Starting phenix.real_space_refine on Thu Jul 2 18:48:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s37_24818/07_2026/7s37_24818.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s37_24818/07_2026/7s37_24818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7s37_24818/07_2026/7s37_24818.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s37_24818/07_2026/7s37_24818.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7s37_24818/07_2026/7s37_24818.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s37_24818/07_2026/7s37_24818.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s37_24818/07_2026/7s37_24818.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s37_24818/07_2026/7s37_24818.map" } resolution = 3.2 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= 0.242 sd= 1.445 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 P 46 5.49 5 S 16 5.16 5 C 5782 2.51 5 N 1655 2.21 5 O 1893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9392 Number of models: 1 Model: "" Number of chains: 2 Chain: "P" Number of atoms: 8401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8401 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 26, 'TRANS': 1006} Chain breaks: 3 Chain: "R" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 991 Classifications: {'RNA': 46} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 25, 'rna3p_pyr': 16} Link IDs: {'rna2p': 5, 'rna3p': 40} Chain breaks: 1 Time building chain proxies: 2.50, per 1000 atoms: 0.27 Number of scatterers: 9392 At special positions: 0 Unit cell: (86.97, 114.845, 123.765, 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 16 16.00 P 46 15.00 O 1893 8.00 N 1655 7.00 C 5782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.00 Conformation dependent library (CDL) restraints added in 333.7 milliseconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 7 sheets defined 56.4% alpha, 9.2% beta 14 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'P' and resid 58 through 64 Processing helix chain 'P' and resid 67 through 92 removed outlier: 4.450A pdb=" N ASN P 88 " --> pdb=" O GLU P 84 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLU P 89 " --> pdb=" O ILE P 85 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS P 92 " --> pdb=" O ASN P 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 132 Processing helix chain 'P' and resid 134 through 145 removed outlier: 3.748A pdb=" N LEU P 138 " --> pdb=" O THR P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 150 through 164 Processing helix chain 'P' and resid 175 through 179 Processing helix chain 'P' and resid 180 through 196 Processing helix chain 'P' and resid 207 through 213 Processing helix chain 'P' and resid 217 through 228 removed outlier: 3.710A pdb=" N GLN P 228 " --> pdb=" O ASN P 224 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 247 Processing helix chain 'P' and resid 252 through 257 Processing helix chain 'P' and resid 270 through 283 Processing helix chain 'P' and resid 286 through 306 Processing helix chain 'P' and resid 315 through 343 Processing helix chain 'P' and resid 346 through 352 removed outlier: 3.520A pdb=" N ILE P 350 " --> pdb=" O LYS P 346 " (cutoff:3.500A) Processing helix chain 'P' and resid 358 through 364 Processing helix chain 'P' and resid 368 through 383 Proline residue: P 378 - end of helix Processing helix chain 'P' and resid 388 through 395 removed outlier: 3.639A pdb=" N LYS P 392 " --> pdb=" O GLU P 388 " (cutoff:3.500A) Processing helix chain 'P' and resid 404 through 410 removed outlier: 3.730A pdb=" N ASN P 407 " --> pdb=" O THR P 404 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY P 408 " --> pdb=" O PHE P 405 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE P 410 " --> pdb=" O ASN P 407 " (cutoff:3.500A) Processing helix chain 'P' and resid 411 through 426 removed outlier: 4.089A pdb=" N HIS P 415 " --> pdb=" O PRO P 411 " (cutoff:3.500A) Processing helix chain 'P' and resid 430 through 436 removed outlier: 3.760A pdb=" N LYS P 434 " --> pdb=" O TYR P 430 " (cutoff:3.500A) Processing helix chain 'P' and resid 436 through 446 Processing helix chain 'P' and resid 719 through 726 Processing helix chain 'P' and resid 730 through 751 Processing helix chain 'P' and resid 774 through 792 Processing helix chain 'P' and resid 794 through 799 Processing helix chain 'P' and resid 804 through 807 removed outlier: 3.595A pdb=" N GLN P 807 " --> pdb=" O THR P 804 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 804 through 807' Processing helix chain 'P' and resid 808 through 817 Processing helix chain 'P' and resid 851 through 853 No H-bonds generated for 'chain 'P' and resid 851 through 853' Processing helix chain 'P' and resid 860 through 865 removed outlier: 3.658A pdb=" N ASN P 863 " --> pdb=" O SER P 860 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG P 864 " --> pdb=" O ASP P 861 " (cutoff:3.500A) Processing helix chain 'P' and resid 872 through 889 removed outlier: 3.504A pdb=" N VAL P 876 " --> pdb=" O SER P 872 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS P 878 " --> pdb=" O GLU P 874 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ASN P 881 " --> pdb=" O LYS P 877 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N TYR P 882 " --> pdb=" O LYS P 878 " (cutoff:3.500A) Processing helix chain 'P' and resid 893 through 901 Processing helix chain 'P' and resid 902 through 906 Processing helix chain 'P' and resid 909 through 922 Processing helix chain 'P' and resid 925 through 940 removed outlier: 3.550A pdb=" N LYS P 929 " --> pdb=" O ARG P 925 " (cutoff:3.500A) Processing helix chain 'P' and resid 959 through 971 removed outlier: 3.994A pdb=" N VAL P 963 " --> pdb=" O LYS P 959 " (cutoff:3.500A) Processing helix chain 'P' and resid 980 through 1001 removed outlier: 4.527A pdb=" N ALA P 984 " --> pdb=" O ASN P 980 " (cutoff:3.500A) Processing helix chain 'P' and