Starting phenix.real_space_refine on Fri Sep 11 14:11:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s37_24818/09_2026/7s37_24818.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s37_24818/09_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_24818/09_2026/7s37_24818.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s37_24818/09_2026/7s37_24818.map" model { file = "/net/cci-nas-00/data/ceres_data/7s37_24818/09_2026/7s37_24818.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s37_24818/09_2026/7s37_24818.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7s37_24818/09_2026/7s37_24818.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s37_24818/09_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-2.2.1-6174/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: {'RNAv2': 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: 1.79, per 1000 atoms: 0.19 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: 0.68 Conformation dependent library (CDL) restraints added in 227.5 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: 1.10 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: 1.60 Time building geometry restraints manager: 0.89 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: 12260 1.96 - 3.93: 789 3.93 - 5.89: 128 5.89 - 7.86: 19 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 - 17.01: 5265 17.01 - 34.03: 373 34.03 - 51.04: 126 51.04 - 68.05: 46 68.05 - 85.07: 12 Dihedral angle restraints: 5822 sinusoidal: 2785 harmonic: 3037 Sorted by residual: dihedral pdb=" C4' A R 88 " pdb=" C3' A R 88 " pdb=" C2' A R 88 " pdb=" C1' A R 88 " ideal model delta sinusoidal sigma weight residual 36.34 -36.12 72.47 1 3.10e+00 1.04e-01 6.98e+02 dihedral pdb=" C4' G R 43 " pdb=" C3' G R 43 " pdb=" C2' G R 43 " pdb=" C1' G R 43 " ideal model delta sinusoidal sigma weight residual 36.34 -35.82 72.17 1 3.10e+00 1.04e-01 6.93e+02 dihedral pdb=" C4' U R 90 " pdb=" C3' U R 90 " pdb=" C2' U R 90 " pdb=" C1' U R 90 " ideal model delta sinusoidal sigma weight residual 36.34 -35.57 71.91 1 3.10e+00 1.04e-01 6.89e+02 ... (remaining 5819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1207 0.066 - 0.133: 216 0.133 - 0.199: 27 0.199 - 0.266: 39 0.266 - 0.332: 17 Chirality restraints: 1506 Sorted by residual: chirality pdb=" P G R 92 " pdb=" OP1 G R 92 " pdb=" OP2 G R 92 " pdb=" O5' G R 92 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" P U R 98 " pdb=" OP1 U R 98 " pdb=" OP2 U R 98 " pdb=" O5' U R 98 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" P U R 80 " pdb=" OP1 U R 80 " pdb=" OP2 U R 80 " pdb=" O5' U R 80 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.32 2.00e-01 2.50e+01 2.54e+00 ... (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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.180 Find NCS groups from input model: 0.020 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.710 ------------------------------------------------------------------------------- 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= 0.291 Angle : 1.078 9.824 13199 Z= 0.567 Chirality : 0.069 0.332 1506 Planarity : 0.006 0.038 1517 Dihedral : 13.992 85.067 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 0.00648 / 0.29 ( 9648) covalent geometry : angle 1.07751 / 0.57 (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 : 0.283 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: 0.1170 time to fit residues: 41.0405 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 : 0.381 ------------------------------------------------------------------------------- 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: 1.