Starting phenix.real_space_refine on Sat Jun 7 14:04:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wyb_32890/06_2025/7wyb_32890_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wyb_32890/06_2025/7wyb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wyb_32890/06_2025/7wyb_32890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wyb_32890/06_2025/7wyb_32890.map" model { file = "/net/cci-nas-00/data/ceres_data/7wyb_32890/06_2025/7wyb_32890_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wyb_32890/06_2025/7wyb_32890_neut.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.05, per 1000 atoms: 0.58 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: 2.03 Conformation dependent library (CDL) restraints added in 945.4 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: 0.94 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: 2.63 Time building geometry restraints manager: 2.43 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: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.290 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:13.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.360 ------------------------------------------------------------------------------- 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 : 5.06 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.002 TRP C 82 HIS 0.008 0.001 HIS R1016 PHE 0.028 0.003 PHE C 222 TYR 0.031 0.002 TYR C 105 ARG 0.006 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.12503 ( 402) hydrogen bonds : angle 5.88914 ( 1104) SS BOND : bond 0.00765 ( 2) SS BOND : angle 1.75124 ( 4) covalent geometry : bond 0.00537 ( 8941) covalent geometry : angle 0.80272 (12099) *********************** 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 : 0.836 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: 0.9925 time to fit residues: 125.9460 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 : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 98 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 B 255 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.189668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.161278 restraints weight = 12025.275| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 2.88 r_work: 0.4160 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.1010 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= 0.175 Angle : 0.652 9.955 12103 Z= 0.347 Chirality : 0.044 0.194 1369 Planarity : 0.004 0.056 1525 Dihedral : 5.348 47.330 1201 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.47 % Allowed : 8.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.25), residues: 1099 helix: 0.67 (0.29), residues: 348 sheet: 0.08 (0.32), residues: 275 loop : -2.02 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 211 HIS 0.006 0.001 HIS R1016 PHE 0.018 0.002 PHE C 253 TYR 0.024 0.002 TYR C 105 ARG 0.004 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.05384 ( 402) hydrogen bonds : angle 4.97819 ( 1104) SS BOND : bond 0.00579 ( 2) SS BOND : angle 1.41924 ( 4) covalent geometry : bond 0.00401 ( 8941) covalent geometry : angle 0.65122 (12099) *********************** 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 125 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: B 240 MET cc_start: 0.5728 (tmm) cc_final: 0.5181 (pp-130) REVERT: B 309 ASP cc_start: 0.5712 (m-30) cc_final: 0.5435 (m-30) REVERT: C 52 ARG cc_start: 0.7334 (mtt90) cc_final: 0.7092 (mtt90) REVERT: C 101 MET cc_start: 0.6241 (mtt) cc_final: 0.5931 (ttm) REVERT: C 219 ARG cc_start: 0.7209 (tpt-90) cc_final: 0.6952 (tpt-90) REVERT: C 239 ASN cc_start: 0.6953 (m-40) cc_final: 0.6230 (t0) REVERT: D 21 MET cc_start: 0.0089 (mtm) cc_final: -0.0393 (mtm) REVERT: E 76 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6744 (mtpp) REVERT: E 246 LYS cc_start: 0.7050 (ttmm) cc_final: 0.6758 (ttmm) REVERT: R 1114 MET cc_start: 0.6944 (tpp) cc_final: 0.6571 (tmm) outliers start: 14 outliers final: 7 residues processed: 114 average time/residue: 1.1585 time to fit residues: 142.0403 Evaluate side-chains 114 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 945 LEU 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 85 