Starting phenix.real_space_refine on Wed Aug 5 15:49:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rx1_54355/08_2026/9rx1_54355.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rx1_54355/08_2026/9rx1_54355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rx1_54355/08_2026/9rx1_54355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rx1_54355/08_2026/9rx1_54355.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rx1_54355/08_2026/9rx1_54355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rx1_54355/08_2026/9rx1_54355.map" } resolution = 4.2 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= 0.025 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: 5 Type Number sf(0) Gaussians S 24 5.16 5 C 3247 2.51 5 N 831 2.21 5 O 870 1.98 5 H 5022 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9994 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 9973 Classifications: {'peptide': 629} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 593} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'P32': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.56, per 1000 atoms: 0.16 Number of scatterers: 9994 At special positions: 0 Unit cell: (76.096, 85.28, 124.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 O 870 8.00 N 831 7.00 C 3247 6.00 H 5022 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS A 199 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 198 " distance=2.04 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: 0.85 Conformation dependent library (CDL) restraints added in 279.7 milliseconds 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1178 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 6 sheets defined 67.9% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 36 through 61 removed outlier: 3.740A pdb=" N GLY A 43 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 47 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET A 48 " --> pdb=" O MET A 44 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 55 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 69 removed outlier: 4.454A pdb=" N ALA A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 74 through 94 removed outlier: 3.681A pdb=" N PHE A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 removed outlier: 3.593A pdb=" N THR A 100 " --> pdb=" O PRO A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 145 removed outlier: 3.562A pdb=" N CYS A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP A 121 " --> pdb=" O TRP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 removed outlier: 4.128A pdb=" N SER A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 179 removed outlier: 3.724A pdb=" N ALA A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N CYS A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TRP A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 186 through 194 removed outlier: 3.973A pdb=" N CYS A 192 " --> pdb=" O GLN A 188 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 216 through 234 Processing helix chain 'A' and resid 236 through 1040 removed outlier: 3.513A pdb=" N THR A1033 " --> pdb=" O HIS A1029 " (cutoff:3.500A) Proline residue: A1034 - end of helix Processing helix chain 'A' and resid 1081 through 1097 removed outlier: 4.250A pdb=" N PHE A1085 " --> pdb=" O VAL A1081 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A1086 " --> pdb=" O SER A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1109 removed outlier: 4.082A pdb=" N TYR A1108 " --> pdb=" O PRO A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1118 Processing helix chain 'A' and resid 1121 through 1127 removed outlier: 4.078A pdb=" N LEU A1125 " --> pdb=" O THR A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1154 Processing helix chain 'A' and resid 1167 through 1179 removed outlier: 3.801A pdb=" N ILE A1171 " --> pdb=" O ALA A1167 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A1173 " --> pdb=" O SER A1169 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A1175 " --> pdb=" O ILE A1171 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A1176 " --> pdb=" O GLY A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1194 Processing helix chain 'A' and resid 1194 through 1199 Processing helix chain 'A' and resid 1208 through 1215 removed outlier: 4.419A pdb=" N LYS A1213 " --> pdb=" O ALA A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1238 removed outlier: 3.623A pdb=" N ALA A1236 " --> pdb=" O LEU A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1255 removed outlier: 3.570A pdb=" N ASN A1253 " --> pdb=" O TRP A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1259 Processing