Starting phenix.real_space_refine on Tue Mar 3 20:55:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x10_32932/03_2026/7x10_32932_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x10_32932/03_2026/7x10_32932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x10_32932/03_2026/7x10_32932_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x10_32932/03_2026/7x10_32932_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x10_32932/03_2026/7x10_32932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x10_32932/03_2026/7x10_32932.map" } resolution = 2.93 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= 0.020 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 61 5.16 5 C 5546 2.51 5 N 1486 2.21 5 O 1581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8674 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1744 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 4, 'TRANS': 206} Chain breaks: 3 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: "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: "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: "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: 2.08, per 1000 atoms: 0.24 Number of scatterers: 8674 At special positions: 0 Unit cell: (90.2, 124.3, 132, 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 61 16.00 O 1581 8.00 N 1486 7.00 C 5546 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=2.05 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: 0.58 Conformation dependent library (CDL) restraints added in 286.0 milliseconds 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2056 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 35.6% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 17 through 39 removed outlier: 3.948A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 66 Processing helix chain 'A' and resid 230 through 235 removed outlier: 4.000A pdb=" N TRP A 234 " --> pdb=" O GLN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.537A pdb=" N ASN A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.778A pdb=" N PHE A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.752A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 322 Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 350 through 371 removed outlier: 3.742A pdb=" N ASN A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL A 362 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 363 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.782A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.876A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.601A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 4.072A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 925 through 930 removed outlier: 3.866A pdb=" N ALA R 930 " --> pdb=" O VAL R 927 " (cutoff:3.500A) Processing helix chain 'R' and resid 940 through 956 removed outlier: 3.990A pdb=" N LEU R 944 " --> pdb=" O VAL R 940 " (cutoff:3.500A) Processing helix chain 'R' and resid 958 through 967 Processing helix chain 'R' and resid 970 through 974 removed outlier: 3.930A pdb=" N LEU R 973 " --> pdb=" O PHE R 970 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN R 974 " --> pdb=" O ARG R 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 970 through 974' Processing helix chain 'R' and resid 975 through 998 Processing helix chain 'R' and resid 1010 through 1038 removed outlier: 4.732A pdb=" N HIS R1016 " --> pdb=" O ALA R1012 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY R1030 " --> pdb=" O MET R1026 " (cutoff:3.500A) Processing helix chain 'R' and resid 1047 through 1070 Proline residue: R1059 - end of helix Processing helix chain 'R' and resid 1086 through 1091 removed outlier: 4.403A pdb=" N ILE R1089 " --> pdb=" O THR R1086 " (cutoff:3.500A) Processing helix chain 'R' and resid 1092 through 1117 removed outlier: 3.735A pdb=" N HIS R1117 " --> pdb=" O LYS R1113 " (cutoff:3.500A) Processing helix chain 'R' and resid 1144 through 1154 removed outlier: 4.002A pdb=" N LEU R1151 " --> pdb=" O ALA R1147 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS R1152 " --> pdb=" O ILE R1148 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU R1153 " --> pdb=" O ALA R1149 " (cutoff:3.500A) Processing helix chain 'R' and resid 1159 through 1164 removed outlier: 3.738A pdb=" N LEU R1162 " --> pdb=" O ALA R1159 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR R1164 " --> pdb=" O GLY R1161 " (cutoff:3.500A) Processing