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.187062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.158747 restraints weight = 12222.794| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 2.88 r_work: 0.4134 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6110 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8943 Z= 0.225 Angle : 0.679 10.575 12103 Z= 0.362 Chirality : 0.045 0.222 1369 Planarity : 0.004 0.052 1525 Dihedral : 5.454 46.119 1201 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.31 % Allowed : 10.92 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.25), residues: 1099 helix: 0.50 (0.28), residues: 356 sheet: -0.04 (0.31), residues: 297 loop : -1.97 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 36 HIS 0.009 0.002 HIS R1016 PHE 0.024 0.003 PHE C 199 TYR 0.035 0.003 TYR C 105 ARG 0.003 0.000 ARG C 283 Details of bonding type rmsd hydrogen bonds : bond 0.05901 ( 402) hydrogen bonds : angle 4.99156 ( 1104) SS BOND : bond 0.00756 ( 2) SS BOND : angle 1.35202 ( 4) covalent geometry : bond 0.00524 ( 8941) covalent geometry : angle 0.67907 (12099) *********************** 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 134 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 MET cc_start: 0.5859 (OUTLIER) cc_final: 0.5189 (ppp) REVERT: B 309 ASP cc_start: 0.5746 (m-30) cc_final: 0.5454 (m-30) REVERT: C 52 ARG cc_start: 0.7374 (mtt90) cc_final: 0.7133 (mtt90) REVERT: C 101 MET cc_start: 0.6276 (mtt) cc_final: 0.5932 (ttm) REVERT: C 219 ARG cc_start: 0.7230 (tpt-90) cc_final: 0.6987 (tpt-90) REVERT: C 239 ASN cc_start: 0.6919 (m-40) cc_final: 0.6221 (t0) REVERT: D 21 MET cc_start: -0.0038 (mtm) cc_final: -0.0444 (mtm) REVERT: E 246 LYS cc_start: 0.7047 (ttmm) cc_final: 0.6798 (ttmm) REVERT: R 1026 MET cc_start: 0.4534 (mtt) cc_final: 0.4328 (mtt) REVERT: R 1114 MET cc_start: 0.7014 (tpp) cc_final: 0.6751 (tmm) REVERT: R 1117 HIS cc_start: 0.7435 (OUTLIER) cc_final: 0.7212 (m-70) outliers start: 22 outliers final: 10 residues processed: 120 average time/residue: 1.0652 time to fit residues: 137.5033 Evaluate side-chains 122 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain R residue 1058 MET Chi-restraints excluded: chain R residue 1109 ILE Chi-restraints excluded: chain R residue 1117 HIS 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 30 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 51 optimal weight: 0.0010 chunk 106 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 75 GLN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 ASN C 340 ASN E 233 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.190018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.161759 restraints weight = 12130.349| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 2.94 r_work: 0.4169 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8943 Z= 0.140 Angle : 0.589 10.600 12103 Z= 0.312 Chirality : 0.042 0.161 1369 Planarity : 0.004 0.046 1525 Dihedral : 4.966 42.292 1201 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.42 % Allowed : 13.24 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.25), residues: 1099 helix: 1.05 (0.29), residues: 347 sheet: 0.13 (0.31), residues: 290 loop : -1.88 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.005 0.001 HIS R1016 PHE 0.015 0.002 PHE C 151 TYR 0.018 0.002 TYR C 105 ARG 0.002 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.04580 ( 402) hydrogen bonds : angle 4.66974 ( 1104) SS BOND : bond 0.00619 ( 2) SS BOND : angle 1.18360 ( 4) covalent geometry : bond 0.00314 ( 8941) covalent geometry : angle 0.58831 (12099) *********************** 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 135 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: B 53 MET cc_start: 0.5817 (ppp) cc_final: 0.5189 (ppp) REVERT: B 186 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: C 52 ARG cc_start: 0.7334 (mtt90) cc_final: 0.7104 (mtt90) REVERT: C 101 MET cc_start: 0.6209 (mtt) cc_final: 0.5941 (mtm) REVERT: C 219 ARG cc_start: 0.7079 (tpt-90) cc_final: 0.6810 (tpt-90) REVERT: C 239 ASN cc_start: 0.6859 (m-40) cc_final: 0.6173 (t0) REVERT: C 268 ASN cc_start: 0.7409 (OUTLIER) cc_final: 0.7112 (t160) REVERT: D 21 MET cc_start: 0.0149 (mtm) cc_final: -0.0324 (mtm) REVERT: E 62 