Starting phenix.real_space_refine on Wed Mar 4 01:08:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s37_24818/03_2026/7s37_24818.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s37_24818/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7s37_24818/03_2026/7s37_24818.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s37_24818/03_2026/7s37_24818.map" model { file = "/net/cci-nas-00/data/ceres_data/7s37_24818/03_2026/7s37_24818.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s37_24818/03_2026/7s37_24818.cif" } 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-5986/lib/python3.9/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: 2.33, per 1000 atoms: 0.25 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: 0.86 Conformation dependent library (CDL) restraints added in 349.4 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: 1.13 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: 2.00 Time building geometry restraints manager: 1.17 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: 5515 20.22 - 40.44: 307 40.44 - 60.65: 99 60.65 - 80.87: 43 80.87 - 101.09: 4 Dihedral angle restraints: 5968 sinusoidal: 2931 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 5965 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.010 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 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 : 14.849 101.089 4004 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 covalent geometry : bond 0.00644 ( 9648) covalent geometry : angle 1.03660 (13199) hydrogen bonds : bond 0.15113 ( 448) hydrogen bonds : angle 6.04757 ( 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 : 0.357 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: 0.1223 time to fit residues: 42.3883 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 : 0.231 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4424 r_free = 0.4424 target = 0.152546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.131182 restraints weight = 27412.111| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 3.55 r_work: 0.4028 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9648 Z= 0.184 Angle : 0.638 7.106 13199 Z= 0.341 Chirality : 0.041 0.211 1506 Planarity : 0.004 0.058 1517 Dihedral : 15.231 96.719 1824 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.28 % Allowed : 11.83 % Favored : 85.88 % 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: -0.09 (0.26), residues: 1025 helix: 0.57 (0.22), residues: 518 sheet: -0.68 (0.44), residues: 131 loop : -0.55 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 400 TYR 0.017 0.002 TYR P1001 PHE 0.042 0.002 PHE P 916 TRP 0.019 0.003 TRP P 883 HIS 0.008 0.001 HIS P 420 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9648) covalent geometry : angle 0.63834 (13199) hydrogen bonds : bond 0.04857 ( 448) hydrogen bonds : angle 4.94848 ( 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 195 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.361 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: P 63 ARG cc_start: 0.7058 (mtp180) cc_final: 0.6508 (mtm180) REVERT: P 72 TYR cc_start: 0.7978 (t80) cc_final: 0.7711 (t80) REVERT: P 75 ARG cc_start: 0.8866 (mtt180) cc_final: 0.8402 (mmt90) REVERT: P 76 LYS cc_start: 0.8648 (mmmt) cc_final: 0.8234 (mmmt) REVERT: P 77 ASN cc_start: 0.8278 (t0) cc_final: 0.7824 (t0) REVERT: P 163 LYS cc_start: 0.7782 (tttt) cc_final: 0.7482 (ttpt) REVERT: P 257 ASP cc_start: 0.7547 (t70) cc_final: 0.7335 (t0) REVERT: P 285 GLN cc_start: 0.8266 (pt0) cc_final: 0.7602 (pm20) REVERT: P 286 TYR cc_start: 0.8079 (m-80) cc_final: 0.7420 (m-10) REVERT: P 300 ILE cc_start: 0.7846 (pt) cc_final: 