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 716 GLN P 930 HIS P1241 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.152702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.131184 restraints weight = 27240.656| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 3.46 r_work: 0.4029 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 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 0.044 9648 Z= 0.201 Angle : 0.790 14.987 13199 Z= 0.379 Chirality : 0.054 0.632 1506 Planarity : 0.004 0.055 1517 Dihedral : 12.024 152.746 1678 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.17 % Allowed : 11.73 % Favored : 86.10 % 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: -0.04 (0.25), residues: 1025 helix: 0.66 (0.23), residues: 506 sheet: -0.66 (0.44), residues: 131 loop : -0.55 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 400 TYR 0.017 0.002 TYR P1001 PHE 0.032 0.002 PHE P 916 TRP 0.020 0.002 TRP P 883 HIS 0.007 0.001 HIS P 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.20 ( 9648) covalent geometry : angle 0.79006 / 0.38 (13199) hydrogen bonds : bond 0.04731 / 3.14 ( 448) hydrogen bonds : angle 4.95971 / 3.54 ( 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 196 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.347 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: 0.7093 (mtp180) cc_final: 0.6575 (mtm180) REVERT: P 72 TYR cc_start: 0.7959 (t80) cc_final: 0.7709 (t80) REVERT: P 75 ARG cc_start: 0.8881 (mtt180) cc_final: 0.8427 (mmt90) REVERT: P 76 LYS cc_start: 0.8653 (mmmt) cc_final: 0.8253 (mmmt) REVERT: P 77 ASN cc_start: 0.8223 (t0) cc_final: 0.7787 (t0) REVERT: P 163 LYS cc_start: 0.7933 (tttt) cc_final: 0.7629 (ttpt) REVERT: P 222 LEU cc_start: 0.8634 (tp) cc_final: 0.8428 (tt) REVERT: P 257 ASP cc_start: 0.7486 (t70) cc_final: 0.7278 (t0) REVERT: P 285 GLN cc_start: 0.8151 (pt0) cc_final: 0.7690 (pm20) REVERT: P 300 ILE cc_start: 0.7885 (pt) cc_final: 0.7673 (pt) REVERT: P 304 ASP cc_start: 0.6744 (t70) cc_final: 0.6544 (t0) REVERT: P 371 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7159 (mm-30) REVERT: P 380 LEU cc_start: 0.7895 (mt) cc_final: 0.7617 (mt) REVERT: P 383 MET cc_start: 0.6556 (mtp) cc_final: 0.6258 (ptp) REVERT: P 394 ASN cc_start: 0.7547 (t0) cc_final: 0.7238 (p0) REVERT: P 418 GLU cc_start: 0.8359 (mp0) cc_final: 0.8027 (mp0) REVERT: P 740 THR cc_start: 0.8126 (m) cc_final: 0.7867 (p) REVERT: P 742 LYS cc_start: 0.7619 (mtmt) cc_final: 0.7133 (mmmt) REVERT: P 766 GLU cc_start: 0.7848 (mp0) cc_final: 0.7637 (mp0) REVERT: P 891 LEU cc_start: 0.7420 (mt) cc_final: 0.7190 (mt) REVERT: P 926 GLN cc_start: 0.7633 (tp-100) cc_final: 0.7198 (tp-100) REVERT: P 937 SER cc_start: 0.7073 (t) cc_final: 0.6736 (m) REVERT: P 981 TYR cc_start: 0.7296 (m-10) cc_final: 0.6837 (m-10) REVERT: P 1171 ARG cc_start: 0.7768 (ttt180) cc_final: 0.7531 (ttp80) outliers start: 20 outliers final: 12 residues processed: 185 average time/residue: 0.1055 time to fit residues: 25.9719 Evaluate side-chains 161 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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: 2.9990 chunk 23 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 91 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 224 ASN P 228 GLN P 309 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 = 0.4354 r_free = 0.4354 target = 0.146647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.124333 restraints weight = 27249.693| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 3.55 r_work: 0.3933 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 9648 Z= 0.254 Angle : 0.834 14.388 13199 Z= 0.400 Chirality : 0.051 0.302 1506 Planarity : 0.005 0.049 1517 Dihedral : 12.512 166.119 1676 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.26 % Allowed : 14.66 % Favored : 82.08 % 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: -0.34 (0.25), residues: 1025 helix: 0.31 (0.22), residues: 531 sheet: -0.36 (0.51), residues: 96 loop : -0.78 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P1335 TYR 0.020 0.002 TYR P 362 PHE 0.029 0.003 PHE P 916 TRP 0.011 0.002 TRP P 883 HIS 0.008 0.002 HIS P1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.25 ( 9648) covalent geometry : angle 0.83400 / 0.40 (13199) hydrogen bonds : bond 0.05253 / 3.56 ( 448) hydrogen bonds : angle 5.17158 / 3.67 ( 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 197 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 77 ASN cc_start: 0.8219 (t0) cc_final: 0.7900 (t0) REVERT: P 257 ASP cc_start: 0.7861 (t70) cc_final: 0.7520 (t0) REVERT: P 285 GLN cc_start: 0.8601 (pt0) cc_final: 0.8286 (pm20) REVERT: P 286 TYR cc_start: 0.8202 (m-10) cc_final: 0.7813 (m-10) REVERT: P 304 ASP cc_start: 0.7181 (t70) cc_final: 0.6875 (t0) REVERT: P 321 MET cc_start: 0.6837 (mmp) cc_final: 0.6393 (mmp) REVERT: P 354 GLN cc_start: 0.7587 (mt0) cc_final: 0.6838 (tm-30) REVERT: P 394 ASN cc_start: 0.7614 (t0) cc_final: 0.7231 (p0) REVERT: P 418 GLU cc_start: 0.8282 (mp0) cc_final: 0.8014 (mm-30) REVERT: P 740 THR cc_start: 0.8212 (m) cc_final: 0.7861 (p) REVERT: P 742 LYS cc_start: 0.7617 (mtmt) cc_final: 0.7155 (mmtt) REVERT: P 749 LYS cc_start: 0.8028 (tttt) cc_final: 0.7777 (tttm) REVERT: P 908 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7471 (mp) REVERT: P 926 GLN cc_start: 0.7964 (tp-100) cc_final: 0.7316 (tp-100) REVERT: P 927 ILE cc_start: 0.8814 (tp) cc_final: 0.8363 (pt) REVERT: P 937 SER cc_start: 0.7440 (t) cc_final: 0.7142 (m) REVERT: P 961 LYS cc_start: 0.7373 (mttt) cc_final: 0.7136 (mtpp) REVERT: P 967 ARG cc_start: 0.7428 (mtt180) cc_final: 0.7093 (mmm-85) REVERT: P 981 TYR cc_start: 0.7536 (m-10) cc_final: 0.7072 (m-10) REVERT: P 1064 GLU cc_start: 0.7606 (tp30) cc_final: 0.7392 (tp30) outliers start: 30 outliers final: 21 residues processed: 186 average time/residue: 0.1098 time to fit residues: 26.9699 Evaluate side-chains 167 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 824 VAL Chi-restraints excluded: chain P residue 842 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 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 1179 ILE 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 1317 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4376 r_free = 0.4376 target = 0.148595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.126972 restraints weight = 27753.478| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 3.49 r_work: 0.3963 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.4964 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= 0.156 Angle : 0.714 10.028 13199 Z= 0.338 Chirality : 0.047 0.276 1506 Planarity : 0.003 0.038 1517 Dihedral : 12.287 166.056 1676 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.15 % Allowed : 15.64 % Favored : 81.22 % 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: -0.04 (0.26), residues: 1025 helix: 0.67 (0.23), residues: 525 sheet: -0.30 (0.51), residues: 98 loop : -0.78 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 400 TYR 0.010 0.001 TYR P 271 PHE 0.037 0.002 PHE P 916 TRP 0.007 0.001 TRP P1074 HIS 0.005 0.001 HIS P1297 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 ( 9648) covalent geometry : angle 0.71445 / 0.34 (13199) hydrogen bonds : bond 0.04222 / 2.82 ( 448) hydrogen bonds : angle 4.78004 / 3.39 ( 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 190 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.332 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 76 LYS cc_start: 0.8557 (mmmt) cc_final: 0.8268 (mmmt) REVERT: P 77 ASN cc_start: 0.8055 (t0) cc_final: 0.7782 (t0) REVERT: P 222 LEU cc_start: 0.8572 (tp) cc_final: 0.8347 (tt) REVERT: P 257 ASP cc_start: 0.7886 (t70) cc_final: 0.7497 (t0) REVERT: P 304 ASP cc_start: 0.7084 (t70) cc_final: 0.6872 (t0) REVERT: P 321 MET cc_start: 0.6949 (mmp) cc_final: 0.6673 (mmp) REVERT: P 354 GLN cc_start: 0.7546 (mt0) cc_final: 0.7118 (tm-30) REVERT: P 394 ASN cc_start: 0.7701 (t0) cc_final: 0.7405 (p0) REVERT: P 418 GLU cc_start: 0.8426 (mp0) cc_final: 0.8138 (mm-30) REVERT: P 740 THR cc_start: 0.8294 (m) cc_final: 0.7980 (p) REVERT: P 742 LYS cc_start: 0.7687 (mtmt) cc_final: 0.7248 (mmtt) REVERT: P 745 ASP cc_start: 0.7991 (m-30) cc_final: 0.7616 (t0) REVERT: P 891 LEU cc_start: 0.7563 (mt) cc_final: 0.7180 (mt) REVERT: P 892 ILE cc_start: 0.4510 (OUTLIER) cc_final: 0.3918 (pt) REVERT: P 926 GLN cc_start: 0.7954 (tp-100) cc_final: 0.7298 (tp-100) REVERT: P 927 ILE cc_start: 0.8777 (tp) cc_final: 0.8324 (pt) REVERT: P 937 SER cc_start: 0.7333 (t) cc_final: 0.7089 (m) REVERT: P 947 ASP cc_start: 0.7191 (t0) cc_final: 0.6989 (t0) REVERT: P 967 ARG cc_start: 0.7403 (mtt180) cc_final: 0.7012 (mmm-85) REVERT: P 981 TYR cc_start: 0.7305 (m-10) cc_final: 0.6865 (m-10) outliers start: 29 outliers final: 20 residues processed: 176 average time/residue: 0.0990 time to fit residues: 23.8925 Evaluate side-chains 162 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 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 922 VAL Chi-restraints excluded: chain P residue 1084 ARG 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 Chi-restraints excluded: chain P residue 1364 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 64 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 22 optimal weight: 0.0060 chunk 8 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 0.0770 chunk 48 optimal weight: 0.9980 overall best weight: 0.5354 ------------------------------------------------------------------------------- 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 = 0.4392 r_free = 0.4392 target = 0.149702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.128281 restraints weight = 27841.345| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 3.51 r_work: 0.3988 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9648 Z= 0.129 Angle : 0.675 9.678 13199 Z= 0.320 Chirality : 0.046 0.263 1506 Planarity : 0.003 0.031 1517 Dihedral : 12.109 168.334 1676 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.50 % Allowed : 17.26 % Favored : 80.24 % 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: 0.95 (0.23), residues: 518 sheet: -0.46 (0.44), residues: 132 loop : -0.71 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 220 TYR 0.020 0.001 TYR P 362 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/Z covalent geometry : bond 0.00275 / 0.13 ( 9648) covalent geometry : angle 0.67471 / 0.32 (13199) hydrogen bonds : bond 0.03882 / 2.61 ( 448) hydrogen bonds : angle 4.61937 / 3.30 ( 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 176 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.239 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: 0.6957 (mtp180) cc_final: 0.6381 (mtm180) REVERT: P 76 LYS cc_start: 0.8563 (mmmt) cc_final: 0.8290 (mmmt) REVERT: P 77 ASN cc_start: 0.7944 (t0) cc_final: 0.7681 (t0) REVERT: P 286 TYR cc_start: 0.8163 (m-10) cc_final: 0.7856 (m-10) REVERT: P 304 ASP cc_start: 0.7105 (t70) cc_final: 0.6900 (t0) REVERT: P 354 GLN cc_start: 0.7672 (mt0) cc_final: 0.7258 (tm-30) REVERT: P 394 ASN cc_start: 0.7663 (t0) cc_final: 0.7324 (p0) REVERT: P 418 GLU cc_start: 0.8403 (mp0) cc_final: 0.8082 (mm-30) REVERT: P 740 THR cc_start: 0.8282 (m) cc_final: 0.7961 (p) REVERT: P 742 LYS cc_start: 0.7660 (mtmt) cc_final: 0.7236 (mmtt) REVERT: P 745 ASP cc_start: 0.7956 (m-30) cc_final: 0.7598 (t0) REVERT: P 908 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7466 (mt) REVERT: P 926 GLN cc_start: 0.7842 (tp-100) cc_final: 0.7266 (tp-100) REVERT: P 927 ILE cc_start: 0.8740 (tp) cc_final: 0.8305 (pt) REVERT: P 937 SER cc_start: 0.7397 (t) cc_final: 0.7131 (m) REVERT: P 947 ASP cc_start: 0.7251 (t0) cc_final: 0.6991 (t0) REVERT: P 981 TYR cc_start: 0.7174 (m-10) cc_final: 0.6664 (m-10) REVERT: P 1237 TYR cc_start: 0.6301 (t80) cc_final: 0.5970 (t80) outliers start: 23 outliers final: 14 residues processed: 168 average time/residue: 0.0999 time to fit residues: 22.4223 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 : 0.256 ------------------------------------------------------------------------------- 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 241 LEU