= 0.464 Chirality : 0.049 0.255 1369 Planarity : 0.005 0.076 1525 Dihedral : 12.351 87.746 3188 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.25), residues: 1099 helix: 0.32 (0.29), residues: 348 sheet: -0.19 (0.32), residues: 276 loop : -2.27 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 304 TYR 0.031 0.002 TYR C 105 PHE 0.028 0.003 PHE C 222 TRP 0.018 0.002 TRP C 82 HIS 0.008 0.001 HIS R1016 Details of bonding type rmsd covalent geometry : bond 0.00537 ( 8941) covalent geometry : angle 0.80272 (12099) SS BOND : bond 0.00765 ( 2) SS BOND : angle 1.75124 ( 4) hydrogen bonds : bond 0.12503 ( 402) hydrogen bonds : angle 5.88914 ( 1104) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.186 Fit side-chains REVERT: B 308 GLU cc_start: 0.6288 (mt-10) cc_final: 0.6083 (mt-10) REVERT: C 101 MET cc_start: 0.5505 (mtt) cc_final: 0.5283 (ttm) REVERT: E 246 LYS cc_start: 0.7146 (ttmm) cc_final: 0.6845 (ttmm) REVERT: R 1180 ASN cc_start: 0.7186 (m-40) cc_final: 0.6938 (m110) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.4663 time to fit residues: 58.8725 Evaluate side-chains 105 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.0040 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS B 255 ASN C 119 ASN C 340 ASN E 233 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.190501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.161858 restraints weight = 12203.804| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 2.92 r_work: 0.4171 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8943 Z= 0.162 Angle : 0.640 9.747 12103 Z= 0.340 Chirality : 0.043 0.197 1369 Planarity : 0.004 0.056 1525 Dihedral : 5.279 46.787 1201 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.58 % Allowed : 8.30 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.25), residues: 1099 helix: 0.69 (0.29), residues: 350 sheet: 0.11 (0.32), residues: 275 loop : -1.96 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 304 TYR 0.021 0.002 TYR C 105 PHE 0.018 0.002 PHE C 253 TRP 0.013 0.001 TRP C 211 HIS 0.005 0.001 HIS R1016 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8941) covalent geometry : angle 0.63947 (12099) SS BOND : bond 0.00545 ( 2) SS BOND : angle 1.39350 ( 4) hydrogen bonds : bond 0.05215 ( 402) hydrogen bonds : angle 4.93846 ( 1104) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: B 240 MET cc_start: 0.5741 (tmm) cc_final: 0.5195 (pp-130) REVERT: B 309 ASP cc_start: 0.5715 (m-30) cc_final: 0.5437 (m-30) REVERT: C 52 ARG cc_start: 0.7339 (mtt90) cc_final: 0.7114 (mtt90) REVERT: C 101 MET cc_start: 0.6227 (mtt) cc_final: 0.5807 (tpt) REVERT: C 219 ARG cc_start: 0.7188 (tpt-90) cc_final: 0.6949 (tpt-90) REVERT: C 239 ASN cc_start: 0.6977 (m-40) cc_final: 0.6267 (t0) REVERT: D 21 MET cc_start: 0.0118 (mtm) cc_final: -0.0375 (mtm) REVERT: E 76 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6749 (mtpp) REVERT: E 246 LYS cc_start: 0.7084 (ttmm) cc_final: 0.6777 (ttmm) REVERT: R 1114 MET cc_start: 0.6894 (tpp) cc_final: 0.6583 (tmm) outliers start: 15 outliers final: 6 residues processed: 116 average time/residue: 0.5162 time to fit residues: 64.1790 Evaluate side-chains 114 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain R residue 1058 MET Chi-restraints excluded: chain R residue 1178 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 64 optimal weight: 0.7980 chunk 86 optimal weight: 0.0030 chunk 8 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 52 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.0170 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 55 optimal weight: 20.0000 overall best weight: 0.2828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS B 255 ASN R1183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.193518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.165184 restraints weight = 12176.607| |-----------------------------------------------------------------------------| r_work (start): 0.4344 rms_B_bonded: 2.91 r_work: 0.4222 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5980 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8943 Z= 0.109 Angle : 0.545 9.882 12103 Z= 0.291 Chirality : 0.041 0.207 1369 Planarity : 0.003 0.047 1525 Dihedral : 4.626 40.568 1201 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.37 % Allowed : 11.34 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.26), residues: 