resid 1004 through 1009 removed outlier: 3.759A pdb=" N PHE P1008 " --> pdb=" O LEU P1004 " (cutoff:3.500A) Processing helix chain 'P' and resid 1041 through 1045 removed outlier: 3.641A pdb=" N ASN P1044 " --> pdb=" O ASN P1041 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N PHE P1045 " --> pdb=" O ILE P1042 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 1041 through 1045' Processing helix chain 'P' and resid 1077 through 1089 Processing helix chain 'P' and resid 1168 through 1177 removed outlier: 4.546A pdb=" N SER P1172 " --> pdb=" O ILE P1168 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER P1173 " --> pdb=" O MET P1169 " (cutoff:3.500A) Processing helix chain 'P' and resid 1177 through 1186 Processing helix chain 'P' and resid 1191 through 1195 removed outlier: 3.724A pdb=" N ILE P1195 " --> pdb=" O LYS P1192 " (cutoff:3.500A) Processing helix chain 'P' and resid 1207 through 1209 No H-bonds generated for 'chain 'P' and resid 1207 through 1209' Processing helix chain 'P' and resid 1229 through 1241 Processing helix chain 'P' and resid 1248 through 1262 removed outlier: 3.505A pdb=" N HIS P1262 " --> pdb=" O PHE P1258 " (cutoff:3.500A) Processing helix chain 'P' and resid 1263 through 1281 removed outlier: 4.315A pdb=" N ASP P1267 " --> pdb=" O LYS P1263 " (cutoff:3.500A) Processing helix chain 'P' and resid 1283 through 1297 Processing helix chain 'P' and resid 1301 through 1313 Processing helix chain 'P' and resid 1314 through 1316 No H-bonds generated for 'chain 'P' and resid 1314 through 1316' Processing helix chain 'P' and resid 1340 through 1344 Processing helix chain 'P' and resid 1363 through 1365 No H-bonds generated for 'chain 'P' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'P' and resid 954 through 957 removed outlier: 6.465A pdb=" N ILE P 7 " --> pdb=" O VAL P 760 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N GLU P 762 " --> pdb=" O ILE P 7 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU P 9 " --> pdb=" O GLU P 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 42 through 46 removed outlier: 10.015A pdb=" N GLU P1357 " --> pdb=" O LYS P 31 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS P 33 " --> pdb=" O GLU P1357 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ARG P1359 " --> pdb=" O LYS P 33 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU P 35 " --> pdb=" O ARG P1359 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP P1361 " --> pdb=" O LEU P 35 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU P1203 " --> pdb=" O ILE P1348 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER P1202 " --> pdb=" O LEU P1214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 837 through 840 Processing sheet with id=AA4, first strand: chain 'P' and resid 1049 through 1051 Processing sheet with id=AA5, first strand: chain 'P' and resid 1063 through 1065 Processing sheet with id=AA6, first strand: chain 'P' and resid 1156 through 1167 removed outlier: 3.523A pdb=" N TYR P1141 " --> pdb=" O ILE P1166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 1324 through 1325 412 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 1.83 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2580 1.34 - 1.46: 1914 1.46 - 1.58: 5028 1.58 - 1.70: 95 1.70 - 1.82: 31 Bond restraints: 9648 Sorted by residual: bond pdb=" CB ILE P 322 " pdb=" CG2 ILE P 322 " ideal model delta sigma weight residual 1.521 1.600 -0.079 3.30e-02 9.18e+02 5.78e+00 bond pdb=" CB ILE P1281 " pdb=" CG2 ILE P1281 " ideal model delta sigma weight residual 1.521 1.581 -0.060 3.30e-02 9.18e+02 3.36e+00 bond pdb=" CB ILE P 950 " pdb=" CG2 ILE P 950 " ideal model delta sigma weight residual 1.521 1.581 -0.060 3.30e-02 9.18e+02 3.32e+00 bond pdb=" C VAL P 842 " pdb=" N PRO P 843 " ideal model delta sigma weight residual 1.332 1.355 -0.024 1.33e-02 5.65e+03 3.18e+00 bond pdb=" CB ILE P1196 " pdb=" CG2 ILE P1196 " ideal model delta sigma weight residual 1.521 1.578 -0.057 3.30e-02 9.18e+02 2.95e+00 ... (remaining 9643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 12375 1.96 - 3.93: 687 3.93 - 5.89: 116 5.89 - 7.86: 18 7.86 - 9.82: 3 Bond angle restraints: 13199 Sorted by residual: angle pdb=" CA GLN P 402 " pdb=" CB GLN P 402 " pdb=" CG GLN P 402 " ideal model delta sigma weight residual 114.10 122.02 -7.92 2.00e+00 2.50e-01 1.57e+01 angle pdb=" N VAL P1280 " pdb=" CA VAL P1280 " pdb=" C VAL P1280 " ideal model delta sigma weight residual 109.34 117.35 -8.01 2.08e+00 2.31e-01 1.48e+01 angle pdb=" CA GLU P 427 " pdb=" CB GLU P 427 " pdb=" CG GLU P 427 " ideal model delta sigma weight residual 114.10 121.70 -7.60 2.00e+00 2.50e-01 1.44e+01 angle pdb=" C TYR P1326 " pdb=" N PHE P1327 " pdb=" CA PHE P1327 " ideal model delta sigma weight residual 121.54 128.42 -6.88 1.91e+00 2.74e-01 1.30e+01 angle pdb=" C THR P 769 " pdb=" N THR P 770 " pdb=" CA THR P 770 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 ... (remaining 13194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.22: 5460 20.22 - 40.44: 279 40.44 - 60.65: 70 60.65 - 80.87: 9 80.87 - 101.09: 4 Dihedral angle restraints: 5822 sinusoidal: 2785 harmonic: 3037 Sorted by residual: dihedral pdb=" CA PHE P1327 " pdb=" C PHE P1327 " pdb=" N ASP P1328 " pdb=" CA ASP P1328 " ideal model delta harmonic sigma weight residual 180.00 162.78 17.22 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" C GLN P 402 " pdb=" N GLN P 402 " pdb=" CA GLN P 402 " pdb=" CB GLN P 402 " ideal model delta harmonic sigma weight residual -122.60 -131.10 8.50 0 2.50e+00 1.60e-01 1.15e+01 dihedral pdb=" CA ASP P 912 " pdb=" CB ASP P 912 " pdb=" CG ASP P 912 " pdb=" OD1 ASP P 912 " ideal model delta sinusoidal sigma weight residual -30.00 -88.34 58.34 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 5819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1018 0.043 - 0.085: 364 0.085 - 0.128: 90 0.128 - 0.170: 29 