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6564 (m-30) REVERT: E 246 LYS cc_start: 0.6964 (ttmm) cc_final: 0.6717 (ttmm) REVERT: R 945 LEU cc_start: 0.6072 (OUTLIER) cc_final: 0.5851 (mp) REVERT: R 1114 MET cc_start: 0.7050 (tpp) cc_final: 0.6798 (tmm) outliers start: 23 outliers final: 11 residues processed: 122 average time/residue: 1.0765 time to fit residues: 141.4191 Evaluate side-chains 122 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 247 MET 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 C residue 268 ASN Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain R residue 945 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 67 optimal weight: 0.4980 chunk 31 optimal weight: 0.4980 chunk 74 optimal weight: 0.9990 chunk 39 optimal weight: 0.0470 chunk 102 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1117 HIS 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 = 0.190353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.161802 restraints weight = 12146.625| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 2.91 r_work: 0.4174 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8943 Z= 0.132 Angle : 0.571 10.480 12103 Z= 0.304 Chirality : 0.041 0.156 1369 Planarity : 0.003 0.043 1525 Dihedral : 4.811 44.080 1201 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.42 % Allowed : 14.29 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.26), residues: 1099 helix: 1.24 (0.29), residues: 347 sheet: 0.12 (0.31), residues: 289 loop : -1.82 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.005 0.001 HIS R1016 PHE 0.018 0.002 PHE C 241 TYR 0.015 0.001 TYR R1112 ARG 0.002 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.04354 ( 402) hydrogen bonds : angle 4.55769 ( 1104) SS BOND : bond 0.00556 ( 2) SS BOND : angle 1.09315 ( 4) covalent geometry : bond 0.00295 ( 8941) covalent geometry : angle 0.57123 (12099) *********************** 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 133 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: B 53 MET cc_start: 0.5743 (ppp) cc_final: 0.5148 (ppp) REVERT: B 198 MET cc_start: 0.7401 (mtp) cc_final: 0.6773 (mtt) REVERT: C 52 ARG cc_start: 0.7264 (mtt90) cc_final: 0.7044 (mtt90) REVERT: C 101 MET cc_start: 0.6225 (mtt) cc_final: 0.5938 (mtm) REVERT: C 219 ARG cc_start: 0.7064 (tpt-90) cc_final: 0.6757 (tpt-90) REVERT: C 239 ASN cc_start: 0.6852 (m-40) cc_final: 0.6166 (t0) REVERT: D 21 MET cc_start: 0.0077 (mtm) cc_final: -0.0357 (mtm) REVERT: E 246 LYS cc_start: 0.6965 (ttmm) cc_final: 0.6735 (ttmm) REVERT: R 945 LEU cc_start: 0.6052 (OUTLIER) cc_final: 0.5851 (mp) outliers start: 23 outliers final: 14 residues processed: 123 average time/residue: 1.0777 time to fit residues: 143.0472 Evaluate side-chains 123 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 E residue 232 MET Chi-restraints excluded: chain R residue 945 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 68 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 98 optimal weight: 0.0000 chunk 12 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1117 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.190589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.162063 restraints weight = 12036.879| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 2.92 r_work: 0.4167 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8943 Z= 0.147 Angle : 0.596 9.642 12103 Z= 0.313 Chirality : 0.042 0.229 1369 Planarity : 0.003 0.042 1525 Dihedral : 4.787 44.286 1201 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.94 % Allowed : 15.44 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.26), residues: 1099 helix: 1.26 (0.29), residues: 347 sheet: 0.05 (0.31), residues: 289 loop : -1.77 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R1143 HIS 0.006 0.001 HIS R1016 PHE 0.018 0.002 PHE B 199 TYR 0.015 0.001 TYR C 105 ARG 0.003 0.000 ARG C 48 Details of bonding type rmsd hydrogen bonds : bond 0.04489 ( 402) hydrogen bonds : angle 4.55531 ( 1104) SS BOND : bond 0.00680 ( 2) SS BOND : angle 1.01269 ( 4) covalent geometry : bond 0.00335 ( 8941) covalent geometry : angle 0.59612 (12099) *********************** 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 136 