0.7624 (pt) REVERT: P 304 ASP cc_start: 0.6750 (t70) cc_final: 0.6549 (t0) REVERT: P 380 LEU cc_start: 0.7871 (mt) cc_final: 0.7599 (mt) REVERT: P 383 MET cc_start: 0.6511 (mtp) cc_final: 0.6217 (ptp) REVERT: P 394 ASN cc_start: 0.7539 (t0) cc_final: 0.7225 (p0) REVERT: P 418 GLU cc_start: 0.8427 (mp0) cc_final: 0.8084 (mp0) REVERT: P 740 THR cc_start: 0.8102 (m) cc_final: 0.7844 (p) REVERT: P 742 LYS cc_start: 0.7699 (mtmt) cc_final: 0.7204 (mmmt) REVERT: P 766 GLU cc_start: 0.7798 (mp0) cc_final: 0.7556 (mp0) REVERT: P 926 GLN cc_start: 0.7696 (tp-100) cc_final: 0.7280 (tp-100) REVERT: P 937 SER cc_start: 0.7112 (t) cc_final: 0.6763 (m) REVERT: P 959 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7693 (mttp) REVERT: P 981 TYR cc_start: 0.7290 (m-10) cc_final: 0.6799 (m-10) REVERT: P 1089 MET cc_start: 0.5911 (mtt) cc_final: 0.5661 (mtp) REVERT: P 1171 ARG cc_start: 0.7782 (ttt180) cc_final: 0.7527 (ttp80) REVERT: P 1305 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7186 (mm110) outliers start: 21 outliers final: 12 residues processed: 184 average time/residue: 0.1229 time to fit residues: 29.4940 Evaluate side-chains 165 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 959 LYS 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 1305 GLN 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: 4.9990 chunk 23 optimal weight: 0.3980 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 2 optimal weight: 0.0370 overall best weight: 1.2864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 167 HIS ** P 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 309 ASN P 758 ASN 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 = 0.4381 r_free = 0.4381 target = 0.148668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.126829 restraints weight = 27618.732| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 3.55 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9648 Z= 0.187 Angle : 0.643 13.648 13199 Z= 0.333 Chirality : 0.041 0.177 1506 Planarity : 0.004 0.040 1517 Dihedral : 15.188 98.508 1822 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.61 % Allowed : 15.09 % Favored : 82.30 % 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: -0.00 (0.25), residues: 1025 helix: 0.64 (0.22), residues: 518 sheet: -0.33 (0.51), residues: 96 loop : -0.63 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P1335 TYR 0.021 0.002 TYR P 362 PHE 0.033 0.002 PHE P 916 TRP 0.008 0.001 TRP P 883 HIS 0.006 0.002 HIS P 799 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 9648) covalent geometry : angle 0.64342 (13199) hydrogen bonds : bond 0.04441 ( 448) hydrogen bonds : angle 4.86371 ( 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 192 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 70 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8108 (mtm180) REVERT: P 76 LYS cc_start: 0.8534 (mmmt) cc_final: 0.8297 (mmmt) REVERT: P 77 ASN cc_start: 0.8005 (t0) cc_final: 0.7687 (t0) REVERT: P 163 LYS cc_start: 0.8137 (tttt) cc_final: 0.7756 (ttpt) REVERT: P 257 ASP cc_start: 0.7382 (t70) cc_final: 0.7083 (t0) REVERT: P 286 TYR cc_start: 0.7835 (m-80) cc_final: 0.7538 (m-10) REVERT: P 304 ASP cc_start: 0.6859 (t70) cc_final: 0.6628 (t0) REVERT: P 321 MET cc_start: 0.6720 (mmp) cc_final: 0.6194 (mmp) REVERT: P 380 LEU cc_start: 0.8054 (mt) cc_final: 0.7825 (mt) REVERT: P 394 ASN cc_start: 0.7844 (t0) cc_final: 0.7444 (p0) REVERT: P 418 GLU cc_start: 0.8069 (mp0) cc_final: 0.7752 (mm-30) REVERT: P 740 THR cc_start: 0.8054 (m) cc_final: 0.7672 (p) REVERT: P 742 LYS cc_start: 0.7532 (mtmt) cc_final: 0.7101 (mmtt) REVERT: P 749 LYS cc_start: 0.8061 (tttt) cc_final: 0.7756 (tttm) REVERT: P 770 THR cc_start: 0.6624 (m) cc_final: 0.6406 (p) REVERT: P 926 GLN cc_start: 0.7757 (tp-100) cc_final: 0.7094 (tp-100) REVERT: P 937 SER cc_start: 0.7110 (t) cc_final: 0.6760 (m) REVERT: P 981 TYR cc_start: 0.7380 (m-10) cc_final: 0.6884 (m-10) REVERT: P 1043 MET cc_start: 0.5354 (ptm) cc_final: 0.5031 (ptp) outliers start: 24 outliers final: 18 residues processed: 183 average time/residue: 0.1184 time to fit residues: 28.5906 Evaluate side-chains 170 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 70 ARG 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 824 VAL Chi-restraints excluded: chain P residue 882 TYR Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 1051 THR Chi-restraints excluded: chain P residue 1087 LEU Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1149 VAL Chi-restraints excluded: chain P residue 1164 LEU 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 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: 7.9990 chunk 44 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 228 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.147981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.126287 restraints weight = 28006.935| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 3.53 r_work: 0.3954 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9648 Z= 0.169 Angle : 0.617 9.356 13199 Z= 0.320 Chirality : 0.040 0.136 1506 Planarity : 0.004 0.045 1517 Dihedral : 15.207 99.050 1822 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.93 % Allowed : 15.96 % Favored : 81.11 % 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: -0.02 (0.26), residues: 1025 helix: 0.70 (0.22), residues: 524 sheet: -0.40 (0.47), residues: 110 loop : -0.77 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 400 TYR 0.020 0.002 TYR P 362 PHE 0.036 0.002 PHE P 916 TRP 0.005 0.001 TRP P1074 HIS 0.005 0.001 HIS P 799 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9648) covalent geometry : angle 0.61724 (13199) hydrogen bonds : bond 0.04269 ( 448) hydrogen bonds : angle 4.76251 ( 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 177 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 75 ARG cc_start: 0.8905 (mtt180) cc_final: 0.8292 (mmm-85) REVERT: P 76 LYS cc_start: 0.8692 (mmmt) cc_final: 0.8250 (mmmt) REVERT: P 77 ASN cc_start: 0.8145 (t0) cc_final: 0.7868 (t0) REVERT: P 163 LYS cc_start: 0.7951 (tttt) cc_final: 0.7430 (ttpt) REVERT: P 304 ASP cc_start: 0.7078 (t70) cc_final: 0.6797 (t0) REVERT: P 321 MET cc_start: 0.7074 (mmp) cc_final: 0.6678 (mmp) REVERT: P 354 GLN cc_start: 0.7633 (mt0) cc_final: 0.7086 (tm-30) REVERT: P 394 ASN cc_start: 0.7665 (t0) cc_final: 0.7221 (p0) REVERT: P 418 GLU cc_start: 0.8332 (mp0) cc_final: 0.8085 (mm-30) REVERT: P 740 THR cc_start: 0.8265 (m) cc_final: 0.7892 (p) REVERT: P 742 LYS cc_start: 0.7661 (mtmt) cc_final: 0.7236 (mmtt) REVERT: P 745 ASP cc_start: 0.8002 (m-30) cc_final: 0.7669 (t0) REVERT: P 781 MET cc_start: 0.6559 (mmm) cc_final: 0.6344 (mtp) REVERT: P 908 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7515 (mp) REVERT: P 926 GLN cc_start: 0.7967 (tp-100) cc_final: 0.7307 (tp-100) REVERT: P 927 ILE cc_start: 0.8784 (tp) cc_final: 0.8337 (pt) REVERT: P 937 SER cc_start: 0.7407 (t) cc_final: 0.7122 (m) REVERT: P 967 ARG cc_start: 0.7480 (mtt180) cc_final: 0.7236 (mmm-85) REVERT: P 981 TYR cc_start: 0.7480 (m-10) cc_final: 0.6967 (m-10) outliers start: 27 outliers final: 17 residues processed: 168 average time/residue: 0.1116 time to fit residues: 24.9284 Evaluate side-chains 162 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 241 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 