helix chain 'R' and resid 1166 through 1168 No H-bonds generated for 'chain 'R' and resid 1166 through 1168' Processing helix chain 'R' and resid 1169 through 1181 removed outlier: 3.874A pdb=" N ALA R1173 " --> pdb=" O THR R1169 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR R1177 " --> pdb=" O ALA R1173 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER R1181 " --> pdb=" O THR R1177 " (cutoff:3.500A) Processing helix chain 'R' and resid 1182 through 1191 removed outlier: 3.536A pdb=" N PHE R1188 " --> pdb=" O GLY R1184 " (cutoff:3.500A) Processing helix chain 'R' and resid 1195 through 1204 removed outlier: 3.758A pdb=" N LYS R1204 " --> pdb=" O LYS R1200 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213 removed outlier: 3.807A pdb=" N SER A 243 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 343 " --> pdb=" O ILE A 287 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.871A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.943A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.881A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 149 removed outlier: 7.056A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.634A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.063A 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: 3.579A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.697A 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: 3.806A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 6.845A 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: 6.246A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 143 through 144 Processing sheet with id=AB3, first strand: chain 'E' and resid 148 through 150 removed outlier: 3.517A pdb=" N VAL E 149 " --> pdb=" O LYS E 246 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU E 248 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU E 180 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU E 189 " --> pdb=" O LEU E 180 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1077 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: 1.16 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2093 1.33 - 1.46: 2466 1.46 - 1.59: 4205 1.59 - 1.71: 0 1.71 - 1.84: 92 Bond restraints: 8856 Sorted by residual: bond pdb=" CA GLN E 113 " pdb=" C GLN E 113 " ideal model delta sigma weight residual 1.521 1.560 -0.039 1.29e-02 6.01e+03 9.08e+00 bond pdb=" CA GLY E 16 " pdb=" C GLY E 16 " ideal model delta sigma weight residual 1.524 1.474 0.050 1.67e-02 3.59e+03 9.06e+00 bond pdb=" CA SER E 186 " pdb=" CB SER E 186 " ideal model delta sigma weight residual 1.532 1.485 0.047 1.58e-02 4.01e+03 8.93e+00 bond pdb=" C LEU E 216 " pdb=" N THR E 217 " ideal model delta sigma weight residual 1.330 1.369 -0.039 1.32e-02 5.74e+03 8.90e+00 bond pdb=" C GLU E 236 " pdb=" O GLU E 236 " ideal model delta sigma weight residual 1.235 1.203 0.032 1.26e-02 6.30e+03 6.55e+00 ... (remaining 8851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 11789 2.73 - 5.45: 165 5.45 - 8.18: 21 8.18 - 10.90: 0 10.90 - 13.63: 1 Bond angle restraints: 11976 Sorted by residual: angle pdb=" N ALA R1009 " pdb=" CA ALA R1009 " pdb=" C ALA R1009 " ideal model delta sigma weight residual 113.51 99.88 13.63 1.52e+00 4.33e-01 8.04e+01 angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 110.61 116.81 -6.20 1.25e+00 6.40e-01 2.46e+01 angle pdb=" C CYS R1008 " pdb=" N ALA R1009 " pdb=" CA ALA R1009 " ideal model delta sigma weight residual 126.86 119.08 7.78 1.57e+00 4.06e-01 2.46e+01 angle pdb=" C GLU E 224 " pdb=" CA GLU E 224 " pdb=" CB GLU E 224 " ideal model delta sigma weight residual 111.26 103.81 7.45 1.67e+00 3.59e-01 1.99e+01 angle pdb=" C PRO E 14 " pdb=" CA PRO E 14 " pdb=" CB PRO E 14 " ideal model delta sigma weight residual 111.39 116.57 -5.18 1.28e+00 6.10e-01 1.64e+01 ... (remaining 11971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4811 17.99 - 35.98: 367 35.98 - 53.97: 47 53.97 - 71.96: 8 71.96 - 89.95: 4 Dihedral angle restraints: 5237 sinusoidal: 2058 harmonic: 3179 Sorted by residual: dihedral pdb=" C CYS R1008 " pdb=" N CYS R1008 " pdb=" CA CYS R1008 " pdb=" CB CYS R1008 " ideal model delta harmonic sigma weight residual -122.60 -132.77 10.17 0 2.50e+00 1.60e-01 1.65e+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 -119.62 33.62 1 1.00e+01 1.00e-02 1.61e+01 dihedral pdb=" CA ASP R1085 " pdb=" C ASP R1085 " pdb=" N THR R1086 " pdb=" CA THR R1086 " ideal model delta harmonic