Chi-restraints excluded: chain P residue 824 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 1084 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 58 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 71 optimal weight: 0.0170 overall best weight: 1.1622 ------------------------------------------------------------------------------- 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 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.147279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.125356 restraints weight = 27480.184| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 3.48 r_work: 0.3949 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9648 Z= 0.177 Angle : 0.707 10.231 13199 Z= 0.338 Chirality : 0.047 0.270 1506 Planarity : 0.004 0.042 1517 Dihedral : 12.125 167.737 1676 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.61 % Allowed : 17.81 % 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: 0.08 (0.26), residues: 1025 helix: 0.77 (0.23), residues: 530 sheet: -0.16 (0.49), residues: 98 loop : -0.78 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 780 TYR 0.017 0.002 TYR P1001 PHE 0.046 0.003 PHE P 916 TRP 0.003 0.001 TRP P 883 HIS 0.007 0.001 HIS P 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 ( 9648) covalent geometry : angle 0.70746 / 0.34 (13199) hydrogen bonds : bond 0.04231 / 2.85 ( 448) hydrogen bonds : angle 4.75748 / 3.39 ( 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: 24 poor density : 149 time to evaluate : 0.334 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: 0.8844 (t) cc_final: 0.8633 (p) REVERT: P 77 ASN cc_start: 0.8126 (t0) cc_final: 0.7834 (t0) REVERT: P 222 LEU cc_start: 0.8640 (tp) cc_final: 0.8386 (tt) REVERT: P 286 TYR cc_start: 0.8219 (m-10) cc_final: 0.7814 (m-10) REVERT: P 304 ASP cc_start: 0.7161 (t70) cc_final: 0.6918 (t0) REVERT: P 321 MET cc_start: 0.7019 (mmp) cc_final: 0.6808 (mmp) REVERT: P 354 GLN cc_start: 0.7804 (mt0) cc_final: 0.7473 (tm-30) REVERT: P 394 ASN cc_start: 0.7848 (t0) cc_final: 0.7529 (p0) REVERT: P 740 THR cc_start: 0.8294 (m) cc_final: 0.7949 (p) REVERT: P 742 LYS cc_start: 0.7661 (mtmt) cc_final: 0.7219 (mmtt) REVERT: P 745 ASP cc_start: 0.8038 (m-30) cc_final: 0.7701 (t0) REVERT: P 781 MET cc_start: 0.6768 (mmm) cc_final: 0.6547 (mmm) REVERT: P 892 ILE cc_start: 0.4619 (OUTLIER) cc_final: 0.3999 (pt) REVERT: P 908 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7564 (mt) REVERT: P 926 GLN cc_start: 0.7914 (tp-100) cc_final: 0.7304 (tp-100) REVERT: P 927 ILE cc_start: 0.8816 (tp) cc_final: 0.8389 (pt) REVERT: P 937 SER cc_start: 0.7426 (t) cc_final: 0.7211 (m) REVERT: P 947 ASP cc_start: 0.7389 (t0) cc_final: 0.7121 (t0) REVERT: P 981 TYR cc_start: 0.7421 (m-10) cc_final: 0.6912 (m-10) REVERT: P 1080 PHE cc_start: 0.5268 (m-80) cc_final: 0.5029 (m-80) REVERT: P 1089 MET cc_start: 0.5789 (mtp) cc_final: 0.5443 (mtp) outliers start: 24 outliers final: 18 residues processed: 164 average time/residue: 0.0992 time to fit residues: 22.3253 Evaluate side-chains 157 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 257 ASP 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 908 LEU Chi-restraints excluded: chain P residue 1084 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 76 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 255 ASN P 721 HIS P 758 ASN ** P 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1305 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.144539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.122469 restraints weight = 27278.922| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 3.45 r_work: 0.3914 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.6140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 9648 Z= 0.259 Angle : 0.805 13.405 13199 Z= 0.388 Chirality : 0.051 0.367 1506 Planarity : 0.005 0.062 1517 Dihedral : 12.385 166.640 1676 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.37 % Allowed : 18.02 % 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: -0.25 (0.25), residues: 1025 helix: 0.48 (0.22), residues: 522 sheet: -0.18 (0.48), residues: 99 loop : -0.91 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG P 967 TYR 0.017 0.002 TYR P 823 PHE 0.045 0.003 PHE P 916 TRP 0.008 0.002 TRP P 18 HIS 0.011 0.002 HIS P 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.26 ( 9648) covalent geometry : angle 0.80545 / 0.39 (13199) hydrogen bonds : bond 0.05092 / 3.47 ( 448) hydrogen bonds : angle 5.07620 / 3.62 ( 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: 31 poor density : 147 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 73 THR cc_start: 0.8874 (t) cc_final: 0.8613 (p) REVERT: P 75 ARG cc_start: 0.9007 (mtt180) cc_final: 0.8587 (mtp85) REVERT: P 76 LYS cc_start: 0.8618 (mmmt) cc_final: 0.8394 (mmmt) REVERT: P 77 ASN cc_start: 0.8269 (t0) cc_final: 0.7943 (t0) REVERT: P 222 LEU cc_start: 0.8690 (tp) cc_final: 0.8383 (tt) REVERT: P 286 TYR cc_start: 0.8331 (m-10) cc_final: 0.7923 (m-10) REVERT: P 354 GLN cc_start: 0.7811 (mt0) cc_final: 0.7490 (tm-30) REVERT: P 394 ASN cc_start: 0.8005 (t0) cc_final: 0.7582 (p0) REVERT: P 742 LYS cc_start: 0.7561 (mtmt) cc_final: 0.7139 (mmtt) REVERT: P 745 ASP cc_start: 0.8101 (m-30) cc_final: 0.7664 (t0) REVERT: P 892 ILE cc_start: 0.4934 (OUTLIER) cc_final: 0.4302 (pt) REVERT: P 908 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7729 (mt) REVERT: P 926 GLN cc_start: 0.8023 (tp-100) cc_final: 0.7402 (tp-100) REVERT: P 927 ILE cc_start: 0.8857 (tp) cc_final: 0.8453 (pt) REVERT: P 937 SER cc_start: 0.7463 (t) cc_final: 0.7227 (m) REVERT: P 947 ASP cc_start: 0.7755 (t0) cc_final: 0.7477 (t0) REVERT: P 981 TYR cc_start: 0.7649 (m-10) cc_final: 0.7203 (m-80) REVERT: P 1189 GLU cc_start: 0.7071 (tp30) cc_final: 0.6831 (tp30) outliers start: 31 outliers final: 19 residues processed: 168 average time/residue: 0.1054 time to fit residues: 23.8963 Evaluate side-chains 160 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 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 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 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 908 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 71 optimal weight: 0.2980 chunk 87 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 255 ASN P 758 ASN ** P 844 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 = 0.4362 r_free = 0.4362 target = 0.147741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.126061 restraints weight = 27035.983| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 3.45 r_work: 0.3959 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.6108 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= 0.140 Angle : 0.721 10.021 13199 Z= 0.345 Chirality : 0.048 0.250 1506 Planarity : 0.004 0.072 1517 Dihedral : 12.175 168.977 1676 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.61 % Allowed : 19.11 % 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: -0.02 (0.26), residues: 1025 helix: 0.69 (0.23), residues: 523 sheet: -0.17 (0.47), residues: 111 loop : -0.82 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG P 780 TYR 0.025 0.002 TYR P 72 PHE 0.044 0.002 PHE P 916 TRP 0.007 0.001 TRP P 883 HIS 0.010 0.001 HIS P 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 9648) covalent geometry : angle 0.72122 / 0.35 (13199) hydrogen bonds : bond 0.04060 / 2.75 ( 448) hydrogen bonds : angle 4.83739 / 3.44 ( 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 170 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 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: 0.8836 (t) cc_final: 0.8563 (p) REVERT: P 75 ARG cc_start: 0.8962 (mtt180) cc_final: 0.8519 (mtp85) REVERT: P 76 LYS cc_start: 0.8597 (mmmt) cc_final: 0.8363 (mmmt) REVERT: P 77 ASN cc_start: 0.8062 (t0) cc_final: 0.7682 (t0) REVERT: P 286 TYR cc_start: 0.8249 (m-10) cc_final: 0.7894 (m-10) REVERT: P 354 GLN cc_start: 0.7900 (mt0) cc_final: 0.7578 (tm-30) REVERT: P 394 ASN cc_start: 0.7961 (t0) cc_final: 0.7555 (p0) REVERT: P 745 ASP cc_start: 0.8026 (m-30) cc_final: 0.7743 (t0) REVERT: P 908 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7874 (mt) REVERT: P 926 GLN cc_start: 0.7902 (tp-100) cc_final: 0.7292 (tp-100) REVERT: P 927 ILE cc_start: 0.8784 (tp) cc_final: 0.8380 (pt) REVERT: P 947 ASP cc_start: 0.7652 (t0) cc_final: 0.7353 (t0) REVERT: P 981 TYR cc_start: 0.7271 (m-10) cc_final: 0.6833 (m-10) outliers start: 24 outliers final: 17 residues processed: 163 average time/residue: 0.0991 time to fit residues: 22.2558 Evaluate side-chains 150 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- 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: 2.9990 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 67 optimal weight: 0.1980 chunk 58 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1054 ASN P1261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.148028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.126359 restraints weight = 26902.350| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 3.38 r_work: 0.3972 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.6194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9648 Z= 0.139 Angle : 0.732 15.162 13199 Z= 0.344 Chirality : 0.048 0.252 1506 Planarity : 0.004 0.039 1517 Dihedral : 12.053 169.455 1676 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.28 % Allowed : 19.44 % 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: 0.07 (0.26), residues: 1025 helix: 0.68 (0.23), residues: 523 sheet: -0.05 (0.48), residues: 111 loop : -0.67 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 780 TYR 0.012 0.001 TYR P 25 PHE 0.051 0.002 PHE P 916 TRP 0.017 0.002 TRP P 18 HIS 0.006 0.001 HIS P 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 9648) covalent geometry : angle 0.73204 / 0.34 (13199) hydrogen bonds : bond 0.04007 / 2.69 ( 448) hydrogen bonds : angle 4.81955 / 3.43 ( 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 165 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 7 ILE cc_start: 0.7781 (mt) cc_final: 0.7578 (pt) REVERT: P 73 THR cc_start: 0.8849 (t) cc_final: 0.8591 (p) REVERT: P 75 ARG cc_start: 0.8946 (mtt180) cc_final: 0.8500 (mtp85) REVERT: P 77 ASN cc_start: 0.8038 (t0) cc_final: 0.7648 (t0) REVERT: P 84 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7840 (pt0) REVERT: P 286 TYR cc_start: 0.8108 (m-10) cc_final: 0.7833 (m-10) REVERT: P 354 GLN cc_start: 0.7785 (mt0) cc_final: 0.7583 (tm-30) REVERT: P 394 ASN cc_start: 0.7962 (t0) cc_final: 0.7564 (p0) REVERT: P 742 LYS cc_start: 0.7438 (mtmt) cc_final: 0.7045 (mmtt) REVERT: P 745 ASP cc_start: 0.8043 (m-30) cc_final: 0.7676 (t0) REVERT: P 908 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7782 (mt) REVERT: P 926 GLN cc_start: 0.7913 (tp-100) cc_final: 0.7300 (tp-100) REVERT: P 927 ILE cc_start: 0.8760 (tp) cc_final: 0.8350 (pt) REVERT: P 947 ASP cc_start: 0.7659 (t0) cc_final: 0.7356 (t0) REVERT: P 981 TYR cc_start: 0.7216 (m-10) cc_final: 0.6523 (m-10) REVERT: P 1189 GLU cc_start: 0.7027 (tp30) cc_final: 0.6795 (tp30) outliers start: 21 outliers final: 20 residues processed: 157 average time/residue: 0.0938 time to fit residues: 20.1996 Evaluate side-chains 155 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 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 198 GLU 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 322 ILE Chi-restraints excluded: chain P residue 776 ASN 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 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: 5.9990 chunk 104 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 79 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 255 ASN ** P 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 983 HIS ** 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 = 0.4337 r_free = 0.4337 target = 0.145780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.123675 restraints weight = 26986.387| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 3.47 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.6471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9648 Z= 0.194 Angle : 0.796 13.518 13199 Z= 0.378 Chirality : 0.050 0.300 1506 Planarity : 0.005 0.105 1517 Dihedral : 12.177 167.926 1676 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.39 % Allowed : 19.65 % Favored : 77.96 % 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: -0.12 (0.26), residues: 1025 helix: 0.50 (0.23), residues: 525 sheet: -0.05 (0.48), residues: 99 loop : -0.74 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG P1333 TYR 0.015 0.002 TYR P1013 PHE 0.050 0.003 PHE P 916 TRP 0.022 0.004 TRP P 18 HIS 0.010 0.001 HIS P 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 ( 9648) covalent geometry : angle 0.79631 / 0.38 (13199) hydrogen bonds : bond 0.04489 / 3.05 ( 448) hydrogen bonds : angle 5.01584 / 3.57 ( 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: 22 poor density : 144 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 73 THR cc_start: 0.8806 (t) cc_final: 0.8538 (p) REVERT: P 75 ARG cc_start: 0.8755 (mtt180) cc_final: 0.8204 (mtp85) REVERT: P 77 ASN cc_start: 0.8032 (t0) cc_final: 0.7633 (t0) REVERT: P 83 GLN cc_start: 0.8188 (tp-100) cc_final: 0.7908 (tp-100) REVERT: P 222 LEU cc_start: 0.8600 (tp) cc_final: 0.8379 (tt) REVERT: P 286 TYR cc_start: 0.7885 (m-10) cc_final: 0.7655 (m-10) REVERT: P 354 GLN cc_start: 0.7714 (mt0) cc_final: 0.7446 (tm-30) REVERT: P 383 MET cc_start: 0.6602 (ptp) cc_final: 0.6324 (ptp) REVERT: P 394 ASN cc_start: 0.7957 (t0) cc_final: 0.7559 (p0) REVERT: P 742 LYS cc_start: 0.7418 (mtmt) cc_final: 0.7062 (mmtt) REVERT: P 745 ASP cc_start: 0.7948 (m-30) cc_final: 0.7557 (t0) REVERT: P 926 GLN cc_start: 0.7847 (tp-100) cc_final: 0.7249 (tp-100) REVERT: P 927 ILE cc_start: 0.8769 (tp) cc_final: 0.8344 (pt) REVERT: P 947 ASP cc_start: 0.7564 (t0) cc_final: 0.7294 (t0) REVERT: P 981 TYR cc_start: 0.7319 (m-10) cc_final: 0.6707 (m-10) outliers start: 22 outliers final: 20 residues processed: 159 average time/residue: 0.1019 time to fit residues: 22.0866 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 : 0.257 ------------------------------------------------------------------------------- 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 320 SER Chi-restraints excluded: chain P residue 322 ILE 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 922 VAL 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: 0.0050 chunk 2 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 805 GLN ** P 844 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 = 0.4362 r_free = 0.4362 target = 0.147787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.126238 restraints weight = 26609.006| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 3.36 r_work: 0.3970 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.6506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9648 Z= 0.142 Angle : 0.748 14.207 13199 Z= 0.354 Chirality : 0.048 0.252 1506 Planarity : 0.005 0.133 1517 Dihedral : 12.115 169.457 1676 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.17 % Allowed : 19.87 % Favored : 77.96 % 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 (0.26), residues: 1025 helix: 0.63 (0.23), residues: 519 sheet: -0.11 (0.46), residues: 123 loop : -0.58 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG P 780 TYR 0.012 0.001 TYR P1013 PHE 0.049 0.002 PHE P 916 TRP 0.025 0.004 TRP P1074 HIS 0.008 0.001 HIS P 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 9648) covalent geometry : angle 0.74834 / 0.35 (13199) hydrogen bonds : bond 0.04026 / 2.71 ( 448) hydrogen bonds : angle 4.85079 / 3.46 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2461.62 seconds wall clock time: 42 minutes 54.95 seconds (2574.95 seconds total)