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 1169 MET Chi-restraints excluded: chain P residue 1259 VAL 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: 0.0670 chunk 70 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 193 ASN ** P1305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.148782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.126971 restraints weight = 27809.274| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 3.53 r_work: 0.3968 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.4986 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= 0.127 Angle : 0.566 8.794 13199 Z= 0.295 Chirality : 0.038 0.168 1506 Planarity : 0.004 0.045 1517 Dihedral : 15.136 99.103 1822 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.82 % Allowed : 17.37 % Favored : 79.80 % 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: 0.91 (0.23), residues: 515 sheet: -0.33 (0.46), residues: 110 loop : -0.67 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 400 TYR 0.012 0.001 TYR P1001 PHE 0.043 0.002 PHE P 916 TRP 0.003 0.001 TRP P1074 HIS 0.006 0.001 HIS P 137 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9648) covalent geometry : angle 0.56593 (13199) hydrogen bonds : bond 0.03766 ( 448) hydrogen bonds : angle 4.62394 ( 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 178 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 63 ARG cc_start: 0.6986 (mtp180) cc_final: 0.6551 (mtm180) REVERT: P 75 ARG cc_start: 0.8913 (mtt180) cc_final: 0.8292 (mmm-85) REVERT: P 76 LYS cc_start: 0.8693 (mmmt) cc_final: 0.8252 (mmmt) REVERT: P 77 ASN cc_start: 0.8049 (t0) cc_final: 0.7784 (t0) REVERT: P 163 LYS cc_start: 0.7862 (tttt) cc_final: 0.7381 (ttpt) REVERT: P 304 ASP cc_start: 0.7080 (t70) cc_final: 0.6796 (t0) REVERT: P 354 GLN cc_start: 0.7601 (mt0) cc_final: 0.7183 (tm-30) REVERT: P 394 ASN cc_start: 0.7636 (t0) cc_final: 0.7300 (p0) REVERT: P 418 GLU cc_start: 0.8404 (mp0) cc_final: 0.8147 (mm-30) REVERT: P 740 THR cc_start: 0.8298 (m) cc_final: 0.7967 (p) REVERT: P 742 LYS cc_start: 0.7714 (mtmt) cc_final: 0.7280 (mmtt) REVERT: P 745 ASP cc_start: 0.7926 (m-30) cc_final: 0.7627 (t0) REVERT: P 908 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7483 (mp) REVERT: P 926 GLN cc_start: 0.7908 (tp-100) cc_final: 0.7242 (tp-100) REVERT: P 927 ILE cc_start: 0.8756 (tp) cc_final: 0.8320 (pt) REVERT: P 937 SER cc_start: 0.7361 (t) cc_final: 0.7122 (m) REVERT: P 947 ASP cc_start: 0.7131 (t0) cc_final: 0.6903 (t0) REVERT: P 981 TYR cc_start: 0.7245 (m-10) cc_final: 0.6740 (m-10) REVERT: P 1043 MET cc_start: 0.5373 (OUTLIER) cc_final: 0.5135 (ptp) REVERT: P 1080 PHE cc_start: 0.5640 (m-80) cc_final: 0.5214 (m-80) REVERT: P 1089 MET cc_start: 0.5757 (mtp) cc_final: 0.5403 (mtp) REVERT: P 1237 TYR cc_start: 0.6385 (t80) cc_final: 0.6023 (t80) outliers start: 26 outliers final: 17 residues processed: 167 average time/residue: 0.1101 time to fit residues: 24.6932 Evaluate side-chains 155 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 322 ILE 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 908 LEU Chi-restraints excluded: chain P residue 1043 MET 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 1317 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 58 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 64 optimal weight: 0.0020 chunk 67 optimal weight: 2.9990 chunk 4 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 193 ASN ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.149309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.127247 restraints weight = 27642.806| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 3.61 