sigma weight residual 180.00 160.12 19.88 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1188 0.075 - 0.150: 158 0.150 - 0.225: 9 0.225 - 0.299: 2 0.299 - 0.374: 1 Chirality restraints: 1358 Sorted by residual: chirality pdb=" CA CYS R1008 " pdb=" N CYS R1008 " pdb=" C CYS R1008 " pdb=" CB CYS R1008 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA SER R1073 " pdb=" N SER R1073 " pdb=" C SER R1073 " pdb=" CB SER R1073 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ALA B 203 " pdb=" N ALA B 203 " pdb=" C ALA B 203 " pdb=" CB ALA B 203 " both_signs ideal model delta sigma weight residual False 2.48 2.25 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1355 not shown) Planarity restraints: 1507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.044 5.00e-02 4.00e+02 6.83e-02 7.46e+00 pdb=" N PRO B 236 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 178 " -0.021 2.00e-02 2.50e+03 1.49e-02 5.56e+00 pdb=" CG TRP E 178 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP E 178 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP E 178 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 178 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 178 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP E 178 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 178 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 178 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 178 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 151 " -0.022 2.00e-02 2.50e+03 1.56e-02 4.25e+00 pdb=" CG PHE B 151 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 151 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 151 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 151 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 151 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 151 " -0.008 2.00e-02 2.50e+03 ... (remaining 1504 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 657 2.73 - 3.28: 8069 3.28 - 3.82: 12848 3.82 - 4.36: 15022 4.36 - 4.90: 27090 Nonbonded interactions: 63686 Sorted by model distance: nonbonded pdb=" O ILE R 962 " pdb=" OG1 THR R 966 " model vdw 2.192 3.040 nonbonded pdb=" O THR R1177 " pdb=" OG SER R1181 " model vdw 2.233 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR R1076 " pdb=" O VAL R1079 " model vdw 2.246 3.040 nonbonded pdb=" O ILE E 100 " pdb=" OG SER E 105 " model vdw 2.248 3.040 ... (remaining 63681 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.010 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 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 0.059 8858 Z= 0.255 Angle : 0.800 13.631 11980 Z= 0.462 Chirality : 0.051 0.374 1358 Planarity : 0.005 0.068 1507 Dihedral : 12.695 89.948 3175 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.18 (0.26), residues: 1078 helix: 0.67 (0.29), residues: 345 sheet: -0.44 (0.31), residues: 266 loop : -2.13 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 356 TYR 0.020 0.002 TYR R1164 PHE 0.033 0.002 PHE B 151 TRP 0.041 0.003 TRP E 178 HIS 0.011 0.002 HIS R1016 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 8856) covalent geometry : angle 0.79892 (11976) SS BOND : bond 0.01654 ( 2) SS BOND : angle 2.19403 ( 4) hydrogen bonds : bond 0.15711 ( 388) hydrogen bonds : angle 6.00888 ( 1077) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.222 Fit side-chains REVERT: E 185 GLN cc_start: 0.8697 (mt0) cc_final: 0.8468 (mt0) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.5512 time to fit residues: 94.5735 Evaluate side-chains 139 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN R1191 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.153478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.130140 restraints weight = 12732.580| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.36 r_work: 0.3606 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8858 Z= 0.164 Angle : 0.622 9.432 11980 Z= 0.335 Chirality : 0.044 0.154 1358 Planarity : 0.005 0.050 1507 Dihedral : 5.165 31.423 1185 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.16 % Allowed : 10.14 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.69 (0.26), residues: 1078 helix: 1.24 (0.29), residues: 343 sheet: -0.25 (0.30), residues: 265 loop : -1.92 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 356 TYR 0.017 0.002 TYR R1112 PHE 0.023 0.002 PHE R1018 TRP 0.023 0.002 TRP E 178 HIS 0.008 0.001 HIS R1016 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8856) covalent