helix chain 'A' and resid 1261 through 1273 removed outlier: 3.554A pdb=" N ILE A1268 " --> pdb=" O LEU A1264 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN A1269 " --> pdb=" O GLN A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1304 removed outlier: 3.823A pdb=" N ILE A1299 " --> pdb=" O ASN A1295 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A1300 " --> pdb=" O PRO A1296 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN A1301 " --> pdb=" O ASP A1297 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP A1304 " --> pdb=" O ILE A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1309 Processing helix chain 'A' and resid 1361 through 285 removed outlier: 3.985A pdb=" N ARG A1365 " --> pdb=" O PRO A1361 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU A 285 " --> pdb=" O ASN A1374 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 316 Proline residue: A 305 - end of helix Processing helix chain 'A' and resid 321 through 334 removed outlier: 3.565A pdb=" N PHE A 325 " --> pdb=" O PRO A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 346 Proline residue: A 340 - end of helix removed outlier: 3.902A pdb=" N ARG A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 346 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 357 Processing sheet with id=AA1, first strand: chain 'A' and resid 1044 through 1050 removed outlier: 3.627A pdb=" N VAL A1342 " --> pdb=" O LYS A1331 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A1344 " --> pdb=" O VAL A1329 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A1329 " --> pdb=" O PHE A1344 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1061 through 1063 removed outlier: 3.525A pdb=" N ASP A1063 " --> pdb=" O GLN A1068 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1076 through 1077 Processing sheet with id=AA4, first strand: chain 'A' and resid 1163 through 1164 removed outlier: 3.542A pdb=" N ARG A1312 " --> pdb=" O ARG A1164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1218 through 1220 Processing sheet with id=AA6, first strand: chain 'A' and resid 1288 through 1289 removed outlier: 7.139A pdb=" N MET A1281 " --> pdb=" O GLN A1277 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLN A1277 " --> pdb=" O MET A1281 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN A1283 " --> pdb=" O TYR A1275 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TYR A1275 " --> pdb=" O ILE A1317 " (cutoff:3.500A) 267 hydrogen bonds defined for protein. 756 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: 1.92 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5016 1.03 - 1.23: 7 1.23 - 1.42: 2126 1.42 - 1.61: 2942 1.61 - 1.81: 38 Bond restraints: 10129 Sorted by residual: bond pdb=" CB CYS A 192 " pdb=" SG CYS A 192 " ideal model delta sigma weight residual 1.808 1.771 0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CG PHE A 306 " pdb=" CD2 PHE A 306 " ideal model delta sigma weight residual 1.384 1.367 0.017 2.10e-02 2.27e+03 6.41e-01 bond pdb=" CB LYS A1115 " pdb=" CG LYS A1115 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 4.77e-01 bond pdb=" CB PHE A 306 " pdb=" CG PHE A 306 " ideal model delta sigma weight residual 1.502 1.487 0.015 2.30e-02 1.89e+03 4.50e-01 bond pdb=" CB GLN A1196 " pdb=" CG GLN A1196 " ideal model delta sigma weight residual 1.520 1.540 -0.020 3.00e-02 1.11e+03 4.36e-01 ... (remaining 10124 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 18174 1.75 - 3.50: 158 3.50 - 5.26: 24 5.26 - 7.01: 1 7.01 - 8.76: 1 Bond angle restraints: 18358 Sorted by residual: angle pdb=" CA CYS A 192 " pdb=" CB CYS A 192 " pdb=" SG CYS A 192 " ideal model delta sigma weight residual 114.40 121.20 -6.80 2.30e+00 1.89e-01 8.74e+00 angle pdb=" C LYS A 191 " pdb=" N CYS A 192 " pdb=" CA CYS A 192 " ideal model delta sigma weight residual 122.54 117.71 4.83 1.65e+00 3.67e-01 8.55e+00 angle pdb=" CB MET A 296 " pdb=" CG MET A 296 " pdb=" SD MET A 296 " ideal model delta sigma weight residual 112.70 121.46 -8.76 3.00e+00 1.11e-01 8.52e+00 angle pdb=" N CYS A 199 " pdb=" CA CYS A 199 " pdb=" C CYS A 199 " ideal model delta sigma weight residual 110.88 108.04 2.84 1.28e+00 6.10e-01 4.94e+00 angle pdb=" N ALA A 288 " pdb=" CA ALA A 288 " pdb=" C ALA A 288 " ideal model delta sigma weight residual 113.28 110.01 3.27 1.57e+00 4.06e-01 4.35e+00 ... (remaining 18353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 4392 16.93 - 33.87: 249 33.87 - 50.80: 83 50.80 - 67.73: 34 67.73 - 84.67: 7 Dihedral angle restraints: 4765 sinusoidal: 2565 harmonic: 2200 Sorted by residual: dihedral pdb=" CA CYS A 192 " pdb=" C CYS A 192 " pdb=" N TYR