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9648 Z= 0.117 Angle : 0.570 8.064 13199 Z= 0.292 Chirality : 0.038 0.204 1506 Planarity : 0.003 0.044 1517 Dihedral : 15.070 99.243 1822 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.50 % Allowed : 17.92 % 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: 0.23 (0.26), residues: 1025 helix: 0.88 (0.23), residues: 522 sheet: -0.40 (0.44), residues: 132 loop : -0.55 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 139 TYR 0.010 0.001 TYR P 823 PHE 0.042 0.002 PHE P 916 TRP 0.004 0.001 TRP P1074 HIS 0.005 0.001 HIS P 167 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9648) covalent geometry : angle 0.57000 (13199) hydrogen bonds : bond 0.03635 ( 448) hydrogen bonds : angle 4.60838 ( 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 173 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 63 ARG cc_start: 0.7011 (mtp180) cc_final: 0.6574 (mtm180) REVERT: P 75 ARG cc_start: 0.8696 (mtt180) cc_final: 0.8004 (mmm-85) REVERT: P 76 LYS cc_start: 0.8629 (mmmt) cc_final: 0.8152 (mmmt) REVERT: P 77 ASN cc_start: 0.7868 (t0) cc_final: 0.7601 (t0) REVERT: P 163 LYS cc_start: 0.7972 (tttt) cc_final: 0.7400 (ttpt) REVERT: P 362 TYR cc_start: 0.7815 (t80) cc_final: 0.7573 (t80) REVERT: P 394 ASN cc_start: 0.7805 (t0) cc_final: 0.7404 (p0) REVERT: P 418 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7837 (mm-30) REVERT: P 722 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7636 (mt-10) REVERT: P 740 THR cc_start: 0.8134 (m) cc_final: 0.7793 (p) REVERT: P 742 LYS cc_start: 0.7544 (mtmt) cc_final: 0.7152 (mmtt) REVERT: P 745 ASP cc_start: 0.7769 (m-30) cc_final: 0.7499 (t0) REVERT: P 781 MET cc_start: 0.6702 (mmm) cc_final: 0.6440 (mmm) REVERT: P 926 GLN cc_start: 0.7743 (tp-100) cc_final: 0.7137 (tp-100) REVERT: P 927 ILE cc_start: 0.8670 (tp) cc_final: 0.8214 (pt) REVERT: P 937 SER cc_start: 0.6980 (t) cc_final: 0.6720 (m) REVERT: P 947 ASP cc_start: 0.6891 (t0) cc_final: 0.6644 (t0) REVERT: P 981 TYR cc_start: 0.7144 (m-10) cc_final: 0.6398 (m-10) REVERT: P 1043 MET cc_start: 0.5239 (ptm) cc_final: 0.5012 (ptp) REVERT: P 1089 MET cc_start: 0.5562 (mtp) cc_final: 0.5196 (mtp) outliers start: 23 outliers final: 14 residues processed: 163 average time/residue: 0.1054 time to fit residues: 23.0849 Evaluate side-chains 154 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 241 LEU Chi-restraints excluded: chain P residue 418 GLU Chi-restraints excluded: chain P residue 776 ASN Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 882 TYR 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 1317 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 76 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 0.0030 chunk 61 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 985 HIS ** P1305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.149071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.127078 restraints weight = 27444.736| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 3.51 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9648 Z= 0.125 Angle : 0.574 8.011 13199 Z= 0.295 Chirality : 0.038 0.152 1506 Planarity : 0.004 0.043 1517 Dihedral : 15.039 99.896 1822 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.93 % Allowed : 17.70 % Favored : 79.37 % 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: 0.94 (0.23), residues: 522 sheet: -0.34 (0.46), residues: 121 loop : -0.55 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 780 TYR 0.012 0.001 TYR P 823 PHE 0.050 0.002 PHE P 916 TRP 0.003 0.001 TRP P1074 HIS 0.005 0.001 HIS P 167 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9648) covalent geometry : angle 0.57383 (13199) hydrogen bonds : bond 0.03650 ( 448) hydrogen bonds : angle 4.62855 ( 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 174 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 76 LYS cc_start: 0.8627 (mmmt) cc_final: 0.8140 (mmmt) REVERT: P 77 ASN cc_start: 0.7865 (t0) cc_final: 0.7599 (t0) REVERT: P 163 LYS cc_start: 0.7997 (tttt) cc_final: 0.7641 (ttpt) REVERT: P 193 ASN cc_start: 0.6253 (m110) cc_final: 0.5748 (m-40) REVERT: P 362 TYR cc_start: 0.7873 (t80) cc_final: 0.7479 (t80) REVERT: P 394 ASN cc_start: 0.7861 (t0) cc_final: 0.7435 (p0) REVERT: P 722 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7581 (mt-10) REVERT: P 740 THR cc_start: 0.8180 (m) cc_final: 0.7848 (p) REVERT: P 742 LYS cc_start: 0.7565 (mtmt) cc_final: 0.7164 (mmtt) REVERT: P 745 ASP cc_start: 0.7813 (m-30) cc_final: 0.7554 (t0) REVERT: P 781 MET cc_start: 0.6702 (mmm) cc_final: 0.6428 (mmm) REVERT: P 782 LYS cc_start: 0.7730 (ttmt) cc_final: 0.7499 (tptp) REVERT: P 892 ILE cc_start: 0.5061 (OUTLIER) cc_final: 0.4572 (pt) REVERT: P 926 GLN cc_start: 0.7758 (tp-100) cc_final: 0.7146 (tp-100) REVERT: P 927 ILE cc_start: 0.8713 (tp) cc_final: 0.8262 (pt) REVERT: P 937 SER cc_start: 0.6992 (t) cc_final: 0.6755 (m) REVERT: P 947 ASP cc_start: 0.7062 (t0) cc_final: 0.6853 (t0) REVERT: P 981 TYR cc_start: 0.7041 (m-10) cc_final: 0.6283 (m-10) REVERT: P 1089 MET cc_start: 0.5639 (mtp) cc_final: 0.5264 (mtp) outliers start: 27 outliers final: 15 residues processed: 164 average time/residue: 0.1013 time to fit residues: 22.6171 Evaluate side-chains 155 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 322 ILE Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 882 TYR Chi-restraints excluded: chain P residue 892 ILE 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 1317 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 57 optimal weight: 0.4980 chunk 32 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 758 ASN ** P 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.145866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.122935 restraints weight = 27169.004| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 3.57 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.5940 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= 0.219 Angle : 0.686 11.042 13199 Z= 0.357 Chirality : 0.042 0.153 1506 Planarity : 0.005 0.069 1517 Dihedral : 15.237 102.117 1822 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.50 % Allowed : 18.13 % Favored : 79.37 % 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: -0.11 (0.25), residues: 1025 helix: 0.58 (0.22), residues: 523 sheet: -0.21 (0.47), residues: 99 loop : -0.79 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P1333 TYR 0.021 0.002 TYR P 823 PHE 0.050 0.003 PHE P 916 TRP 0.010 0.002 TRP P1074 HIS 0.006 0.002 HIS P 412 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 9648) covalent geometry : angle 0.68631 (13199) hydrogen bonds : bond 0.04578 ( 448) hydrogen bonds : angle 5.01277 ( 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 172 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 76 LYS cc_start: 0.8639 (mmmt) cc_final: 0.8116 (mmmt) REVERT: P 77 ASN cc_start: 0.8016 (t0) cc_final: 0.7705 (t0) REVERT: P 163 LYS cc_start: 0.8025 (tttt) cc_final: 0.7776 (ttpt) REVERT: P 394 ASN cc_start: 0.8035 (t0) cc_final: 0.7612 (p0) REVERT: P 745 ASP cc_start: 0.7937 (m-30) cc_final: 0.7629 (t0) REVERT: P 781 MET cc_start: 0.6421 (mmm) cc_final: 0.6065 (mtp) REVERT: P 782 LYS cc_start: 0.7531 (ttmt) cc_final: 0.7328 (tptp) REVERT: P 892 ILE cc_start: 0.5100 (OUTLIER) cc_final: 0.4532 (pt) REVERT: P 926 GLN cc_start: 0.7876 (tp-100) cc_final: 