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: B 53 MET cc_start: 0.5577 (ppp) cc_final: 0.4969 (ppp) REVERT: B 198 MET cc_start: 0.7279 (mtp) cc_final: 0.6626 (mtt) REVERT: C 52 ARG cc_start: 0.7264 (mtt90) cc_final: 0.7025 (mtt90) REVERT: C 101 MET cc_start: 0.6179 (mtt) cc_final: 0.5879 (ttm) REVERT: C 219 ARG cc_start: 0.7068 (tpt-90) cc_final: 0.6746 (tpt-90) REVERT: C 239 ASN cc_start: 0.6844 (m-40) cc_final: 0.6158 (t0) REVERT: D 21 MET cc_start: 0.0033 (mtm) cc_final: -0.0402 (mtm) REVERT: R 945 LEU cc_start: 0.6054 (OUTLIER) cc_final: 0.5842 (mp) REVERT: R 1081 TRP cc_start: 0.6679 (t60) cc_final: 0.6449 (t60) outliers start: 28 outliers final: 18 residues processed: 122 average time/residue: 0.9949 time to fit residues: 131.3800 Evaluate side-chains 127 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET 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 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 69 THR 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 E residue 232 MET Chi-restraints excluded: chain R residue 945 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 90 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 22 optimal weight: 40.0000 chunk 57 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 0.0670 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.189535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.160847 restraints weight = 12154.222| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 2.92 r_work: 0.4165 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 moved from start: 0.2013 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 : 0.613 10.851 12103 Z= 0.320 Chirality : 0.042 0.193 1369 Planarity : 0.003 0.041 1525 Dihedral : 4.839 44.474 1201 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.94 % Allowed : 16.70 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.26), residues: 1099 helix: 1.12 (0.29), residues: 353 sheet: -0.04 (0.31), residues: 294 loop : -1.74 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.006 0.001 HIS R1191 PHE 0.017 0.002 PHE C 241 TYR 0.018 0.002 TYR R1112 ARG 0.002 0.000 ARG C 48 Details of bonding type rmsd hydrogen bonds : bond 0.04702 ( 402) hydrogen bonds : angle 4.54362 ( 1104) SS BOND : bond 0.00674 ( 2) SS BOND : angle 1.03667 ( 4) covalent geometry : bond 0.00374 ( 8941) covalent geometry : angle 0.61243 (12099) *********************** 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 137 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: B 53 MET cc_start: 0.5525 (ppp) cc_final: 0.4962 (ppp) REVERT: B 186 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: B 198 MET cc_start: 0.7258 (mtp) cc_final: 0.6595 (mtt) REVERT: B 353 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6474 (mp) REVERT: C 101 MET cc_start: 0.6207 (mtt) cc_final: 0.5928 (ttm) REVERT: C 219 ARG cc_start: 0.7074 (tpt-90) cc_final: 0.6707 (tpt-90) REVERT: C 239 ASN cc_start: 0.6834 (m-40) cc_final: 0.6156 (t0) REVERT: D 21 MET cc_start: 0.0177 (mtm) cc_final: -0.0260 (mtm) REVERT: E 194 MET cc_start: 0.6708 (OUTLIER) cc_final: 0.6322 (tmm) REVERT: R 945 LEU cc_start: 0.6055 (OUTLIER) cc_final: 0.5825 (mp) outliers start: 28 outliers final: 17 residues processed: 124 average time/residue: 1.0893 time to fit residues: 146.2779 Evaluate side-chains 126 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 GLU 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 B residue 307 PHE Chi-restraints excluded: chain B residue 353 LEU 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 E residue 69 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain R residue 945 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 50 optimal weight: 0.2980 chunk 73 optimal weight: 0.4980 chunk 67 optimal weight: 0.6980 chunk 55 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 87 optimal weight: 0.4980 chunk 92 optimal weight: 0.9990 chunk 29 optimal weight: 0.1980 chunk 105 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.192719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.163876 restraints weight = 12295.669| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 2.91 r_work: 0.4189 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8943 Z= 0.127 