1099 helix: 1.24 (0.29), residues: 347 sheet: 0.34 (0.32), residues: 278 loop : -1.71 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 304 TYR 0.017 0.001 TYR R1112 PHE 0.016 0.002 PHE C 241 TRP 0.011 0.001 TRP C 211 HIS 0.002 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8941) covalent geometry : angle 0.54483 (12099) SS BOND : bond 0.00603 ( 2) SS BOND : angle 1.09094 ( 4) hydrogen bonds : bond 0.03837 ( 402) hydrogen bonds : angle 4.48951 ( 1104) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: B 53 MET cc_start: 0.5756 (ppp) cc_final: 0.5043 (pp-130) REVERT: B 198 MET cc_start: 0.7167 (mtp) cc_final: 0.6669 (mtt) REVERT: B 289 GLU cc_start: 0.7886 (mp0) cc_final: 0.7666 (mp0) REVERT: B 309 ASP cc_start: 0.5714 (m-30) cc_final: 0.5430 (m-30) REVERT: C 52 ARG cc_start: 0.7294 (mtt90) cc_final: 0.7076 (mtt90) REVERT: C 101 MET cc_start: 0.6174 (mtt) cc_final: 0.5671 (tpt) REVERT: C 239 ASN cc_start: 0.6969 (m-40) cc_final: 0.6342 (t0) REVERT: D 21 MET cc_start: 0.0081 (mtm) cc_final: -0.0414 (mtm) REVERT: E 246 LYS cc_start: 0.6991 (ttmm) cc_final: 0.6673 (tttp) REVERT: R 1081 TRP cc_start: 0.6452 (t60) cc_final: 0.6202 (t60) REVERT: R 1114 MET cc_start: 0.7052 (tpp) cc_final: 0.6838 (tmm) outliers start: 13 outliers final: 4 residues processed: 119 average time/residue: 0.5109 time to fit residues: 65.2351 Evaluate side-chains 115 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain R residue 1058 MET Chi-restraints excluded: chain R residue 1178 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 73 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 13 optimal weight: 0.0980 chunk 28 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 46 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: B 213 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.190405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.161660 restraints weight = 12275.318| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 2.92 r_work: 0.4178 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6043 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8943 Z= 0.157 Angle : 0.590 9.116 12103 Z= 0.313 Chirality : 0.042 0.158 1369 Planarity : 0.004 0.043 1525 Dihedral : 4.813 45.928 1201 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.10 % Allowed : 12.71 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.26), residues: 1099 helix: 1.43 (0.29), residues: 339 sheet: 0.21 (0.31), residues: 289 loop : -1.75 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 219 TYR 0.023 0.002 TYR C 105 PHE 0.018 0.002 PHE C 253 TRP 0.009 0.001 TRP C 211 HIS 0.007 0.001 HIS R1016 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8941) covalent geometry : angle 0.59008 (12099) SS BOND : bond 0.00708 ( 2) SS BOND : angle 1.05012 ( 4) hydrogen bonds : bond 0.04658 ( 402) hydrogen bonds : angle 4.54824 ( 1104) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: B 53 MET cc_start: 0.5621 (ppp) cc_final: 0.5010 (pp-130) REVERT: B 309 ASP cc_start: 0.5732 (m-30) cc_final: 0.5254 (m-30) REVERT: C 101 MET cc_start: 0.6265 (mtt) cc_final: 0.5387 (tpt) REVERT: C 239 ASN cc_start: 0.6828 (m-40) cc_final: 0.6150 (t0) REVERT: D 21 MET cc_start: 0.0073 (mtm) cc_final: -0.0407 (mtm) REVERT: E 76 LYS cc_start: 0.6965 (OUTLIER) cc_final: 0.6684 (mtpp) REVERT: E 246 LYS cc_start: 0.6992 (ttmm) cc_final: 0.6767 (ttmm) REVERT: R 1113 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6482 (mppt) outliers start: 20 outliers final: 11 residues processed: 115 average time/residue: 0.4691 time to fit residues: 58.0347 Evaluate side-chains 117 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain R residue 1058 MET Chi-restraints excluded: chain R residue 1079 VAL Chi-restraints excluded: chain R residue 1109 ILE Chi-restraints excluded: chain R residue 1113 LYS Chi-restraints excluded: chain R residue 1178 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 57 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.192086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.163309 restraints weight = 12231.926| |-----------------------------------------------------------------------------| r_work (start): 0.4305 rms_B_bonded: 2.93 r_work: 0.4184 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8943 Z= 0.140 Angle : 0.575 10.741 12103 Z= 0.304 Chirality : 0.041 0.147 1369 Planarity : 0.003 0.042 1525 Dihedral : 4.701 44.545 1201 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.89 % Allowed : 13.66 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.26), residues: 1099 helix: 1.37 (0.29), residues: 345 sheet: 0.19 (0.31), residues: 289 loop : -1.68 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 283 TYR 0.018 0.002 TYR C 105 PHE 0.017 0.002 PHE C 241 TRP 0.015 0.001 TRP R1143 HIS 0.005 0.001 HIS R1016 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8941) covalent geometry : angle 0.57476 (12099) SS BOND : bond 0.00487 ( 2) SS BOND : angle 0.98958 ( 4) hydrogen bonds : bond 0.04375 ( 402) hydrogen bonds : angle 4.47840 ( 1104) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: B 53 MET cc_start: 0.5498 (ppp) cc_final: 0.4975 (pp-130) REVERT: B 198 MET cc_start: 0.7416 (mtp) cc_final: 0.6760 (mtt) REVERT: C 52 ARG cc_start: 0.7190 (mtt90) cc_final: 0.6961 (mtt90) REVERT: C 239 ASN cc_start: 0.6821 (m-40) cc_final: 0.6168 (t0) REVERT: D 21 MET cc_start: 0.0029 (mtm) cc_final: -0.0419 (mtm) REVERT: E 194 MET cc_start: 0.6667 (ttp) cc_final: 0.6258 (tmm) REVERT: R 1185 MET cc_start: 0.6163 (tmm) cc_final: 0.5930 (tmm) outliers start: 18 outliers final: 13 residues processed: 118 average time/residue: 0.4790 time to fit residues: 60.9488 Evaluate side-chains 120 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain R residue 1058 MET Chi-restraints excluded: chain R residue 1079 VAL Chi-restraints excluded: chain R residue 1109 ILE Chi-restraints excluded: chain R residue 1178 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 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 213 HIS R1183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.190623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.162189 restraints weight = 12167.349| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 2.87 r_work: 0.4163 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6059 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8943 Z= 0.162 Angle : 0.602 10.919 12103 Z= 0.316 Chirality : 0.042 0.154 1369 Planarity : 0.004 0.041 1525 Dihedral : 4.788 44.736 1201 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.05 % Allowed : 14.29 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.26), residues: 1099 helix: 1.34 (0.29), residues: 345 sheet: 0.07 (0.31), residues: 289 loop : -1.67 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 314 TYR 0.021 0.002 TYR C 105 PHE 0.017 0.002 PHE C 151 TRP 0.012 0.001 TRP C 211 HIS 0.006 0.001 HIS R1016 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8941) covalent geometry : angle 0.60210 (12099) SS BOND : bond 0.00690 ( 2) SS BOND : angle 1.05898 ( 4) hydrogen bonds : bond 0.04734 ( 402) hydrogen bonds : angle 4.52822 ( 1104) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: B 53 MET cc_start: 0.5438 (ppp) cc_final: 0.4982 (pp-130) REVERT: B 309 ASP cc_start: 0.5752 (m-30) cc_final: 0.5386 (m-30) REVERT: C 239 ASN cc_start: 0.6825 (m-40) cc_final: 0.6142 (t0) REVERT: E 62 ASP cc_start: 0.6940 (OUTLIER) cc_final: 0.6500 (m-30) REVERT: E 76 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6712 (mtpp) REVERT: R 1081 TRP cc_start: 0.6527 (t60) cc_final: 0.6286 (t60) outliers start: 29 outliers final: 18 residues processed: 116 average time/residue: 0.4245 time to fit residues: 53.3924 Evaluate side-chains 118 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain R residue 928 LEU Chi-restraints excluded: chain R residue 1058 MET Chi-restraints excluded: chain R residue 1079 VAL Chi-restraints excluded: chain R residue 1109 ILE Chi-restraints excluded: chain R residue 1178 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 102 optimal weight: 0.0770 chunk 70 optimal weight: 0.5980 chunk 77 optimal weight: 0.0070 chunk 103 optimal weight: 0.7980 chunk 59 optimal weight: 0.0050 chunk 97 optimal weight: 0.9990 chunk 32 optimal weight: 0.0870 chunk 20 optimal weight: 0.0070 chunk 107 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 overall best weight: 0.0366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS C 75 GLN C 119 ASN D 18 GLN E 234 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.197340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.168942 restraints weight = 12420.725| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 3.00 r_work: 0.4264 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5899 