0.7284 (tp-100) REVERT: P 927 ILE cc_start: 0.8760 (tp) cc_final: 0.8330 (pt) REVERT: P 937 SER cc_start: 0.7027 (t) cc_final: 0.6826 (m) REVERT: P 947 ASP cc_start: 0.7506 (t0) cc_final: 0.7289 (t0) REVERT: P 981 TYR cc_start: 0.7327 (m-10) cc_final: 0.6642 (m-10) REVERT: P 1089 MET cc_start: 0.5629 (mtp) cc_final: 0.5183 (mtp) outliers start: 23 outliers final: 18 residues processed: 164 average time/residue: 0.1025 time to fit residues: 22.8895 Evaluate side-chains 157 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 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 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 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: 0.4980 chunk 105 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 73 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 758 ASN ** P 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.147548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.125894 restraints weight = 27361.119| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 3.49 r_work: 0.3945 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.5966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9648 Z= 0.148 Angle : 0.640 9.966 13199 Z= 0.328 Chirality : 0.040 0.205 1506 Planarity : 0.004 0.064 1517 Dihedral : 15.134 100.019 1822 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.39 % Allowed : 18.68 % Favored : 78.94 % 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: 0.01 (0.26), residues: 1025 helix: 0.69 (0.23), residues: 519 sheet: -0.28 (0.46), residues: 111 loop : -0.70 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 780 TYR 0.013 0.001 TYR P 823 PHE 0.052 0.002 PHE P 916 TRP 0.014 0.002 TRP P1074 HIS 0.005 0.001 HIS P1297 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9648) covalent geometry : angle 0.63958 (13199) hydrogen bonds : bond 0.04027 ( 448) hydrogen bonds : angle 4.82048 ( 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 166 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 63 ARG cc_start: 0.7134 (mtp180) cc_final: 0.6490 (mtm180) REVERT: P 70 ARG cc_start: 0.8646 (mtp180) cc_final: 0.8408 (mtp180) REVERT: P 76 LYS cc_start: 0.8737 (mmmt) cc_final: 0.8194 (mmmt) REVERT: P 77 ASN cc_start: 0.8107 (t0) cc_final: 0.7754 (t0) REVERT: P 163 LYS cc_start: 0.7784 (tttt) cc_final: 0.7517 (ttpt) REVERT: P 383 MET cc_start: 0.6453 (ptp) cc_final: 0.6167 (ptp) REVERT: P 394 ASN cc_start: 0.7953 (t0) cc_final: 0.7469 (p0) REVERT: P 722 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8210 (mt-10) REVERT: P 745 ASP cc_start: 0.8042 (m-30) cc_final: 0.7745 (t0) REVERT: P 781 MET cc_start: 0.6571 (mmm) cc_final: 0.6192 (mtp) REVERT: P 782 LYS cc_start: 0.7626 (ttmt) cc_final: 0.7409 (tptp) REVERT: P 926 GLN cc_start: 0.7928 (tp-100) cc_final: 0.7341 (tp-100) REVERT: P 927 ILE cc_start: 0.8791 (tp) cc_final: 0.8384 (pt) REVERT: P 937 SER cc_start: 0.7472 (t) cc_final: 0.7256 (m) REVERT: P 947 ASP cc_start: 0.7619 (t0) cc_final: 0.7341 (t0) REVERT: P 981 TYR cc_start: 0.6973 (m-10) cc_final: 0.6422 (m-10) outliers start: 22 outliers final: 19 residues processed: 159 average time/residue: 0.1073 time to fit residues: 23.2457 Evaluate side-chains 158 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 194 GLN 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 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 893 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 1317 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 82 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 844 GLN ** 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 = 0.4349 r_free = 0.4349 target = 