Starting phenix.real_space_refine on Sun Jul 27 22:08:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s37_24818/07_2025/7s37_24818.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s37_24818/07_2025/7s37_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_24818/07_2025/7s37_24818.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s37_24818/07_2025/7s37_24818.map" model { file = "/net/cci-nas-00/data/ceres_data/7s37_24818/07_2025/7s37_24818.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s37_24818/07_2025/7s37_24818.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.242 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.61, per 1000 atoms: 0.60 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: 2.44 Conformation dependent library (CDL) restraints added in 967.5 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: 3.29 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: 4.06 Time building geometry restraints manager: 2.81 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: 1.300 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.060 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.270 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (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 TRP 0.010 0.002 TRP P 883 HIS 0.016 0.002 HIS P 137 PHE 0.032 0.002 PHE P1313 TYR 0.015 0.002 TYR P 132 ARG 0.016 0.001 ARG P1060 Details of bonding type rmsd hydrogen bonds : bond 0.15113 ( 448) hydrogen bonds : angle 6.04757 ( 1260) covalent geometry : bond 0.00644 ( 9648) covalent geometry : angle 1.03660 (13199) *********************** 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 : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 0.7188 (t80) REVERT: P 75 ARG cc_start: 0.8450 (mtt180) cc_final: 0.7938 (mmt90) REVERT: P 76 LYS cc_start: 0.8480 (mmmt) cc_final: 0.8164 (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: 0.7652 (ttpt) REVERT: P 222 LEU cc_start: 0.8416 (tp) cc_final: 0.8196 (tt) REVERT: P 286 TYR cc_start: 0.7743 (m-80) cc_final: 0.7405 (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: 0.7186 (mmmt) REVERT: P 751 MET cc_start: 0.6756 (mmt) cc_final: 0.6061 (mmt) REVERT: P 763 MET cc_start: 0.8020 (mmt) cc_final: 0.7818 (mmm) REVERT: P 937 SER cc_start: 0.6958 (t) cc_final: 0.6667 (m) outliers start: 1 outliers final: 1 residues processed: 269 average time/residue: 0.3056 time to fit residues: 105.8983 Evaluate side-chains 166 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 90 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** P 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1241 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.153913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.132664 restraints weight = 27263.581| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 3.53 r_work: 0.4051 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9648 Z= 0.158 Angle : 0.617 6.900 13199 Z= 0.330 Chirality : 0.041 0.211 1506 Planarity : 0.004 0.056 1517 Dihedral : 15.184 95.393 1824 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.85 % Allowed : 11.94 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1025 helix: 0.67 (0.23), residues: 507 sheet: -0.69 (0.43), residues: 131 loop : -0.56 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P 883 HIS 0.008 0.001 HIS P 420 PHE 0.043 0.002 PHE P 916 TYR 0.016 0.001 TYR P1001 ARG 0.013 0.001 ARG P 400 Details of bonding type rmsd hydrogen bonds : bond 0.04569 ( 448) hydrogen bonds : angle 4.86444 ( 1260) covalent geometry : bond 0.00346 ( 9648) covalent geometry : angle 0.61696 (13199) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 1.038 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: 0.7095 (mtp180) cc_final: 0.6567 (mtm180) REVERT: P 72 TYR cc_start: 0.7961 (t80) cc_final: 0.7701 (t80) REVERT: P 76 LYS cc_start: 0.8638 (mmmt) cc_final: 0.8238 (mmmt) REVERT: P 77 ASN cc_start: 0.8237 (t0) cc_final: 0.7765 (t0) REVERT: P 163 LYS cc_start: 0.7916 (tttt) cc_final: 