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8943 Z= 0.096 Angle : 0.546 10.535 12103 Z= 0.281 Chirality : 0.040 0.149 1369 Planarity : 0.003 0.038 1525 Dihedral : 4.171 36.807 1201 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.37 % Allowed : 17.23 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.26), residues: 1099 helix: 1.80 (0.30), residues: 342 sheet: 0.16 (0.32), residues: 284 loop : -1.33 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 314 TYR 0.018 0.001 TYR R1112 PHE 0.018 0.001 PHE C 241 TRP 0.016 0.001 TRP C 211 HIS 0.004 0.001 HIS E 234 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 8941) covalent geometry : angle 0.54582 (12099) SS BOND : bond 0.00499 ( 2) SS BOND : angle 0.98793 ( 4) hydrogen bonds : bond 0.02967 ( 402) hydrogen bonds : angle 4.21920 ( 1104) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: B 53 MET cc_start: 0.5432 (ppp) cc_final: 0.4881 (pp-130) REVERT: B 198 MET cc_start: 0.7098 (mtp) cc_final: 0.6480 (mtt) REVERT: C 52 ARG cc_start: 0.7076 (mtt90) cc_final: 0.6834 (mtt90) REVERT: C 239 ASN cc_start: 0.6650 (m-40) cc_final: 0.5987 (t0) REVERT: C 300 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7978 (tm) REVERT: E 186 SER cc_start: 0.7800 (m) cc_final: 0.7516 (t) REVERT: R 1081 TRP cc_start: 0.6413 (t60) cc_final: 0.6044 (t60) outliers start: 13 outliers final: 6 residues processed: 119 average time/residue: 0.4870 time to fit residues: 62.5560 Evaluate side-chains 115 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain R residue 1058 MET Chi-restraints excluded: chain R residue 1178 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 90 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.189608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.161495 restraints weight = 12095.399| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 2.92 r_work: 0.4171 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6043 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8943 Z= 0.179 Angle : 0.625 10.350 12103 Z= 0.327 Chirality : 0.042 0.148 1369 Planarity : 0.004 0.038 1525 Dihedral : 4.717 46.325 1201 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.89 % Allowed : 18.38 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.26), residues: 1099 helix: 1.57 (0.29), residues: 339 sheet: 0.02 (0.31), residues: 285 loop : -1.43 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 15 TYR 0.019 0.002 TYR C 105 PHE 0.018 0.002 PHE C 151 TRP 0.010 0.002 TRP C 211 HIS 0.008 0.001 HIS R1016 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8941) covalent geometry : angle 0.62503 (12099) SS BOND : bond 0.00550 ( 2) SS BOND : angle 0.81385 ( 4) hydrogen bonds : bond 0.04779 ( 402) hydrogen bonds : angle 4.49348 ( 1104) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: B 53 MET cc_start: 0.5452 (ppp) cc_final: 0.4921 (pp-130) REVERT: B 198 MET cc_start: 0.7255 (mtp) cc_final: 0.6574 (mtt) REVERT: B 309 ASP cc_start: 0.5758 (m-30) cc_final: 0.5303 (m-30) REVERT: C 239 ASN cc_start: 0.6829 (m-40) cc_final: 0.6116 (t0) REVERT: E 76 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6706 (mtpp) REVERT: R 1081 TRP cc_start: 0.6582 (t60) cc_final: 0.6375 (t60) REVERT: R 1180 ASN cc_start: 0.7080 (m-40) cc_final: 0.6617 (m110) outliers start: 18 outliers final: 13 residues processed: 109 average time/residue: 0.5090 time to fit residues: 59.5861 Evaluate side-chains 111 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 188 GLN Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain R residue 1058 MET Chi-restraints excluded: chain R residue 1178 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 69 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.190758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.162771 restraints weight = 12008.655| |-----------------------------------------------------------------------------| r_work (start): 0.4305 rms_B_bonded: 2.82 r_work: 0.4187 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6052 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8943 Z= 0.164 Angle : 0.626 11.745 12103 Z= 0.322 Chirality : 0.042 0.141 1369 Planarity : 0.003 0.039 1525 Dihedral : 4.700 44.459 1201 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.00 % Allowed : 18.07 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.26), residues: 1099 helix: 1.24 (0.29), residues: 352 