0.145806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.122508 restraints weight = 27339.253| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 3.50 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.6167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9648 Z= 0.173 Angle : 0.672 10.106 13199 Z= 0.344 Chirality : 0.041 0.210 1506 Planarity : 0.004 0.042 1517 Dihedral : 15.151 100.620 1822 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.06 % Allowed : 19.33 % 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: -0.08 (0.26), residues: 1025 helix: 0.54 (0.22), residues: 526 sheet: -0.01 (0.48), residues: 99 loop : -0.74 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 967 TYR 0.015 0.002 TYR P 823 PHE 0.051 0.002 PHE P 916 TRP 0.020 0.003 TRP P 18 HIS 0.005 0.001 HIS P 167 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9648) covalent geometry : angle 0.67243 (13199) hydrogen bonds : bond 0.04218 ( 448) hydrogen bonds : angle 4.90418 ( 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 160 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 70 ARG cc_start: 0.8590 (mtp180) cc_final: 0.8303 (mtp180) REVERT: P 76 LYS cc_start: 0.8651 (mmmt) cc_final: 0.8114 (mmmt) REVERT: P 77 ASN cc_start: 0.7998 (t0) cc_final: 0.7612 (t0) REVERT: P 163 LYS cc_start: 0.7888 (tttt) cc_final: 0.7629 (ttpt) REVERT: P 383 MET cc_start: 0.6149 (ptp) cc_final: 0.5907 (ptp) REVERT: P 394 ASN cc_start: 0.8077 (t0) cc_final: 0.7608 (p0) REVERT: P 722 GLU cc_start: 0.8458 (mt-10) cc_final: 0.7959 (mt-10) REVERT: P 742 LYS cc_start: 0.7518 (mtmt) cc_final: 0.7132 (mmtt) REVERT: P 745 ASP cc_start: 0.7933 (m-30) cc_final: 0.7589 (t0) REVERT: P 781 MET cc_start: 0.6330 (mmm) cc_final: 0.6019 (mtp) REVERT: P 926 GLN cc_start: 0.7819 (tp-100) cc_final: 0.7245 (tp-100) REVERT: P 927 ILE cc_start: 0.8758 (tp) cc_final: 0.8345 (pt) REVERT: P 947 ASP cc_start: 0.7450 (t0) cc_final: 0.7208 (t0) REVERT: P 981 TYR cc_start: 0.6866 (m-10) cc_final: 0.6329 (m-10) outliers start: 19 outliers final: 19 residues processed: 153 average time/residue: 0.1119 time to fit residues: 23.1214 Evaluate side-chains 151 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 194 GLN 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 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 893 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 1317 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 85 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 844 GLN ** 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 = 0.4349 r_free = 0.4349 target = 0.146640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.124630 restraints weight = 27372.318| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 3.41 r_work: 0.3933 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.6325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9648 Z= 0.178 Angle : 0.704 16.221 13199 Z= 0.358 Chirality : 0.042 0.206 1506 Planarity : 0.005 0.067 1517 Dihedral : 15.172 100.471 1822 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.06 % Allowed : 20.20 % Favored : 77.74 % 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: 0.50 (0.22), residues: 525 sheet: -0.01 (0.48), residues: 99 loop : -0.68 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 780 TYR 0.014 0.002 TYR P 823 PHE 0.051 0.002 PHE P 916 TRP 0.022 0.003 TRP P 18 HIS 0.007 0.001 HIS P 167 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9648) covalent geometry : angle 0.70363 (13199) hydrogen bonds : bond 0.04294 ( 448) hydrogen bonds : angle 4.93844 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2417.91 seconds wall clock time: 42 minutes 10.95 seconds (2530.95 seconds total)