A 193 " pdb=" CA TYR A 193 " ideal model delta harmonic sigma weight residual 180.00 154.86 25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA TYR A1360 " pdb=" C TYR A1360 " pdb=" N PRO A1361 " pdb=" CA PRO A1361 " ideal model delta harmonic sigma weight residual -180.00 -158.56 -21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA CYS A 198 " pdb=" C CYS A 198 " pdb=" N CYS A 199 " pdb=" CA CYS A 199 " ideal model delta harmonic sigma weight residual 180.00 158.73 21.27 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 4762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 467 0.027 - 0.053: 185 0.053 - 0.080: 80 0.080 - 0.107: 40 0.107 - 0.134: 20 Chirality restraints: 792 Sorted by residual: chirality pdb=" CA VAL A1207 " pdb=" N VAL A1207 " pdb=" C VAL A1207 " pdb=" CB VAL A1207 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE A1120 " pdb=" N ILE A1120 " pdb=" C ILE A1120 " pdb=" CB ILE A1120 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE A1259 " pdb=" N ILE A1259 " pdb=" C ILE A1259 " pdb=" CB ILE A1259 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 ... (remaining 789 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 292 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C LEU A 292 " 0.038 2.00e-02 2.50e+03 pdb=" O LEU A 292 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY A 293 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A1041 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A1042 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A1042 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1042 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A1360 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO A1361 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A1361 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1361 " -0.021 5.00e-02 4.00e+02 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.34: 2890 2.34 - 2.90: 22773 2.90 - 3.47: 25133 3.47 - 4.03: 32345 4.03 - 4.60: 48711 Nonbonded interactions: 131852 Sorted by model distance: nonbonded pdb="HD22 ASN A 313 " pdb=" HD2 PHE A 325 " model vdw 1.771 2.100 nonbonded pdb=" HG1 THR A 74 " pdb=" H ASN A 77 " model vdw 1.795 2.100 nonbonded pdb=" O ASN A 329 " pdb="HD21 ASN A 329 " model vdw 1.863 2.450 nonbonded pdb=" HG1 THR A1335 " pdb=" H GLY A1337 " model vdw 1.870 2.100 nonbonded pdb=" HA THR A1127 " pdb="HE22 GLN A1283 " model vdw 1.898 2.270 ... (remaining 131847 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 0.480 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: 0.040 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.320 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 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 : 0.002 0.037 5109 Z= 0.104 Angle : 0.533 8.758 6979 Z= 0.275 Chirality : 0.041 0.134 792 Planarity : 0.004 0.046 867 Dihedral : 11.097 75.748 1818 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.89 (0.33), residues: 627 helix: 1.24 (0.29), residues: 310 sheet: -1.56 (0.79), residues: 40 loop : 0.34 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1248 TYR 0.012 0.001 TYR A1061 PHE 0.009 0.001 PHE A 307 TRP 0.013 0.001 TRP A 323 HIS 0.004 0.001 HIS A1029 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 ( 5107) covalent geometry : angle 0.52817 / 0.27 ( 6975) SS BOND : bond 0.00921 / 0.44 ( 2) SS BOND : angle 3.05940 / 0.92 ( 4) hydrogen bonds : bond 0.26691 / 18.09 ( 267) hydrogen bonds : angle 8.49388 / 6.17 ( 756) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 VAL cc_start: 0.8126 (t) cc_final: 0.7902 (m) REVERT: A 77 ASN cc_start: 0.9188 (m-40) cc_final: 0.8770 (t0) REVERT: A 97 PHE cc_start: 0.8480 (m-80) cc_final: 0.8006 (m-10) REVERT: A 138 ASP cc_start: 0.8732 (t70) cc_final: 0.8313 (t70) REVERT: A 178 MET cc_start: 0.7660 (mpp) cc_final: 0.7258 (mpp) REVERT: A 192 CYS cc_start: 0.7889 (p) cc_final: 0.7664 (p) REVERT: A 1260 ASN cc_start: 0.8336 (m-40) cc_final: 0.7651 (p0) REVERT: A 1273 SER cc_start: 0.9231 (t) cc_final: 0.8879 (p) REVERT: A 1282 TYR cc_start: 0.8682 (m-80) cc_final: 0.8322 (m-80) REVERT: A 331 LEU cc_start: 0.9185 (tp) cc_final: 0.8967 (tp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1273 time to fit residues: 19.3772 Evaluate side-chains 93 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 0.5980 chunk 24 optimal weight: 0.0870 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.0770 chunk 16 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.116453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.093721 restraints weight = 43582.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.099322 restraints weight = 20579.