0.170 - 0.213: 5 Chirality restraints: 1506 Sorted by residual: chirality pdb=" CA GLN P 402 " pdb=" N GLN P 402 " pdb=" C GLN P 402 " pdb=" CB GLN P 402 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB ILE P 956 " pdb=" CA ILE P 956 " pdb=" CG1 ILE P 956 " pdb=" CG2 ILE P 956 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE P 950 " pdb=" N ILE P 950 " pdb=" C ILE P 950 " pdb=" CB ILE P 950 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 1503 not shown) Planarity restraints: 1517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE P1270 " -0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" C ILE P1270 " 0.066 2.00e-02 2.50e+03 pdb=" O ILE P1270 " -0.025 2.00e-02 2.50e+03 pdb=" N GLU P1271 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A R 32 " 0.026 2.00e-02 2.50e+03 2.19e-02 1.31e+01 pdb=" N9 A R 32 " -0.059 2.00e-02 2.50e+03 pdb=" C8 A R 32 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A R 32 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A R 32 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A R 32 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A R 32 " 0.002 2.00e-02 2.50e+03 pdb=" N1 A R 32 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A R 32 " -0.005 2.00e-02 2.50e+03 pdb=" N3 A R 32 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A R 32 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU P 275 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C LEU P 275 " -0.062 2.00e-02 2.50e+03 pdb=" O LEU P 275 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP P 276 " 0.021 2.00e-02 2.50e+03 ... (remaining 1514 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 838 2.75 - 3.29: 9239 3.29 - 3.82: 15062 3.82 - 4.36: 18525 4.36 - 4.90: 30526 Nonbonded interactions: 74190 Sorted by model distance: nonbonded pdb=" O GLN P 817 " pdb=" OH TYR P 882 " model vdw 2.211 3.040 nonbonded pdb=" OE2 GLU P 762 " pdb=" OG SER P 960 " model vdw 2.214 3.040 nonbonded pdb=" OD1 ASN P 199 " pdb=" NH1 ARG P 783 " model vdw 2.243 3.120 nonbonded pdb=" OG SER P 867 " pdb=" OD1 ASN P 869 " model vdw 2.245 3.040 nonbonded pdb=" OD1 ASP P1267 " pdb=" OH TYR P1294 " model vdw 2.256 3.040 ... (remaining 74185 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.480 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 9648 Z= 0.290 Angle : 1.037 9.824 13199 Z= 0.564 Chirality : 0.049 0.213 1506 Planarity : 0.006 0.038 1517 Dihedral : 12.764 101.089 3858 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.11 % Allowed : 4.78 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.23), residues: 1025 helix: -0.83 (0.20), residues: 508 sheet: -0.90 (0.43), residues: 127 loop : -0.96 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG P1060 TYR 0.015 0.002 TYR P 132 PHE 0.032 0.002 PHE P1313 TRP 0.010 0.002 TRP P 883 HIS 0.016 0.002 HIS P 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.29 ( 9648) covalent geometry : angle 1.03660 / 0.56 (13199) hydrogen bonds : bond 0.15113 / 9.33 ( 448) hydrogen bonds : angle 6.04757 / 4.33 ( 1260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 54 ASP cc_start: 0.7533 (t0) cc_final: 0.7330 (t0) REVERT: P 60 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7270 (pt0) REVERT: P 72 TYR cc_start: 0.7405 (t80) cc_final: 0.7187 (t80) REVERT: P 75 ARG cc_start: 0.8450 (mtt180) cc_final: 0.7937 (mmt90) REVERT: P 76 LYS cc_start: 0.8480 (mmmt) cc_final: 0.8163 (mmmt) REVERT: P 77 ASN cc_start: 0.8123 (t0) cc_final: 0.7854 (t0) REVERT: P 163 LYS cc_start: 0.8136 (tttt) cc_final: 0.7651 (ttpt) REVERT: P 222 LEU cc_start: 0.8416 (tp) cc_final: 0.8196 (tt) REVERT: P 285 GLN cc_start: 0.8078 (pt0) cc_final: 0.7864 (pt0) REVERT: P 286 TYR cc_start: 0.7743 (m-80) cc_final: 0.7092 (m-10) REVERT: P 394 ASN cc_start: 0.7609 (t0) cc_final: 0.7235 (p0) REVERT: P 742 LYS cc_start: 0.7705 (mtmt) cc_final: 0.7187 (mmmt) REVERT: P 751 MET cc_start: 0.6756 (mmt) cc_final: 0.6069 (mmt) REVERT: P 763 MET cc_start: 0.8020 (mmt) cc_final: 0.7817 (mmm) REVERT: P 937 SER cc_start: 0.6958 (t) cc_final: 0.6664 (m) REVERT: P 966 PHE cc_start: 0.7147 (t80) cc_final: 0.6547 (t80) outliers start: 1 outliers final: 1 residues processed: 269 average time/residue: 0.1212 time to fit residues: 42.4616 Evaluate side-chains 165 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 1008 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 224 ASN ** P 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 716 GLN P 930 HIS P1241 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.152173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.130587 restraints weight = 27537.364| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 3.52 r_work: 0.4022 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9648 Z= 0.182 Angle : 0.641 7.568 13199 Z= 0.342 Chirality : 0.041 0.212 1506 Planarity : 0.004 0.065 1517 Dihedral : 10.445 96.665 1678 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.17 % Allowed : 11.83 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.25), residues: 1025 helix: 0.63 (0.23), residues: 507 sheet: -0.67 (0.44), residues: 131 loop : -0.55 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG P 400 TYR 0.016 0.002 TYR P1001 PHE 0.038 0.002 PHE P 916 TRP 0.020 0.003 TRP P 883 HIS 0.008 0.001 HIS P 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 ( 9648) covalent geometry : angle 0.64074 / 0.34 (13199) hydrogen bonds : bond 0.04728 / 3.13 ( 448) hydrogen bonds : angle 4.94165 / 3.52 ( 1260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.282 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: P 63 ARG cc_start: 0.7087 (mtp180) cc_final: 0.6524 (mtm180) REVERT: P 72 TYR cc_start: 0.7969 (t80) cc_final: 0.7724 (t80) REVERT: P 75 ARG cc_start: 0.8865 (mtt180) cc_final: 0.8401 (mmt90) REVERT: P 76 LYS cc_start: 0.8655 (mmmt) cc_final: 0.8440 (mmmt) REVERT: P 77 ASN cc_start: 0.8267 (t0) cc_final: 0.7825 (t0) REVERT: P 163 LYS cc_start: 0.7865 (tttt) cc_final: 0.7554 (ttpt) REVERT: P 257 ASP cc_start: 0.7542 (t70) cc_final: 0.7328 (t0) REVERT: P 285 GLN cc_start: 0.8188 (pt0) cc_final: 0.7622 (pm20) REVERT: P 286 TYR cc_start: 0.8064 (m-80) cc_final: 0.7451 (m-10) REVERT: P 300 ILE cc_start: 0.7870 (pt) cc_final: 0.7665 (pt) REVERT: P 380 LEU cc_start: 0.7885 (mt) cc_final: 0.7617 (mt) REVERT: P 383 MET cc_start: 0.6521 (mtp) cc_final: 0.6230 (ptp) REVERT: P 394 ASN cc_start: 0.7558 (t0) cc_final: 0.7218 (p0) REVERT: P 418 GLU cc_start: 0.8418 (mp0) cc_final: 0.8063 (mp0) REVERT: P 740 THR cc_start: 0.8158 (m) cc_final: 0.7782 (p) REVERT: P 742 LYS cc_start: 0.7658 (mtmt) cc_final: 0.7154 (mmmt) REVERT: P 766 GLU cc_start: 0.7884 (mp0) cc_final: 0.7660 (mp0) REVERT: P 926 GLN cc_start: 0.7820 (tp-100) cc_final: 0.7411 (tp-100) REVERT: P 937 SER cc_start: 0.7097 (t) cc_final: 0.6764 (m) REVERT: P 970 PHE cc_start: 0.7074 (m-80) cc_final: 0.6815 (m-80) REVERT: P 981 TYR cc_start: 0.7283 (m-10) cc_final: 0.6867 (m-80) REVERT: P 1089 MET cc_start: 0.5914 (mtt) cc_final: 0.5690 (mtp) REVERT: P 1171 ARG cc_start: 0.7719 (ttt180) cc_final: 0.7509 (ttp80) outliers start: 20 outliers final: 12 residues processed: 189 average time/residue: 0.1064 time to fit residues: 26.7885 Evaluate side-chains 167 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 217 SER Chi-restraints excluded: chain P residue 301 LEU Chi-restraints excluded: chain P residue 776 ASN Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 1051 THR Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1169 MET Chi-restraints excluded: chain P residue 1259 VAL Chi-restraints excluded: chain P residue 1364 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 97 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 228 GLN P 309 ASN P 758 ASN ** P 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1044 ASN P1221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.144237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.121972 restraints weight = 27109.599| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 3.54 r_work: 0.3902 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 9648 Z= 0.307 Angle : 0.790 13.449 13199 Z= 0.417 Chirality : 0.046 0.188 1506 Planarity : 0.005 0.059 1517 Dihedral : 10.898 100.759 1676 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.80 % Allowed : 15.20 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.25), residues: 1025 helix: 0.05 (0.21), residues: 531 sheet: -0.36 (0.51), residues: 96 loop : -0.92 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 70 TYR 0.022 0.003 TYR P 823 PHE 0.036 0.003 PHE P 916 TRP 0.009 0.002 TRP P1074 HIS 0.010 0.002 HIS P1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.31 ( 9648) covalent geometry : angle 0.79026 / 0.42 (13199) hydrogen bonds : bond 0.05666 / 3.86 ( 448) hydrogen bonds : angle 5.38098 / 3.82 ( 1260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 18 TRP cc_start: 0.7183 (p-90) cc_final: 0.6441 (p-90) REVERT: P 30 LYS cc_start: 0.7661 (mtpt) cc_final: 0.7453 (tttp) REVERT: P 77 ASN cc_start: 0.8323 (t0) cc_final: 0.7949 (t0) REVERT: P 222 LEU cc_start: 0.8698 (tp) cc_final: 0.8471 (tt) REVERT: P 257 ASP cc_start: 0.7907 (t70) cc_final: 0.7574 (t0) REVERT: P 286 TYR cc_start: 0.8242 (m-80) cc_final: 0.7773 (m-10) REVERT: P 321 MET cc_start: 0.6717 (mmp) cc_final: 0.6270 (mmp) REVERT: P 354 GLN cc_start: 0.7663 (mt0) cc_final: 0.6958 (tm-30) REVERT: P 380 LEU cc_start: 0.8266 (mt) cc_final: 0.8047 (mm) REVERT: P 394 ASN cc_start: 0.7730 (t0) cc_final: 0.7340 (p0) REVERT: P 418 GLU cc_start: 0.8331 (mp0) cc_final: 0.8075 (mm-30) REVERT: P 742 LYS cc_start: 0.7721 (mtmt) cc_final: 0.7226 (mmtt) REVERT: P 745 ASP cc_start: 0.8065 (m-30) cc_final: 0.7682 (t0) REVERT: P 749 LYS cc_start: 0.8093 (tttt) cc_final: 0.7822 (tttm) REVERT: P 766 GLU cc_start: 0.8138 (mp0) cc_final: 0.7870 (tm-30) REVERT: P 908 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7540 (mt) REVERT: P 926 GLN cc_start: 0.8050 (tp-100) cc_final: 0.7342 (tp-100) REVERT: P 927 ILE cc_start: 0.8843 (tp) cc_final: 0.8389 (pt) REVERT: P 937 SER cc_start: 0.7453 (t) cc_final: 0.7124 (m) REVERT: P 961 LYS cc_start: 0.7406 (mttt) cc_final: 0.7126 (mtpp) REVERT: P 981 TYR cc_start: 0.7499 (m-10) cc_final: 0.7156 (m-10) REVERT: P 1064 GLU cc_start: 0.7611 (tp30) cc_final: 0.7194 (tp30) REVERT: P 1333 ARG cc_start: 0.8097 (ttp-110) cc_final: 0.7838 (ttp80) outliers start: 35 outliers final: 25 residues processed: 189 average time/residue: 0.1103 time to fit residues: 27.4331 Evaluate side-chains 170 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 217 SER Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 301 LEU Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 842 VAL Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 882 TYR Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 908 LEU Chi-restraints excluded: chain P residue 922 VAL Chi-restraints excluded: chain P residue 1051 THR Chi-restraints excluded: chain P residue 1065 THR Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1149 VAL Chi-restraints excluded: chain P residue 1168 ILE Chi-restraints excluded: chain P residue 1169 MET Chi-restraints excluded: chain P residue 1259 VAL Chi-restraints excluded: chain P residue 1284 ASP Chi-restraints excluded: chain P residue 1288 ASP Chi-restraints excluded: chain P residue 1309 ILE Chi-restraints excluded: chain P residue 1317 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 100 optimal weight: 0.0980 chunk 102 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.147993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.126342 restraints weight = 27838.502| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 3.80 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9648 Z= 0.138 Angle : 0.605 10.130 13199 Z= 0.314 Chirality : 0.039 0.137 1506 