sheet: -0.05 (0.31), residues: 284 loop : -1.43 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 314 TYR 0.021 0.002 TYR R1112 PHE 0.019 0.002 PHE C 241 TRP 0.012 0.002 TRP C 211 HIS 0.006 0.001 HIS R1191 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8941) covalent geometry : angle 0.62602 (12099) SS BOND : bond 0.00545 ( 2) SS BOND : angle 0.90823 ( 4) hydrogen bonds : bond 0.04530 ( 402) hydrogen bonds : angle 4.45052 ( 1104) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: B 53 MET cc_start: 0.5382 (ppp) cc_final: 0.4944 (pp-130) REVERT: B 198 MET cc_start: 0.7194 (mtp) cc_final: 0.6551 (mtt) REVERT: C 217 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7732 (pp-130) REVERT: C 239 ASN cc_start: 0.6849 (m-40) cc_final: 0.6175 (t0) outliers start: 19 outliers final: 12 residues processed: 112 average time/residue: 0.4713 time to fit residues: 57.0092 Evaluate side-chains 112 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain R residue 1058 MET Chi-restraints excluded: chain R residue 1178 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 87 optimal weight: 0.0870 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.191267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.162766 restraints weight = 12105.434| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 2.92 r_work: 0.4188 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6033 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8943 Z= 0.149 Angle : 0.622 13.152 12103 Z= 0.319 Chirality : 0.042 0.141 1369 Planarity : 0.003 0.038 1525 Dihedral : 4.675 43.896 1201 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.58 % Allowed : 18.91 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.26), residues: 1099 helix: 1.37 (0.29), residues: 344 sheet: -0.03 (0.31), residues: 283 loop : -1.43 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 67 TYR 0.017 0.002 TYR C 105 PHE 0.018 0.002 PHE B 199 TRP 0.013 0.001 TRP C 211 HIS 0.007 0.001 HIS R1016 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8941) covalent geometry : angle 0.62143 (12099) SS BOND : bond 0.00571 ( 2) SS BOND : angle 0.95095 ( 4) hydrogen bonds : bond 0.04343 ( 402) hydrogen bonds : angle 4.42192 ( 1104) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: B 53 MET cc_start: 0.5408 (ppp) cc_final: 0.4892 (pp-130) REVERT: B 198 MET cc_start: 0.7118 (mtp) cc_final: 0.6423 (mtt) REVERT: B 229 ASP cc_start: 0.7519 (t0) cc_final: 0.7269 (t70) REVERT: C 124 TYR cc_start: 0.5771 (m-80) cc_final: 0.5267 (m-80) REVERT: C 217 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7718 (pp-130) REVERT: C 239 ASN cc_start: 0.6845 (m-40) cc_final: 0.6164 (t0) outliers start: 15 outliers final: 13 residues processed: 111 average time/residue: 0.4939 time to fit residues: 59.1084 Evaluate side-chains 113 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain R residue 1058 MET Chi-restraints excluded: chain R residue 1178 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 65 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 52 optimal weight: 0.0570 chunk 88 optimal weight: 0.7980 chunk 22 optimal weight: 20.0000 chunk 93 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.191730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.163391 restraints weight = 12051.434| |-----------------------------------------------------------------------------| r_work (start): 0.4320 rms_B_bonded: 2.91 r_work: 0.4197 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8943 Z= 0.132 Angle : 0.603 12.349 12103 Z= 0.309 Chirality : 0.041 0.138 1369 Planarity : 0.003 0.038 1525 Dihedral : 4.563 43.760 1201 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.68 % Allowed : 18.91 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.26), residues: 1099 helix: 1.56 (0.29), residues: 338 sheet: 0.00 (0.32), residues: 283 loop : -1.41 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 72 TYR 0.023 0.002 TYR R1074 PHE 0.020 0.002 PHE C 241 TRP 0.013 0.001 TRP C 211 HIS 0.005 0.001 HIS R1016 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8941) covalent geometry : angle 0.60289 (12099) SS BOND : bond 0.00522 ( 2) SS BOND : angle 0.71453 ( 4) hydrogen bonds : bond 0.04091 ( 402) hydrogen bonds : angle 4.34315 ( 1104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3319.25 seconds wall clock time: 57 minutes 9.17 seconds (3429.17 seconds total)