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.102980 restraints weight = 11856.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.105585 restraints weight = 7758.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.107143 restraints weight = 5508.683| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5109 Z= 0.149 Angle : 0.575 6.608 6979 Z= 0.312 Chirality : 0.041 0.159 792 Planarity : 0.004 0.033 867 Dihedral : 5.283 37.756 683 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.23 (0.33), residues: 627 helix: 1.33 (0.28), residues: 330 sheet: -0.75 (0.82), residues: 35 loop : 0.56 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1365 TYR 0.007 0.001 TYR A 231 PHE 0.011 0.001 PHE A 325 TRP 0.010 0.001 TRP A 323 HIS 0.001 0.001 HIS A1124 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 ( 5107) covalent geometry : angle 0.57444 / 0.31 ( 6975) SS BOND : bond 0.00206 / 0.10 ( 2) SS BOND : angle 1.42012 / 0.48 ( 4) hydrogen bonds : bond 0.07453 / 4.97 ( 267) hydrogen bonds : angle 5.80770 / 4.15 ( 756) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.4655 (ptt) cc_final: 0.4210 (ptt) REVERT: A 52 VAL cc_start: 0.8216 (t) cc_final: 0.8005 (m) REVERT: A 77 ASN cc_start: 0.9241 (m110) cc_final: 0.8700 (t0) REVERT: A 97 PHE cc_start: 0.8427 (m-80) cc_final: 0.8122 (m-80) REVERT: A 138 ASP cc_start: 0.8926 (t70) cc_final: 0.8537 (t70) REVERT: A 1056 TYR cc_start: 0.7788 (m-10) cc_final: 0.7457 (m-10) REVERT: A 1173 LEU cc_start: 0.9734 (tp) cc_final: 0.9510 (tt) REVERT: A 1244 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8291 (mp0) REVERT: A 1245 ASP cc_start: 0.8778 (m-30) cc_final: 0.8563 (m-30) REVERT: A 1273 SER cc_start: 0.9221 (t) cc_final: 0.8982 (p) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1274 time to fit residues: 20.0175 Evaluate side-chains 90 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 48 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.115937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.092439 restraints weight = 46178.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.097896 restraints weight = 22529.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.101639 restraints weight = 13409.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.104119 restraints weight = 8918.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.105496 restraints weight = 6479.000| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5109 Z= 0.134 Angle : 0.532 4.595 6979 Z= 0.287 Chirality : 0.040 0.142 792 Planarity : 0.004 0.034 867 Dihedral : 5.260 38.263 683 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.19 % Allowed : 0.38 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.17 (0.33), residues: 627 helix: 1.36 (0.29), residues: 331 sheet: -0.60 (0.76), residues: 35 loop : 0.38 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 155 TYR 0.011 0.001 TYR A1282 PHE 0.005 0.001 PHE A 325 TRP 0.008 0.001 TRP A 323 HIS 0.002 0.001 HIS A1124 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 5107) covalent geometry : angle 0.52985 / 0.29 ( 6975) SS BOND : bond 0.00731 / 0.35 ( 2) SS BOND : angle 1.86329 / 0.90 ( 4) hydrogen bonds : bond 0.05804 / 3.84 ( 267) hydrogen bonds : angle 5.44002 / 3.89 ( 756) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.4741 (ptt) cc_final: 0.4483 (ptt) REVERT: A 77 ASN cc_start: 0.9309 (m110) cc_final: 0.8767 (t0) REVERT: A 97 PHE cc_start: 0.8479 (m-80) cc_final: 0.8199 (m-80) REVERT: A 138 ASP cc_start: 0.8878 (t70) cc_final: 0.8547 (t70) REVERT: A 192 CYS cc_start: 0.8162 (p) cc_final: 0.7902 (p) REVERT: A 1050 TYR cc_start: 0.8155 (t80) cc_final: 0.7941 (t80) REVERT: A 1202 HIS cc_start: 0.7735 (m-70) cc_final: 0.7246 (m-70) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.1186 time to fit residues: 17.2156 Evaluate side-chains 81 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 39 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 57 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1051 GLN A1251 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.116364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.092762 restraints weight = 46305.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.098305 restraints weight = 22426.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.101994 restraints weight = 13272.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.104636 restraints weight = 8859.