Planarity : 0.004 0.043 1517 Dihedral : 10.408 97.988 1676 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.28 % Allowed : 17.05 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.26), residues: 1025 helix: 0.53 (0.22), residues: 527 sheet: -0.49 (0.47), residues: 122 loop : -0.82 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 967 TYR 0.018 0.001 TYR P 362 PHE 0.038 0.002 PHE P 916 TRP 0.007 0.001 TRP P1074 HIS 0.006 0.001 HIS P 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 9648) covalent geometry : angle 0.60504 / 0.31 (13199) hydrogen bonds : bond 0.04054 / 2.67 ( 448) hydrogen bonds : angle 4.76477 / 3.37 ( 1260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.213 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: P 63 ARG cc_start: 0.7098 (mtp180) cc_final: 0.6390 (mtm180) REVERT: P 77 ASN cc_start: 0.7960 (t0) cc_final: 0.7681 (t0) REVERT: P 222 LEU cc_start: 0.8592 (tp) cc_final: 0.8344 (tt) REVERT: P 354 GLN cc_start: 0.7472 (mt0) cc_final: 0.7233 (tm-30) REVERT: P 394 ASN cc_start: 0.7891 (t0) cc_final: 0.7487 (p0) REVERT: P 418 GLU cc_start: 0.8115 (mp0) cc_final: 0.7848 (mm-30) REVERT: P 722 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: P 740 THR cc_start: 0.7999 (m) cc_final: 0.7743 (p) REVERT: P 742 LYS cc_start: 0.7461 (mtmt) cc_final: 0.7041 (mmtt) REVERT: P 745 ASP cc_start: 0.7799 (m-30) cc_final: 0.7490 (t0) REVERT: P 749 LYS cc_start: 0.7959 (tttt) cc_final: 0.7729 (tttm) REVERT: P 926 GLN cc_start: 0.7864 (tp-100) cc_final: 0.7192 (tp-100) REVERT: P 927 ILE cc_start: 0.8722 (tp) cc_final: 0.8263 (pt) REVERT: P 937 SER cc_start: 0.7070 (t) cc_final: 0.6825 (m) REVERT: P 967 ARG cc_start: 0.7155 (mtt180) cc_final: 0.6924 (mmm-85) REVERT: P 981 TYR cc_start: 0.7286 (m-10) cc_final: 0.6805 (m-10) REVERT: P 1043 MET cc_start: 0.5367 (OUTLIER) cc_final: 0.5159 (ptp) REVERT: P 1064 GLU cc_start: 0.6767 (tp30) cc_final: 0.6493 (tp30) outliers start: 21 outliers final: 11 residues processed: 176 average time/residue: 0.1036 time to fit residues: 24.1485 Evaluate side-chains 159 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 217 SER Chi-restraints excluded: chain P residue 224 ASN Chi-restraints excluded: chain P residue 722 GLU Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 882 TYR Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 1043 MET Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1169 MET Chi-restraints excluded: chain P residue 1317 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 64 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 53 optimal weight: 0.0270 chunk 32 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 193 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.148329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.126487 restraints weight = 27858.614| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 3.52 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9648 Z= 0.126 Angle : 0.572 8.484 13199 Z= 0.297 Chirality : 0.038 0.151 1506 Planarity : 0.004 0.045 1517 Dihedral : 10.259 98.738 1676 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.50 % Allowed : 17.59 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.26), residues: 1025 helix: 0.81 (0.23), residues: 518 sheet: -0.14 (0.48), residues: 108 loop : -0.81 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 400 TYR 0.019 0.001 TYR P 362 PHE 0.043 0.002 PHE P 916 TRP 0.005 0.001 TRP P1074 HIS 0.005 0.001 HIS P 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 9648) covalent geometry : angle 0.57210 / 0.30 (13199) hydrogen bonds : bond 0.03789 / 2.53 ( 448) hydrogen bonds : angle 4.61745 / 3.27 ( 1260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 63 ARG cc_start: 0.7034 (mtp180) cc_final: 0.6534 (mtm180) REVERT: P 77 ASN cc_start: 0.7953 (t0) cc_final: 0.7652 (t0) REVERT: P 222 LEU cc_start: 0.8549 (tp) cc_final: 0.8287 (tt) REVERT: P 354 GLN cc_start: 0.7725 (mt0) cc_final: 0.7426 (tm-30) REVERT: P 394 ASN cc_start: 0.7819 (t0) cc_final: 0.7415 (p0) REVERT: P 740 THR cc_start: 0.8128 (m) cc_final: 0.7878 (p) REVERT: P 742 LYS cc_start: 0.7517 (mtmt) cc_final: 0.7116 (mmtt) REVERT: P 745 ASP cc_start: 0.7843 (m-30) cc_final: 0.7556 (t0) REVERT: P 783 ARG cc_start: 0.6795 (ttm170) cc_final: 0.6586 (ptm160) REVERT: P 892 ILE cc_start: 0.4836 (OUTLIER) cc_final: 0.4561 (pt) REVERT: P 926 GLN cc_start: 0.7806 (tp-100) cc_final: 0.7135 (tp-100) REVERT: P 927 ILE cc_start: 0.8708 (tp) cc_final: 0.8254 (pt) REVERT: P 937 SER cc_start: 0.7021 (t) cc_final: 0.6781 (m) REVERT: P 981 TYR cc_start: 0.7130 (m-10) cc_final: 0.6660 (m-10) REVERT: P 1043 MET cc_start: 0.5250 (ptm) cc_final: 0.5016 (ptp) REVERT: P 1080 PHE cc_start: 0.5606 (m-80) cc_final: 0.5077 (m-80) REVERT: P 1333 ARG cc_start: 0.7746 (ttp80) cc_final: 0.7329 (ttp80) outliers start: 23 outliers final: 16 residues processed: 170 average time/residue: 0.0948 time to fit residues: 21.8483 Evaluate side-chains 164 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 224 ASN Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 320 SER Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 842 VAL Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 882 TYR Chi-restraints excluded: chain P residue 892 ILE Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1169 MET Chi-restraints excluded: chain P residue 1259 VAL Chi-restraints excluded: chain P residue 1317 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 58 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 64 optimal weight: 0.0060 chunk 67 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1305 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 = 0.4319 r_free = 0.4319 target = 0.143902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.121853 restraints weight = 28253.083| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 3.50 r_work: 0.3894 