geometry : angle 0.62122 (11976) SS BOND : bond 0.01429 ( 2) SS BOND : angle 1.83411 ( 4) hydrogen bonds : bond 0.06287 ( 388) hydrogen bonds : angle 4.84904 ( 1077) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.358 Fit side-chains REVERT: A 215 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8176 (ptmm) REVERT: A 270 MET cc_start: 0.7695 (mtt) cc_final: 0.7384 (mtm) REVERT: A 293 LYS cc_start: 0.8169 (mttt) cc_final: 0.7916 (mttm) REVERT: B 283 ARG cc_start: 0.7659 (tpt-90) cc_final: 0.7281 (tpt170) REVERT: B 323 ASP cc_start: 0.7785 (p0) cc_final: 0.7545 (p0) REVERT: E 38 ARG cc_start: 0.7890 (ttp-170) cc_final: 0.7401 (ttm170) REVERT: E 142 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.5397 (mtp) REVERT: E 194 MET cc_start: 0.4091 (ttt) cc_final: 0.2970 (tpt) outliers start: 11 outliers final: 4 residues processed: 156 average time/residue: 0.6359 time to fit residues: 105.2239 Evaluate side-chains 149 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain R residue 955 LEU Chi-restraints excluded: chain R residue 1162 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 16 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 67 optimal weight: 0.0970 chunk 14 optimal weight: 0.7980 chunk 92 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.153271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.130194 restraints weight = 12596.505| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.32 r_work: 0.3613 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8858 Z= 0.159 Angle : 0.598 9.575 11980 Z= 0.323 Chirality : 0.043 0.146 1358 Planarity : 0.004 0.046 1507 Dihedral : 4.956 29.069 1185 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.22 % Allowed : 12.88 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.48 (0.26), residues: 1078 helix: 1.49 (0.30), residues: 344 sheet: -0.17 (0.30), residues: 274 loop : -1.86 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 356 TYR 0.021 0.002 TYR R1112 PHE 0.024 0.002 PHE B 151 TRP 0.020 0.002 TRP B 82 HIS 0.008 0.001 HIS R1016 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8856) covalent geometry : angle 0.59772 (11976) SS BOND : bond 0.01368 ( 2) SS BOND : angle 1.77568 ( 4) hydrogen bonds : bond 0.05969 ( 388) hydrogen bonds : angle 4.67551 ( 1077) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.353 Fit side-chains REVERT: A 270 MET cc_start: 0.7632 (mtt) cc_final: 0.7358 (mtm) REVERT: B 283 ARG cc_start: 0.7644 (tpt-90) cc_final: 0.7203 (tpt170) REVERT: B 323 ASP cc_start: 0.7696 (p0) cc_final: 0.7458 (p0) REVERT: E 142 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.5369 (mtp) REVERT: E 194 MET cc_start: 0.3976 (ttt) cc_final: 0.2803 (tpt) outliers start: 21 outliers final: 10 residues processed: 157 average time/residue: 0.6184 time to fit residues: 103.0941 Evaluate side-chains 159 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 178 TRP Chi-restraints excluded: chain R residue 955 LEU Chi-restraints excluded: chain R residue 957 LEU Chi-restraints excluded: chain R residue 966 THR Chi-restraints excluded: chain R residue 968 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 936 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.152485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.129332 restraints weight = 12703.431| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.33 r_work: 0.3602 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8858 Z= 0.178 Angle : 0.607 9.579 11980 Z= 0.328 Chirality : 0.044 0.148 1358 Planarity : 0.004 0.045 1507 Dihedral : 4.998 29.415 1185 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.11 % Allowed : 16.05 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.46 (0.26), residues: 1078 helix: 1.51 (0.30), residues: 345 sheet: -0.25 (0.30), residues: 278 loop : -1.81 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 356 TYR 0.021 0.002 TYR R1112 PHE 0.027 0.002 PHE B 151 TRP 0.019 0.002 TRP B 82 HIS 0.010 0.001 HIS R1016 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 8856) covalent geometry : angle 0.60557 (11976) SS BOND : bond 0.01440 ( 2) SS BOND : angle 1.97210 ( 4) hydrogen bonds : bond 0.06259 ( 388) hydrogen bonds : angle 4.67867 ( 1077) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.343 Fit side-chains REVERT: A 220 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8307 (ttmm) REVERT: A 270 MET cc_start: 0.7690 (mtt) cc_final: 0.7409 (mtm) REVERT: B 137 ARG cc_start: 0.7772 (ttm170) cc_final: 0.7531 (mmt90) REVERT: B 214 ARG cc_start: 0.7588 (mtm180) cc_final: 0.7297 (mtt180) REVERT: E 142 MET cc_start: 0.6885 (OUTLIER) cc_final: 0.5396 (mtp) REVERT: E 194 MET cc_start: 0.4135 (ttt) cc_final: 0.3665 (tpt) outliers start: 20 outliers final: 12 residues processed: 158 average time/residue: 0.6190 time to fit residues: 103.7067 Evaluate side-chains 164 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 178 TRP Chi-restraints excluded: chain R residue 955 LEU Chi-restraints excluded: chain R residue 957 LEU Chi-restraints excluded: chain R residue 966 THR Chi-restraints excluded: chain R residue 968 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 39 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 15 optimal weight: 0.0170 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 chunk 92 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 36 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 974 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.155472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.132505 restraints weight = 12685.586| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.31 r_work: 0.3644 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8858 Z= 0.116 Angle : 0.541 9.820 11980 Z= 0.292 Chirality : 0.042 0.158 1358 Planarity : 0.004 0.043 1507 Dihedral : 4.636 26.237 1185 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.32 % Allowed : 17.21 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.23 (0.27), residues: 1078 helix: 1.73 (0.30), residues: 345 sheet: -0.14 (0.30), residues: 281 loop : -1.69 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 356 TYR 0.008 0.001 TYR E 192 PHE 0.024 0.001 PHE R 989 TRP 0.021 0.002 TRP B 82 HIS 0.005 0.001 HIS R1016 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8856) covalent geometry : angle 0.54082 (11976) SS BOND : bond 0.01200 ( 2) SS BOND : angle 1.52265 ( 4) hydrogen bonds : bond 0.04814 ( 388) hydrogen bonds : angle 4.37939 ( 1077) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.363 Fit side-chains REVERT: A 58 LYS cc_start: 0.7931 (tmmm) cc_final: 0.7575 (ttpp) REVERT: A 220 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8359 (ttmm) REVERT: A 270 MET cc_start: 0.7653 (mtt) cc_final: 0.7409 (mtm) REVERT: B 170 ASP cc_start: 0.8129 (t70) cc_final: 0.7893 (OUTLIER) REVERT: B 214 ARG cc_start: 0.7524 (mtm180) cc_final: 0.7270 (mtt180) REVERT: E 7 SER cc_start: 0.8111 (t) cc_final: 0.7754 (p) REVERT: E 194 MET cc_start: 0.3917 (ttt) cc_final: 0.2918 (tpt) REVERT: R 936 HIS cc_start: 0.6845 (OUTLIER) cc_final: 0.6582 (t-90) outliers start: 22 outliers final: 13 residues processed: 160 average time/residue: 0.6207 time to fit residues: 105.3855 Evaluate side-chains 165 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 178 TRP Chi-restraints excluded: chain R residue 936 HIS Chi-restraints excluded: chain R residue 955 LEU Chi-restraints excluded: chain R residue 957 LEU Chi-restraints excluded: chain R residue 966 THR Chi-restraints excluded: chain R residue 1035 ILE Chi-restraints excluded: chain R residue 1162 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 105 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 936 HIS R 974 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.150693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.127455 restraints weight = 12544.485| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.33 r_work: 0.3571 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 8858 Z= 0.259 Angle : 0.681 9.248 11980 Z= 0.366 Chirality : 0.046 0.167 1358 Planarity : 0.005 0.046 1507 Dihedral : 5.210 31.523 1185 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.06 % Allowed : 18.06 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.47 (0.26), residues: 1078 helix: 1.50 (0.30), residues: 344 sheet: -0.27 (0.30), residues: 277 loop : -1.80 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 356 TYR 0.019 0.002 TYR E 192 PHE 0.037 0.003 PHE B 151 TRP 0.020 0.002 TRP E 178 HIS 0.009 0.002 HIS R1016 Details of bonding type rmsd covalent geometry : bond 0.00621 ( 8856) covalent geometry : angle 0.67996 (11976) SS BOND : bond 0.01708 ( 2) SS BOND : angle 2.59178 ( 4) hydrogen bonds : bond 0.07237 ( 388) hydrogen bonds : angle 4.83999 ( 1077) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.324 Fit side-chains REVERT: A 38 ARG cc_start: 0.8010 (ttm110) cc_final: 0.7761 (ttp80) REVERT: A 58 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7666 (ttpp) REVERT: A 220 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8222 (ttmm) REVERT: A 221 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7796 (mtt) REVERT: B 262 MET cc_start: 0.7749 (tpp) cc_final: 0.7105 (mpt) REVERT: E 7 SER cc_start: 0.8183 (t) cc_final: 0.7793 (p) REVERT: E 38 ARG cc_start: 0.7768 (ttp-170) cc_final: 0.7292 (ttm170) REVERT: E 142 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.5488 (mtp) REVERT: E 194 MET cc_start: 0.4319 (ttt) cc_final: 0.3760 (tpt) REVERT: R 1086 THR cc_start: 0.7808 (m) cc_final: 0.7521 (t) outliers start: 29 outliers final: 18 residues processed: 169 average time/residue: 0.5615 time to fit residues: 101.2882 Evaluate side-chains 173 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 178 TRP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 955 LEU Chi-restraints excluded: chain R residue 957 LEU Chi-restraints excluded: chain R residue 966 THR Chi-restraints excluded: chain R residue 968 CYS Chi-restraints excluded: chain R residue 1035 ILE Chi-restraints excluded: chain R residue 1162 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 103 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 974 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.153173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.129877 restraints weight = 12767.189| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.35 r_work: 0.3608 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8858 Z= 0.153 Angle : 0.600 9.914 11980 Z= 0.322 Chirality : 0.043 0.178 1358 Planarity : 0.004 0.046 1507 Dihedral : 4.887 29.810 1185 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.53 % Allowed : 19.11 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.40 (0.26), residues: 1078 helix: 1.60 (0.30), residues: 345 sheet: -0.20 (0.30), residues: 277 loop : -1.81 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 356 TYR 0.011 0.001 TYR E 192 PHE 0.026 0.002 PHE R 989 TRP 0.020 0.002 TRP B 82 HIS 0.007 0.001 HIS R1016 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8856) covalent geometry : angle 0.59942 (11976) SS BOND : bond 0.01464 ( 2) SS BOND : angle 2.05278 ( 4) hydrogen bonds : bond 0.05748 ( 388) hydrogen bonds : angle 4.59946 ( 1077) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.235 Fit side-chains REVERT: A 38 ARG cc_start: 0.7873 (ttm110) cc_final: 0.7602 (ttp80) REVERT: A 58 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7595 (ttpp) REVERT: A 220 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8298 (ttmm) REVERT: A 221 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7726 (mtt) REVERT: B 214 ARG cc_start: 0.7527 (mtm180) cc_final: 0.7282 (mtt180) REVERT: E 7 SER cc_start: 0.8126 (t) cc_final: 0.7760 (p) REVERT: E 38 ARG cc_start: 0.7712 (ttp-170) cc_final: 0.7266 (ttm170) REVERT: E 194 MET cc_start: 0.4192 (ttt) cc_final: 0.2964 (tpt) REVERT: R 936 HIS cc_start: 0.6916 (OUTLIER) cc_final: 0.6648 (t-90) REVERT: R 1086 THR cc_start: 0.7709 (m) cc_final: 0.7362 (t) outliers start: 24 outliers final: 16 residues processed: 159 average time/residue: 0.5966 time to fit residues: 100.7689 Evaluate side-chains 166 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 178 TRP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 936 HIS Chi-restraints excluded: chain R residue 955 LEU Chi-restraints excluded: chain R residue 957 LEU Chi-restraints excluded: chain R residue 966 THR Chi-restraints excluded: chain R residue 1020 LEU Chi-restraints excluded: chain R residue 1035 ILE Chi-restraints excluded: chain R residue 1162 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 974 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.152466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.129277 restraints weight = 12566.573| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.32 r_work: 0.3600 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8858 Z= 0.185 Angle : 0.633 9.984 11980 Z= 0.338 Chirality : 0.044 0.208 1358 Planarity : 0.004 0.045 1507 Dihedral : 4.958 30.069 1185 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.96 % Allowed : 19.32 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.46 (0.26), residues: 1078 helix: 1.52 (0.30), residues: 345 sheet: -0.24 (0.30), residues: 277 loop : -1.81 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 356 TYR 0.014 0.002 TYR E 192 PHE 0.028 0.002 