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.106474 restraints weight = 6324.561| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5109 Z= 0.111 Angle : 0.501 4.782 6979 Z= 0.267 Chirality : 0.039 0.135 792 Planarity : 0.004 0.036 867 Dihedral : 5.034 32.470 683 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.38 % Allowed : 0.38 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.46 (0.34), residues: 627 helix: 1.52 (0.29), residues: 326 sheet: -0.33 (0.76), residues: 35 loop : 0.62 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1365 TYR 0.007 0.001 TYR A1341 PHE 0.011 0.001 PHE A 201 TRP 0.009 0.001 TRP A 323 HIS 0.001 0.000 HIS A1226 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 5107) covalent geometry : angle 0.50019 / 0.27 ( 6975) SS BOND : bond 0.00209 / 0.10 ( 2) SS BOND : angle 1.44856 / 0.60 ( 4) hydrogen bonds : bond 0.04892 / 3.27 ( 267) hydrogen bonds : angle 5.06560 / 3.62 ( 756) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.4984 (ptt) cc_final: 0.4746 (ptt) REVERT: A 77 ASN cc_start: 0.9265 (m110) cc_final: 0.8701 (t0) REVERT: A 97 PHE cc_start: 0.8452 (m-80) cc_final: 0.8208 (m-80) REVERT: A 138 ASP cc_start: 0.8923 (t70) cc_final: 0.8629 (t70) REVERT: A 1245 ASP cc_start: 0.8743 (m-30) cc_final: 0.8292 (m-30) outliers start: 2 outliers final: 0 residues processed: 104 average time/residue: 0.1240 time to fit residues: 17.4262 Evaluate side-chains 81 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 0.8980 chunk 12 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.115147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.092363 restraints weight = 44703.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.097661 restraints weight = 21415.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.101305 restraints weight = 12643.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.103804 restraints weight = 8342.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.105228 restraints weight = 5972.010| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5109 Z= 0.106 Angle : 0.487 4.558 6979 Z= 0.257 Chirality : 0.039 0.136 792 Planarity : 0.004 0.037 867 Dihedral : 4.835 27.363 683 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.56 (0.34), residues: 627 helix: 1.58 (0.29), residues: 326 sheet: -0.26 (0.74), residues: 35 loop : 0.70 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 229 TYR 0.008 0.001 TYR A1056 PHE 0.005 0.001 PHE A 201 TRP 0.017 0.001 TRP A 323 HIS 0.001 0.000 HIS A1226 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 5107) covalent geometry : angle 0.48630 / 0.26 ( 6975) SS BOND : bond 0.00202 / 0.11 ( 2) SS BOND : angle 1.32506 / 0.57 ( 4) hydrogen bonds : bond 0.04343 / 2.90 ( 267) hydrogen bonds : angle 4.89900 / 3.51 ( 756) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.9282 (m110) cc_final: 0.8729 (t0) REVERT: A 97 PHE cc_start: 0.8587 (m-80) cc_final: 0.8310 (m-80) REVERT: A 138 ASP cc_start: 0.8995 (t70) cc_final: 0.8707 (t70) REVERT: A 224 ILE cc_start: 0.8712 (pt) cc_final: 0.8286 (tp) REVERT: A 1245 ASP cc_start: 0.8709 (m-30) cc_final: 0.8257 (m-30) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1261 time to fit residues: 17.1113 Evaluate side-chains 77 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.115461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.092075 restraints weight = 45684.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.097394 restraints weight = 22290.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.100969 restraints weight = 13310.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.103451 restraints weight = 8939.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.105352 restraints weight = 6497.290| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5109 Z= 0.103 Angle : 0.477 4.681 6979 Z= 0.251 Chirality : 0.038 0.133 792 Planarity : 0.004 0.038 867 Dihedral : 4.668 31.098 683 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.19 % Allowed : 0.57 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.66 (0.34), residues: 627 helix: 1.61 (0.29), residues: 332 sheet: -0.07 (0.75), residues: 35 loop : 0.77 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1365 TYR 0.018 0.001 TYR A1050 PHE 0.005 0.001 PHE A 201 TRP 0.011 0.001 TRP A 323 HIS 0.001 0.000 HIS A1226 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 5107) covalent geometry : angle 0.47640 / 0.25 ( 6975) SS BOND : bond 0.00097 / 0.05 ( 2) SS BOND : angle 1.13410 / 0.50 ( 4) hydrogen bonds : bond 0.04039 / 2.69 ( 267) hydrogen bonds : angle 4.83581 / 3.47 ( 756) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.9276 (m110) cc_final: 0.8737 (t0) REVERT: A 97 PHE cc_start: 0.8659 (m-80) cc_final: 0.8400 (m-80) REVERT: A 178 MET cc_start: 0.7943 (mpp) cc_final: 0.7719 (mpp) REVERT: A 224 ILE cc_start: 0.8713 (pt) cc_final: 0.8295 (tp) REVERT: A 1244 GLU cc_start: 0.8965 (mp0) cc_final: 0.8744 (mp0) REVERT: A 1245 ASP cc_start: 0.8697 (m-30) cc_final: 0.8265 (m-30) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.1385 time to fit residues: 19.0740 Evaluate side-chains 83 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 53 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.114874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.090844 restraints weight = 45340.