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.5920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 9648 Z= 0.277 Angle : 0.728 13.037 13199 Z= 0.379 Chirality : 0.043 0.189 1506 Planarity : 0.005 0.081 1517 Dihedral : 10.687 102.242 1676 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.58 % Allowed : 16.83 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.25), residues: 1025 helix: 0.36 (0.22), residues: 522 sheet: -0.49 (0.49), residues: 95 loop : -1.01 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 139 TYR 0.019 0.002 TYR P 823 PHE 0.046 0.003 PHE P 916 TRP 0.018 0.003 TRP P 18 HIS 0.009 0.002 HIS P 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.28 ( 9648) covalent geometry : angle 0.72803 / 0.38 (13199) hydrogen bonds : bond 0.05166 / 3.54 ( 448) hydrogen bonds : angle 5.20600 / 3.68 ( 1260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 73 THR cc_start: 0.8830 (t) cc_final: 0.8561 (p) REVERT: P 77 ASN cc_start: 0.8265 (t0) cc_final: 0.7923 (t0) REVERT: P 222 LEU cc_start: 0.8704 (tp) cc_final: 0.8468 (tt) REVERT: P 354 GLN cc_start: 0.7874 (mt0) cc_final: 0.7466 (tm-30) REVERT: P 394 ASN cc_start: 0.7951 (t0) cc_final: 0.7558 (p0) REVERT: P 740 THR cc_start: 0.8232 (m) cc_final: 0.7981 (p) REVERT: P 742 LYS cc_start: 0.7590 (mtmt) cc_final: 0.7133 (mmtt) REVERT: P 745 ASP cc_start: 0.8183 (m-30) cc_final: 0.7743 (t0) REVERT: P 749 LYS cc_start: 0.8032 (tttt) cc_final: 0.7751 (tttm) REVERT: P 892 ILE cc_start: 0.4872 (OUTLIER) cc_final: 0.4205 (pt) REVERT: P 926 GLN cc_start: 0.8024 (tp-100) cc_final: 0.7407 (tp-100) REVERT: P 927 ILE cc_start: 0.8862 (tp) cc_final: 0.8453 (pt) REVERT: P 937 SER cc_start: 0.7582 (t) cc_final: 0.7325 (m) REVERT: P 947 ASP cc_start: 0.7844 (t0) cc_final: 0.7632 (t0) REVERT: P 961 LYS cc_start: 0.7391 (mttt) cc_final: 0.7017 (mmmm) REVERT: P 981 TYR cc_start: 0.7643 (m-10) cc_final: 0.7172 (m-10) REVERT: P 1043 MET cc_start: 0.5479 (OUTLIER) cc_final: 0.5116 (ptp) outliers start: 33 outliers final: 21 residues processed: 178 average time/residue: 0.0991 time to fit residues: 23.6879 Evaluate side-chains 165 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 217 SER Chi-restraints excluded: chain P residue 224 ASN Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 257 ASP Chi-restraints excluded: chain P residue 813 LEU Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 842 VAL Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 882 TYR Chi-restraints excluded: chain P residue 892 ILE Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 1043 MET Chi-restraints excluded: chain P residue 1051 THR Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1149 VAL Chi-restraints excluded: chain P residue 1169 MET Chi-restraints excluded: chain P residue 1259 VAL Chi-restraints excluded: chain P residue 1284 ASP Chi-restraints excluded: chain P residue 1317 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 76 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 0.0010 chunk 61 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 240 ASN P 255 ASN ** P 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1261 GLN P1305 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.146985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.125528 restraints weight = 27707.604| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 3.48 r_work: 0.3945 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.5926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9648 Z= 0.138 Angle : 0.631 12.064 13199 Z= 0.321 Chirality : 0.040 0.174 1506 Planarity : 0.004 0.054 1517 Dihedral : 10.332 99.514 1676 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.82 % Allowed : 18.46 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.26), residues: 1025 helix: 0.63 (0.23), residues: 523 sheet: -0.42 (0.45), residues: 123 loop : -0.91 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 780 TYR 0.012 0.001 TYR P 823 PHE 0.043 0.002 PHE P 916 TRP 0.019 0.003 TRP P1074 HIS 0.009 0.002 HIS P 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 9648) covalent geometry : angle 0.63107 / 0.32 (13199) hydrogen bonds : bond 0.03983 / 2.67 ( 448) hydrogen bonds : angle 4.85930 / 3.42 ( 1260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 73 THR cc_start: 0.8809 (t) cc_final: 0.8548 (p) REVERT: P 77 ASN cc_start: 0.8133 (t0) cc_final: 0.7829 (t0) REVERT: P 222 LEU cc_start: 0.8633 (tp) cc_final: 0.8402 (tt) REVERT: P 354 GLN cc_start: 0.7838 (mt0) cc_final: 0.7459 (tm-30) REVERT: P 394 ASN cc_start: 0.7953 (t0) cc_final: 0.7565 (p0) REVERT: P 740 THR cc_start: 0.8256 (m) cc_final: 0.7953 (p) REVERT: P 742 LYS cc_start: 0.7647 (mtmt) cc_final: 0.7212 (mmtt) REVERT: P 745 ASP cc_start: 0.8068 (m-30) cc_final: 0.7765 (t0) REVERT: P 766 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7719 (pm20) REVERT: P 795 ILE cc_start: 0.6364 (OUTLIER) cc_final: 0.3999 (tt) REVERT: P 809 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7400 (mm-30) REVERT: P 926 GLN cc_start: 0.7946 (tp-100) cc_final: 0.7319 (tp-100) REVERT: P 927 ILE cc_start: 0.8785 (tp) cc_final: 0.8373 (pt) REVERT: P 937 SER cc_start: 0.7467 (t) cc_final: 0.7258 (m) REVERT: P 947 ASP cc_start: 0.7714 (t0) cc_final: 0.7430 (t0) REVERT: P 981 TYR cc_start: 0.7203 (m-10) cc_final: 0.6593 (m-10) REVERT: P 1043 MET cc_start: 0.5517 (OUTLIER) cc_final: 0.5256 (ptp) REVERT: P 1305 GLN cc_start: 0.7202 (OUTLIER) cc_final: 0.6906 (mm-40) REVERT: P 1333 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7811 (ttp80) outliers start: 26 outliers final: 18 residues processed: 168 average time/residue: 0.0863 time to fit residues: 19.7175 Evaluate side-chains 165 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 198 GLU Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 217 SER Chi-restraints excluded: chain P residue 224 ASN Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 766 GLU Chi-restraints excluded: chain P residue 795 ILE Chi-restraints excluded: chain P residue 813 LEU Chi-restraints excluded: chain P residue 842 VAL Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 882 TYR Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 922 VAL Chi-restraints excluded: chain P residue 1043 MET Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1169 MET Chi-restraints excluded: chain P residue 1305 GLN Chi-restraints excluded: chain P residue 1317 ASN Chi-restraints excluded: chain P residue 1364 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 96 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 32 optimal weight: 0.0170 chunk 0 optimal weight: 6.9990 chunk 72 optimal weight: 0.5980 chunk 71 optimal weight: 0.1980 chunk 87 optimal weight: 2.