PHE B 151 TRP 0.017 0.002 TRP B 82 HIS 0.009 0.001 HIS E 234 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 8856) covalent geometry : angle 0.63132 (11976) SS BOND : bond 0.01528 ( 2) SS BOND : angle 2.22425 ( 4) hydrogen bonds : bond 0.06212 ( 388) hydrogen bonds : angle 4.71493 ( 1077) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.332 Fit side-chains REVERT: A 38 ARG cc_start: 0.7884 (ttm110) cc_final: 0.7579 (mtp-110) REVERT: A 58 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7649 (ttpp) REVERT: A 215 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8147 (mtpp) REVERT: A 220 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8262 (ttmm) REVERT: A 221 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7774 (mtt) REVERT: B 214 ARG cc_start: 0.7544 (mtm180) cc_final: 0.7300 (mtt180) REVERT: B 262 MET cc_start: 0.7765 (tpp) cc_final: 0.7117 (mpt) REVERT: E 7 SER cc_start: 0.8130 (t) cc_final: 0.7771 (p) REVERT: E 38 ARG cc_start: 0.7725 (ttp-170) cc_final: 0.7269 (ttm170) REVERT: E 142 MET cc_start: 0.6885 (OUTLIER) cc_final: 0.5302 (mtp) REVERT: E 194 MET cc_start: 0.4201 (ttt) cc_final: 0.3025 (tpt) REVERT: R 936 HIS cc_start: 0.6996 (OUTLIER) cc_final: 0.6635 (t-90) REVERT: R 1086 THR cc_start: 0.7717 (m) cc_final: 0.7367 (t) outliers start: 28 outliers final: 17 residues processed: 154 average time/residue: 0.6275 time to fit residues: 102.5748 Evaluate side-chains 168 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 178 TRP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 936 HIS Chi-restraints excluded: chain R residue 955 LEU Chi-restraints excluded: chain R residue 957 LEU Chi-restraints excluded: chain R residue 966 THR Chi-restraints excluded: chain R residue 968 CYS Chi-restraints excluded: chain R residue 999 ILE Chi-restraints excluded: chain R residue 1020 LEU Chi-restraints excluded: chain R residue 1035 ILE Chi-restraints excluded: chain R residue 1162 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 58 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 974 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.152947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.129801 restraints weight = 12651.726| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.31 r_work: 0.3609 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8858 Z= 0.163 Angle : 0.622 10.968 11980 Z= 0.333 Chirality : 0.044 0.184 1358 Planarity : 0.004 0.045 1507 Dihedral : 4.885 29.553 1185 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.85 % Allowed : 19.85 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.43 (0.26), residues: 1078 helix: 1.52 (0.30), residues: 345 sheet: -0.28 (0.30), residues: 281 loop : -1.76 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 356 TYR 0.013 0.001 TYR E 192 PHE 0.028 0.002 PHE R 989 TRP 0.019 0.002 TRP B 82 HIS 0.008 0.001 HIS R1016 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8856) covalent geometry : angle 0.62089 (11976) SS BOND : bond 0.01458 ( 2) SS BOND : angle 2.09495 ( 4) hydrogen bonds : bond 0.05896 ( 388) hydrogen bonds : angle 4.69193 ( 1077) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.230 Fit side-chains REVERT: A 38 ARG cc_start: 0.7872 (ttm110) cc_final: 0.7558 (mtp-110) REVERT: A 58 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7664 (ttpp) REVERT: A 215 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8146 (mtpp) REVERT: A 220 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8294 (ttmm) REVERT: A 221 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7745 (mtt) REVERT: B 214 ARG cc_start: 0.7544 (mtm180) cc_final: 0.7318 (mtt180) REVERT: B 262 MET cc_start: 0.7752 (tpp) cc_final: 0.7312 (mpp) REVERT: E 7 SER cc_start: 0.8113 (t) cc_final: 0.7756 (p) REVERT: E 38 ARG cc_start: 0.7722 (ttp-170) cc_final: 0.7276 (ttm170) REVERT: E 194 MET cc_start: 0.4207 (ttt) cc_final: 0.3006 (tpt) REVERT: R 936 HIS cc_start: 0.6953 (OUTLIER) cc_final: 0.6617 (t-90) outliers start: 27 outliers final: 20 residues processed: 155 average time/residue: 0.5769 time to fit residues: 94.8985 Evaluate side-chains 170 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 178 TRP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 936 HIS Chi-restraints excluded: chain R residue 955 LEU Chi-restraints excluded: chain R residue 957 LEU Chi-restraints excluded: chain R residue 966 THR Chi-restraints excluded: chain R residue 968 CYS Chi-restraints excluded: chain