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.096210 restraints weight = 22212.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.099735 restraints weight = 13409.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.102189 restraints weight = 9178.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.103796 restraints weight = 6773.782| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5109 Z= 0.098 Angle : 0.480 5.028 6979 Z= 0.251 Chirality : 0.039 0.144 792 Planarity : 0.004 0.037 867 Dihedral : 4.563 33.257 683 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.73 (0.34), residues: 627 helix: 1.71 (0.29), residues: 332 sheet: -0.12 (0.75), residues: 35 loop : 0.77 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1365 TYR 0.011 0.001 TYR A1050 PHE 0.004 0.001 PHE A 307 TRP 0.012 0.001 TRP A 323 HIS 0.001 0.000 HIS A1226 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 5107) covalent geometry : angle 0.47885 / 0.25 ( 6975) SS BOND : bond 0.00246 / 0.12 ( 2) SS BOND : angle 1.37666 / 0.57 ( 4) hydrogen bonds : bond 0.03774 / 2.54 ( 267) hydrogen bonds : angle 4.75530 / 3.42 ( 756) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.9300 (m110) cc_final: 0.8695 (t0) REVERT: A 138 ASP cc_start: 0.9112 (t70) cc_final: 0.8628 (t70) REVERT: A 224 ILE cc_start: 0.8721 (pt) cc_final: 0.8312 (tp) REVERT: A 1244 GLU cc_start: 0.8970 (mp0) cc_final: 0.8732 (mp0) REVERT: A 1245 ASP cc_start: 0.8680 (m-30) cc_final: 0.8277 (m-30) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1260 time to fit residues: 18.0800 Evaluate side-chains 83 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.113041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.088938 restraints weight = 45429.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.094135 restraints weight = 22375.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.097714 restraints weight = 13601.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.100046 restraints weight = 9286.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.101894 restraints weight = 6933.674| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5109 Z= 0.123 Angle : 0.493 4.942 6979 Z= 0.259 Chirality : 0.038 0.134 792 Planarity : 0.004 0.037 867 Dihedral : 4.598 31.867 683 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.19 % Allowed : 0.38 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.68 (0.34), residues: 627 helix: 1.70 (0.29), residues: 330 sheet: -0.42 (0.68), residues: 42 loop : 0.79 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 155 TYR 0.011 0.001 TYR A1050 PHE 0.016 0.001 PHE A 201 TRP 0.012 0.001 TRP A 323 HIS 0.002 0.001 HIS A 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 5107) covalent geometry : angle 0.49169 / 0.26 ( 6975) SS BOND : bond 0.00389 / 0.20 ( 2) SS BOND : angle 1.46640 / 0.65 ( 4) hydrogen bonds : bond 0.03656 / 2.44 ( 267) hydrogen bonds : angle 4.77543 / 3.43 ( 756) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.9235 (m110) cc_final: 0.8633 (t0) REVERT: A 138 ASP cc_start: 0.9097 (t70) cc_final: 0.8598 (t70) REVERT: A 174 PHE cc_start: 0.8800 (m-10) cc_final: 0.8561 (m-80) REVERT: A 224 ILE cc_start: 0.8756 (pt) cc_final: 0.8355 (tp) REVERT: A 1128 TYR cc_start: 0.8722 (m-80) cc_final: 0.8322 (m-80) REVERT: A 1244 GLU cc_start: 0.8963 (mp0) cc_final: 0.8739 (mp0) REVERT: A 1245 ASP cc_start: 0.8691 (m-30) cc_final: 0.8284 (m-30) outliers start: 1 outliers final: 0 residues processed: 103 average time/residue: 0.1213 time to fit residues: 17.2245 Evaluate side-chains 80 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 48 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.111346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.089155 restraints weight = 44295.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.094179 restraints weight = 20764.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.097670 restraints weight = 12156.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.099976 restraints weight = 8057.