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1305 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.148215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.126774 restraints weight = 27629.878| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 3.49 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.5958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9648 Z= 0.125 Angle : 0.626 14.250 13199 Z= 0.316 Chirality : 0.039 0.171 1506 Planarity : 0.004 0.065 1517 Dihedral : 10.158 99.256 1676 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.71 % Allowed : 18.89 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.26), residues: 1025 helix: 0.82 (0.23), residues: 511 sheet: -0.29 (0.45), residues: 123 loop : -0.77 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG P 780 TYR 0.011 0.001 TYR P1013 PHE 0.040 0.002 PHE P 916 TRP 0.015 0.002 TRP P1074 HIS 0.006 0.001 HIS P 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 9648) covalent geometry : angle 0.62604 / 0.32 (13199) hydrogen bonds : bond 0.03786 / 2.54 ( 448) hydrogen bonds : angle 4.80009 / 3.40 ( 1260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 4 LYS cc_start: 0.8416 (ttmt) cc_final: 0.8049 (ttmm) REVERT: P 77 ASN cc_start: 0.7913 (t0) cc_final: 0.7588 (t0) REVERT: P 193 ASN cc_start: 0.6218 (m110) cc_final: 0.5651 (m-40) REVERT: P 222 LEU cc_start: 0.8530 (tp) cc_final: 0.8316 (tt) REVERT: P 354 GLN cc_start: 0.7811 (mt0) cc_final: 0.7560 (tm-30) REVERT: P 362 TYR cc_start: 0.7796 (t80) cc_final: 0.7567 (t80) REVERT: P 383 MET cc_start: 0.6571 (ptp) cc_final: 0.6306 (ptp) REVERT: P 394 ASN cc_start: 0.8031 (t0) cc_final: 0.7606 (p0) REVERT: P 740 THR cc_start: 0.8073 (m) cc_final: 0.7774 (p) REVERT: P 742 LYS cc_start: 0.7433 (mtmt) cc_final: 0.7059 (mmtt) REVERT: P 745 ASP cc_start: 0.7913 (m-30) cc_final: 0.7606 (t0) REVERT: P 766 GLU cc_start: 0.7987 (mp0) cc_final: 0.7564 (pm20) REVERT: P 795 ILE cc_start: 0.6335 (OUTLIER) cc_final: 0.4039 (tt) REVERT: P 926 GLN cc_start: 0.7775 (tp-100) cc_final: 0.7134 (tp-100) REVERT: P 927 ILE cc_start: 0.8697 (tp) cc_final: 0.8263 (pt) REVERT: P 947 ASP cc_start: 0.7344 (t0) cc_final: 0.7049 (t0) REVERT: P 981 TYR cc_start: 0.6998 (m-10) cc_final: 0.6337 (m-10) REVERT: P 1333 ARG cc_start: 0.7726 (ttp80) cc_final: 0.7447 (ttp80) outliers start: 25 outliers final: 15 residues processed: 164 average time/residue: 0.1015 time to fit residues: 22.4195 Evaluate side-chains 161 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 217 SER Chi-restraints excluded: chain P residue 224 ASN Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 776 ASN Chi-restraints excluded: chain P residue 782 LYS Chi-restraints excluded: chain P residue 795 ILE Chi-restraints excluded: chain P residue 813 LEU Chi-restraints excluded: chain P residue 842 VAL Chi-restraints excluded: chain P residue 882 TYR Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1169 MET Chi-restraints excluded: chain P residue 1317 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 92 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1221 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 = 0.4340 r_free = 0.4340 target = 0.145537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.123295 restraints weight = 27317.855| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 3.49 r_work: 0.3921 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.6251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9648 Z= 0.194 Angle : 0.681 13.256 13199 Z= 0.348 Chirality : 0.041 0.209 1506 Planarity : 0.004 0.062 1517 Dihedral : 10.287 100.990 1676 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.28 % Allowed : 19.33 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.26), residues: 1025 helix: 0.57 (0.23), residues: 522 sheet: -0.18 (0.46), residues: 109 loop : -0.96 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 780 TYR 0.015 0.002 TYR P1013 PHE 0.051 0.003 PHE P 916 TRP 0.020 0.003 TRP P 18 HIS 0.009 0.001 HIS P 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 ( 9648) covalent geometry : angle 0.68078 / 0.35 (13199) hydrogen bonds : bond 0.04376 / 2.94 ( 448) hydrogen bonds : angle 5.05604 / 3.57 ( 1260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 73 THR cc_start: 0.8799 (t) cc_final: 0.8529 (p) REVERT: P 77 ASN cc_start: 0.8164 (t0) cc_final: 0.7827 (t0) REVERT: P 222 LEU cc_start: 0.8660 (tp) cc_final: 0.8418 (tt) REVERT: P 354 GLN cc_start: 0.7809 (mt0) cc_final: 0.7456 (tm-30) REVERT: P 383 MET cc_start: 0.6569 (ptp) cc_final: 0.6251 (ptp) REVERT: P 394 ASN cc_start: 0.8014 (t0) cc_final: 0.7606 (p0) REVERT: P 734 LYS cc_start: 0.8940 (mtpt) cc_final: 0.8733 (mtpp) REVERT: P 740 THR cc_start: 0.8197 (m) cc_final: 0.7894 (p) REVERT: P 742 LYS cc_start: 0.7564 (mtmt) cc_final: 0.7145 (mmtt) REVERT: P 745 ASP cc_start: 0.8136 (m-30) cc_final: 0.7701 (t0) REVERT: P 766 GLU cc_start: 0.8262 (mp0) cc_final: 0.7854 (pm20) REVERT: P 795 ILE cc_start: 0.6362 (OUTLIER) cc_final: 0.3975 (tt) REVERT: P 926 GLN cc_start: 0.7966 (tp-100) cc_final: 0.7364 (tp-100) REVERT: P 927 ILE cc_start: 0.8816 (tp) cc_final: 0.8409 (pt) REVERT: P 947 ASP cc_start: 