Angle : 0.588 10.528 12103 Z= 0.305 Chirality : 0.041 0.161 1369 Planarity : 0.003 0.040 1525 Dihedral : 4.643 43.766 1201 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.84 % Allowed : 17.33 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.26), residues: 1099 helix: 1.37 (0.29), residues: 345 sheet: -0.00 (0.31), residues: 289 loop : -1.65 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 211 HIS 0.004 0.001 HIS R1191 PHE 0.016 0.002 PHE B 199 TYR 0.011 0.001 TYR C 105 ARG 0.002 0.000 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 402) hydrogen bonds : angle 4.37979 ( 1104) SS BOND : bond 0.00588 ( 2) SS BOND : angle 0.95662 ( 4) covalent geometry : bond 0.00285 ( 8941) covalent geometry : angle 0.58794 (12099) *********************** 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 125 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: B 53 MET cc_start: 0.5476 (ppp) cc_final: 0.4949 (pp-130) REVERT: B 198 MET cc_start: 0.7108 (mtp) cc_final: 0.6452 (mtt) REVERT: B 353 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6745 (mp) REVERT: C 101 MET cc_start: 0.6154 (mtt) cc_final: 0.5882 (mtm) REVERT: C 219 ARG cc_start: 0.7060 (tpt-90) cc_final: 0.6771 (tpt-90) REVERT: C 239 ASN cc_start: 0.6823 (m-40) cc_final: 0.6174 (t0) REVERT: D 21 MET cc_start: 0.0192 (mtm) cc_final: -0.0210 (mtm) outliers start: 27 outliers final: 18 residues processed: 112 average time/residue: 1.0571 time to fit residues: 127.7743 Evaluate side-chains 114 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET 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 B residue 307 PHE Chi-restraints excluded: chain B residue 353 LEU 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 E residue 69 THR 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 1011 PHE Chi-restraints excluded: chain R residue 1058 MET Chi-restraints excluded: chain R residue 1079 VAL 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 46 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 6 optimal weight: 0.0370 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.0040 chunk 106 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 overall best weight: 0.5270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.191984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.163036 restraints weight = 12175.006| |-----------------------------------------------------------------------------| r_work (start): 0.4307 rms_B_bonded: 2.89 r_work: 0.4185 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6040 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8943 Z= 0.138 Angle : 0.607 12.108 12103 Z= 0.312 Chirality : 0.041 0.167 1369 Planarity : 0.003 0.040 1525 Dihedral : 4.643 44.391 1201 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.42 % Allowed : 18.49 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1099 helix: 1.38 (0.29), residues: 345 sheet: -0.06 (0.31), residues: 289 loop : -1.58 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 211 HIS 0.005 0.001 HIS R1191 PHE 0.028 0.002 PHE B 199 TYR 0.019 0.001 TYR R1112 ARG 0.001 0.000 ARG C 48 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 402) hydrogen bonds : angle 4.37738 ( 1104) SS BOND : bond 0.00613 ( 2) SS BOND : angle 0.91747 ( 4) covalent geometry : bond 0.00313 ( 8941) covalent geometry : angle 0.60735 (12099) *********************** 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 121 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: B 53 MET cc_start: 0.5538 (ppp) cc_final: 0.5031 (pp-130) REVERT: B 198 MET cc_start: 0.7013 (mtp) cc_final: 0.6424 (mtt) REVERT: B 353 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6760 (mp) REVERT: C 101 MET cc_start: 0.6200 (mtt) cc_final: 0.5912 (mtm) REVERT: C 219 ARG cc_start: 0.7070 (tpt-90) cc_final: 0.6781 (tpt-90) REVERT: C 239 ASN cc_start: 0.6833 (m-40) cc_final: 0.6206 (t0) REVERT: D 21 MET cc_start: 0.0191 (mtm) cc_final: -0.0217 (mtm) REVERT: E 174 THR cc_start: 0.7492 (OUTLIER) cc_final: 0.7223 (p) outliers start: 23 outliers final: 16 residues processed: 111 average time/residue: 1.0130 time to fit residues: 121.5328 Evaluate side-chains 117 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET 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 B residue 307 PHE Chi-restraints excluded: chain B residue 353 LEU 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 E residue 69 THR 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 1011 PHE Chi-restraints excluded: chain R residue 1058 MET Chi-restraints excluded: chain R residue 1079 VAL 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 38 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 98 optimal weight: 0.2980 chunk 105 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 100 optimal weight: 0.2980 chunk 78 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.192993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.164503 restraints weight = 12143.845| |-----------------------------------------------------------------------------| r_work (start): 0.4320 rms_B_bonded: 2.82 r_work: 0.4203 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8943 Z= 0.126 Angle : 0.595 11.189 12103 Z= 0.306 Chirality : 0.041 0.150 1369 Planarity : 0.003 0.040 1525 Dihedral : 4.549 44.316 1201 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.10 % Allowed : 18.59 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.26), residues: 1099 helix: 1.45 (0.29), residues: 345 sheet: -0.05 (0.31), residues: 288 loop : -1.46 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R1081 HIS 0.005 0.001 HIS R1016 PHE 0.032 0.002 PHE B 199 TYR 0.011 0.001 TYR C 105 ARG 0.002 0.000 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 402) hydrogen bonds : angle 4.30991 ( 1104) SS BOND : bond 0.00615 ( 2) SS BOND : angle 0.93846 ( 4) covalent geometry : bond 0.00284 ( 8941) covalent geometry : angle 0.59521 (12099) ********************** 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 120 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: B 53 MET cc_start: 0.5478 (ppp) cc_final: 0.4973 (pp-130) REVERT: B 198 MET cc_start: 0.6916 (mtp) cc_final: 0.6278 (mtt) REVERT: B 353 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6761 (mt) REVERT: C 101 MET cc_start: 0.6108 (mtt) cc_final: 0.5808 (ttm) REVERT: C 219 ARG cc_start: 0.7000 (tpt-90) cc_final: 0.6712 (tpt-90) REVERT: C 239 ASN cc_start: 0.6790 (m-40) cc_final: 0.6154 (t0) REVERT: D 21 MET cc_start: 0.0195 (mtm) cc_final: -0.0207 (mtm) outliers start: 20 outliers final: 17 residues processed: 111 average time/residue: 1.1088 time to fit residues: 133.8291 Evaluate side-chains 118 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET 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 B residue 307 PHE Chi-restraints excluded: chain B residue 353 LEU 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 E residue 69 THR 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 1011 PHE Chi-restraints excluded: chain R residue 1058 MET Chi-restraints excluded: chain R residue 1079 VAL 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 37 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 0.0870 chunk 34 optimal weight: 0.0070 chunk 30 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.193129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.164605 restraints weight = 12210.490| |-----------------------------------------------------------------------------| r_work (start): 0.4320 rms_B_bonded: 2.88 r_work: 0.4200 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8943 Z= 0.128 Angle : 0.605 12.389 12103 Z= 0.309 Chirality : 0.041 0.153 1369 Planarity : 0.003 0.040 1525 Dihedral : 4.550 44.527 1201 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.10 % Allowed : 19.22 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.26), residues: 1099 helix: 1.50 (0.29), residues: 344 sheet: -0.04 (0.31), residues: 288 loop : -1.44 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R1081 HIS 0.005 0.001 HIS R1016 PHE 0.034 0.002 PHE B 199 TYR 0.021 0.001 TYR R1112 ARG 0.002 0.000 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 402) hydrogen bonds : angle 4.33547 ( 1104) SS BOND : bond 0.00577 ( 2) SS BOND : angle 0.87700 ( 4) covalent geometry : bond 0.00289 ( 8941) covalent geometry : angle 0.60452 (12099) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7525.95 seconds wall clock time: 131 minutes 21.70 seconds (7881.70 seconds total)