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.101755 restraints weight = 5841.797| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5109 Z= 0.122 Angle : 0.490 4.962 6979 Z= 0.258 Chirality : 0.039 0.166 792 Planarity : 0.004 0.037 867 Dihedral : 4.619 28.323 683 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.19 % Allowed : 0.19 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.69 (0.34), residues: 627 helix: 1.72 (0.29), residues: 329 sheet: -0.52 (0.68), residues: 42 loop : 0.79 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 155 TYR 0.009 0.001 TYR A1050 PHE 0.006 0.001 PHE A 307 TRP 0.014 0.001 TRP A 181 HIS 0.004 0.001 HIS A1202 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 5107) covalent geometry : angle 0.48895 / 0.26 ( 6975) SS BOND : bond 0.00126 / 0.06 ( 2) SS BOND : angle 1.08254 / 0.41 ( 4) hydrogen bonds : bond 0.03613 / 2.43 ( 267) hydrogen bonds : angle 4.76965 / 3.43 ( 756) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.9256 (m110) cc_final: 0.8652 (t0) REVERT: A 138 ASP cc_start: 0.9080 (t70) cc_final: 0.8583 (t70) REVERT: A 224 ILE cc_start: 0.8768 (pt) cc_final: 0.8322 (tp) REVERT: A 1244 GLU cc_start: 0.9005 (mp0) cc_final: 0.8774 (mp0) REVERT: A 1245 ASP cc_start: 0.8755 (m-30) cc_final: 0.8401 (m-30) outliers start: 1 outliers final: 0 residues processed: 103 average time/residue: 0.1189 time to fit residues: 17.0053 Evaluate side-chains 79 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 0.0470 chunk 50 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 40 optimal weight: 0.0570 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.112529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.089560 restraints weight = 44952.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.094687 restraints weight = 21589.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.098253 restraints weight = 12889.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.100370 restraints weight = 8641.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.102330 restraints weight = 6436.718| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5109 Z= 0.092 Angle : 0.477 5.844 6979 Z= 0.247 Chirality : 0.039 0.133 792 Planarity : 0.004 0.038 867 Dihedral : 4.514 35.378 683 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.88 (0.34), residues: 627 helix: 1.86 (0.29), residues: 330 sheet: -0.41 (0.68), residues: 42 loop : 0.91 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1365 TYR 0.011 0.001 TYR A1056 PHE 0.006 0.001 PHE A 201 TRP 0.013 0.001 TRP A 323 HIS 0.002 0.001 HIS A1202 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 ( 5107) covalent geometry : angle 0.47677 / 0.25 ( 6975) SS BOND : bond 0.00056 / 0.03 ( 2) SS BOND : angle 1.03444 / 0.46 ( 4) hydrogen bonds : bond 0.03431 / 2.30 ( 267) hydrogen bonds : angle 4.60484 / 3.31 ( 756) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.9266 (m110) cc_final: 0.8646 (t0) REVERT: A 138 ASP cc_start: 0.9079 (t70) cc_final: 0.8592 (t70) REVERT: A 224 ILE cc_start: 0.8746 (pt) cc_final: 0.8355 (tp) REVERT: A 1128 TYR cc_start: 0.8803 (m-80) cc_final: 0.8367 (m-80) REVERT: A 1245 ASP cc_start: 0.8692 (m-30) cc_final: 0.8342 (m-30) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1198 time to fit residues: 17.1532 Evaluate side-chains 81 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 55 optimal weight: 0.0070 chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.110992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.088740 restraints weight = 44484.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.093769 restraints weight = 20771.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.097185 restraints weight = 12142.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.099639 restraints weight = 8049.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.101056 restraints weight = 5779.238| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5109 Z= 0.125 Angle : 0.493 5.689 6979 Z= 0.260 Chirality : 0.039 0.143 792 Planarity : 0.004 0.037 867 Dihedral : 4.545 31.299 683 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.75 (0.34), residues: 627 helix: 1.75 (0.29), residues: 330 sheet: -0.48 (0.70), residues: 42 loop : 0.86 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1365 TYR 0.008 0.001 TYR A1341 PHE 0.006 0.001 PHE A 201 TRP 0.013 0.001 TRP A 323 HIS 0.002 0.001 HIS A 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 ( 5107) covalent geometry : angle 0.49135 / 0.26 ( 6975) SS BOND : bond 0.00030 / 0.02 ( 2) SS BOND : angle 1.52507 / 0.55 ( 4) hydrogen bonds : bond 0.03374 / 2.27 ( 267) hydrogen bonds : angle 4.70918 / 3.38 ( 756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1780.10 seconds wall clock time: 30 minutes 56.97 seconds (1856.97 seconds total)