0.7818 (t0) cc_final: 0.7537 (t0) REVERT: P 981 TYR cc_start: 0.7185 (m-10) cc_final: 0.6553 (m-10) REVERT: P 1333 ARG cc_start: 0.8204 (ttp80) cc_final: 0.7777 (ttp80) outliers start: 21 outliers final: 19 residues processed: 160 average time/residue: 0.1032 time to fit residues: 22.3423 Evaluate side-chains 161 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 198 GLU Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 217 SER Chi-restraints excluded: chain P residue 224 ASN Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 776 ASN Chi-restraints excluded: chain P residue 782 LYS Chi-restraints excluded: chain P residue 795 ILE Chi-restraints excluded: chain P residue 813 LEU Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 842 VAL Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 882 TYR Chi-restraints excluded: chain P residue 922 VAL Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1169 MET Chi-restraints excluded: chain P residue 1317 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 82 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 60 optimal weight: 0.3980 chunk 84 optimal weight: 0.0870 chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.6964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 721 HIS P 726 ASN ** P 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1221 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 = 0.4321 r_free = 0.4321 target = 0.144046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.121469 restraints weight = 27130.009| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 3.48 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.6609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 9648 Z= 0.229 Angle : 0.735 13.566 13199 Z= 0.375 Chirality : 0.043 0.228 1506 Planarity : 0.005 0.072 1517 Dihedral : 10.504 101.261 1676 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.28 % Allowed : 19.11 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.25), residues: 1025 helix: 0.34 (0.23), residues: 517 sheet: -0.31 (0.48), residues: 99 loop : -1.07 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 780 TYR 0.017 0.002 TYR P1013 PHE 0.050 0.003 PHE P 916 TRP 0.025 0.004 TRP P 18 HIS 0.012 0.002 HIS P 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.23 ( 9648) covalent geometry : angle 0.73482 / 0.38 (13199) hydrogen bonds : bond 0.04771 / 3.20 ( 448) hydrogen bonds : angle 5.27359 / 3.73 ( 1260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 73 THR cc_start: 0.8821 (t) cc_final: 0.8543 (p) REVERT: P 77 ASN cc_start: 0.8057 (t0) cc_final: 0.7730 (t0) REVERT: P 83 GLN cc_start: 0.8194 (tp-100) cc_final: 0.7920 (tp-100) REVERT: P 222 LEU cc_start: 0.8602 (tp) cc_final: 0.8371 (tt) REVERT: P 354 GLN cc_start: 0.7681 (mt0) cc_final: 0.7370 (tm-30) REVERT: P 383 MET cc_start: 0.6542 (ptp) cc_final: 0.6285 (ptp) REVERT: P 394 ASN cc_start: 0.7919 (t0) cc_final: 0.7561 (p0) REVERT: P 722 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7931 (mt-10) REVERT: P 734 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8411 (mtpp) REVERT: P 740 THR cc_start: 0.8100 (m) cc_final: 0.7760 (p) REVERT: P 742 LYS cc_start: 0.7452 (mtmt) cc_final: 0.7027 (mmtt) REVERT: P 745 ASP cc_start: 0.8002 (m-30) cc_final: 0.7590 (t0) REVERT: P 766 GLU cc_start: 0.8086 (mp0) cc_final: 0.7608 (pm20) REVERT: P 795 ILE cc_start: 0.6507 (OUTLIER) cc_final: 0.4165 (tt) REVERT: P 926 GLN cc_start: 0.7892 (tp-100) cc_final: 0.7482 (tp-100) REVERT: P 927 ILE cc_start: 0.8798 (tp) cc_final: 0.8374 (pt) REVERT: P 939 MET cc_start: 0.7281 (mtp) cc_final: 0.7060 (mtp) REVERT: P 981 TYR cc_start: 0.7161 (m-10) cc_final: 0.6631 (m-10) REVERT: P 1333 ARG cc_start: 0.7626 (ttp80) cc_final: 0.7378 (ttp80) outliers start: 21 outliers final: 17 residues processed: 158 average time/residue: 0.1089 time to fit residues: 23.3447 Evaluate side-chains 157 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 198 GLU Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 217 SER Chi-restraints excluded: chain P residue 224 ASN Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 776 ASN Chi-restraints excluded: chain P residue 782 LYS Chi-restraints excluded: chain P residue 795 ILE Chi-restraints excluded: chain P residue 813 LEU Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 922 VAL Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1169 MET Chi-restraints excluded: chain P residue 1317 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 85 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 103 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 80 optimal weight: 0.0770 chunk 9 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 329 HIS P 726 ASN P 758 ASN ** P 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.146701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.124846 restraints weight = 27073.193| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 3.42 r_work: 0.3946 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.6600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9648 Z= 0.146 Angle : 0.671 14.373 13199 Z= 0.341 Chirality : 0.040 0.196 1506 Planarity : 0.005 0.097 1517 Dihedral : 10.218 99.501 1676 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.17 % Allowed : 19.54 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.26), residues: 1025 helix: 0.50 (0.23), residues: 520 sheet: -0.41 (0.45), residues: 123 loop : -0.97 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 780 TYR 0.013 0.001 TYR P1013 PHE 0.048 0.002 PHE P 916 TRP 0.017 0.003 TRP P 18 HIS 0.009 0.001 HIS P 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 9648) covalent geometry : angle 0.67112 / 0.34 (13199) hydrogen bonds : bond 0.04006 / 2.64 ( 448) hydrogen bonds : angle 5.01770 / 3.54 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2345.55 seconds wall clock time: 40 minutes 59.43 seconds (2459.43 seconds total)