R residue 999 ILE Chi-restraints excluded: chain R residue 1020 LEU Chi-restraints excluded: chain R residue 1035 ILE Chi-restraints excluded: chain R residue 1040 VAL Chi-restraints excluded: chain R residue 1162 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 50 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 72 optimal weight: 0.0060 chunk 88 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 974 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.153584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.130470 restraints weight = 12646.356| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.31 r_work: 0.3619 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8858 Z= 0.152 Angle : 0.616 12.245 11980 Z= 0.330 Chirality : 0.043 0.188 1358 Planarity : 0.004 0.045 1507 Dihedral : 4.813 28.691 1185 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.75 % Allowed : 20.27 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.38 (0.26), residues: 1078 helix: 1.55 (0.30), residues: 345 sheet: -0.20 (0.30), residues: 280 loop : -1.74 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 356 TYR 0.012 0.001 TYR E 192 PHE 0.029 0.002 PHE R 989 TRP 0.020 0.002 TRP B 82 HIS 0.007 0.001 HIS R1016 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8856) covalent geometry : angle 0.61455 (11976) SS BOND : bond 0.01422 ( 2) SS BOND : angle 2.01261 ( 4) hydrogen bonds : bond 0.05659 ( 388) hydrogen bonds : angle 4.65836 ( 1077) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.345 Fit side-chains REVERT: A 58 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7668 (ttpp) REVERT: A 215 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8130 (mtpp) REVERT: A 220 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8291 (ttmm) REVERT: A 221 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7743 (mtt) REVERT: B 214 ARG cc_start: 0.7535 (mtm180) cc_final: 0.7312 (mtt180) REVERT: B 262 MET cc_start: 0.7743 (tpp) cc_final: 0.7298 (mpp) REVERT: E 7 SER cc_start: 0.8124 (t) cc_final: 0.7766 (p) REVERT: E 38 ARG cc_start: 0.7724 (ttp-170) cc_final: 0.7441 (ttm170) REVERT: E 194 MET cc_start: 0.4188 (ttt) cc_final: 0.2996 (tpt) REVERT: E 239 LEU cc_start: 0.7510 (mt) cc_final: 0.7169 (mt) REVERT: R 936 HIS cc_start: 0.6987 (OUTLIER) cc_final: 0.6636 (t-90) outliers start: 26 outliers final: 20 residues processed: 156 average time/residue: 0.5985 time to fit residues: 99.0168 Evaluate side-chains 173 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 178 TRP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 936 HIS Chi-restraints excluded: chain R residue 955 LEU Chi-restraints excluded: chain R residue 957 LEU Chi-restraints excluded: chain R residue 966 THR Chi-restraints excluded: chain R residue 968 CYS Chi-restraints excluded: chain R residue 999 ILE Chi-restraints excluded: chain R residue 1020 LEU Chi-restraints excluded: chain R residue 1035 ILE Chi-restraints excluded: chain R residue 1036 MET Chi-restraints excluded: chain R residue 1040 VAL Chi-restraints excluded: chain R residue 1162 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 94 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 90 optimal weight: 0.0970 chunk 18 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 974 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.153948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.130708 restraints weight = 12571.059| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.32 r_work: 0.3623 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8858 Z= 0.149 Angle : 0.618 12.615 11980 Z= 0.329 Chirality : 0.043 0.188 1358 Planarity : 0.004 0.044 1507 Dihedral : 4.776 28.253 1185 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.17 % Allowed : 19.96 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.36 (0.26), residues: 1078 helix: 1.55 (0.30), residues: 346 sheet: -0.16 (0.30), residues: 280 loop : -1.75 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 356 TYR 0.012 0.001 TYR E 192 PHE 0.029 0.002 PHE R 989 TRP 0.020 0.002 TRP B 82 HIS 0.007 0.001 HIS R1016 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8856) covalent geometry : angle 0.61709 (11976) SS BOND : bond 0.01409 ( 2) SS BOND : angle 1.97887 ( 4) hydrogen bonds : bond 0.05543 ( 388) hydrogen bonds : angle 4.63319 ( 1077) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3526.22 seconds wall clock time: 60 minutes 38.29 seconds (3638.29 seconds total)