0.7624 (ttpt) REVERT: P 257 ASP cc_start: 0.7425 (t70) cc_final: 0.7213 (t0) REVERT: P 285 GLN cc_start: 0.8593 (pt0) cc_final: 0.7870 (pm20) REVERT: P 286 TYR cc_start: 0.8081 (m-80) cc_final: 0.7499 (m-10) REVERT: P 300 ILE cc_start: 0.7865 (pt) cc_final: 0.7648 (pt) REVERT: P 380 LEU cc_start: 0.7885 (mt) cc_final: 0.7604 (mt) REVERT: P 394 ASN cc_start: 0.7503 (t0) cc_final: 0.7247 (p0) REVERT: P 418 GLU cc_start: 0.8395 (mp0) cc_final: 0.8034 (mp0) REVERT: P 740 THR cc_start: 0.8087 (m) cc_final: 0.7832 (p) REVERT: P 742 LYS cc_start: 0.7663 (mtmt) cc_final: 0.7174 (mmmt) REVERT: P 766 GLU cc_start: 0.7858 (mp0) cc_final: 0.7622 (mp0) REVERT: P 891 LEU cc_start: 0.7388 (mt) cc_final: 0.7169 (mt) REVERT: P 926 GLN cc_start: 0.7737 (tp-100) cc_final: 0.7364 (tp-100) REVERT: P 937 SER cc_start: 0.7111 (t) cc_final: 0.6788 (m) REVERT: P 959 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7667 (mttp) REVERT: P 966 PHE cc_start: 0.7570 (t80) cc_final: 0.6883 (t80) REVERT: P 981 TYR cc_start: 0.7227 (m-10) cc_final: 0.6700 (m-10) REVERT: P 1064 GLU cc_start: 0.7575 (tp30) cc_final: 0.7110 (tp30) REVERT: P 1171 ARG cc_start: 0.7708 (ttt180) cc_final: 0.7501 (ttp80) REVERT: P 1305 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7282 (mm110) outliers start: 17 outliers final: 11 residues processed: 190 average time/residue: 0.2746 time to fit residues: 68.4504 Evaluate side-chains 165 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 959 LYS Chi-restraints excluded: chain P residue 1051 THR Chi-restraints excluded: chain P residue 1145 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 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 100 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 45 optimal weight: 0.0870 chunk 82 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 overall best weight: 0.7960 ------------------------------------------------------------------------------- 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 ** P 946 ASN ** 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 = 0.4417 r_free = 0.4417 target = 0.151635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.130447 restraints weight = 27702.435| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 3.51 r_work: 0.4019 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9648 Z= 0.139 Angle : 0.593 14.339 13199 Z= 0.304 Chirality : 0.039 0.161 1506 Planarity : 0.004 0.038 1517 Dihedral : 15.088 97.026 1822 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.71 % Allowed : 13.90 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 1025 helix: 0.85 (0.23), residues: 515 sheet: -0.41 (0.48), residues: 110 loop : -0.44 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 883 HIS 0.004 0.001 HIS P 412 PHE 0.034 0.002 PHE P 916 TYR 0.020 0.001 TYR P 362 ARG 0.006 0.001 ARG P 967 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 448) hydrogen bonds : angle 4.68853 ( 1260) covalent geometry : bond 0.00287 ( 9648) covalent geometry : angle 0.59313 (13199) *********************** 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 187 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 72 TYR cc_start: 0.7960 (t80) cc_final: 0.7721 (t80) REVERT: P 75 ARG cc_start: 0.8959 (mtt180) cc_final: 0.8362 (mmm-85) REVERT: P 76 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8274 (mmmt) REVERT: P 77 ASN cc_start: 0.7976 (t0) cc_final: 0.7728 (t0) REVERT: P 163 LYS cc_start: 0.8003 (tttt) cc_final: 0.7480 (ttpt) REVERT: P 257 ASP cc_start: 0.7624 (t70) cc_final: 0.7303 (t0) REVERT: P 286 TYR cc_start: 0.8060 (m-80) cc_final: 0.7834 (m-10) REVERT: P 394 ASN cc_start: 0.7566 (t0) cc_final: 0.7228 (p0) REVERT: P 418 GLU cc_start: 0.8257 (mp0) cc_final: 0.7936 (mm-30) REVERT: P 740 THR cc_start: 0.8122 (m) cc_final: 0.7758 (p) REVERT: P 742 LYS cc_start: 0.7621 (mtmt) cc_final: 0.7218 (mmtt) REVERT: P 891 LEU cc_start: 0.7489 (mt) cc_final: 0.7217 (mt) REVERT: P 926 GLN cc_start: 0.7688 (tp-100) cc_final: 0.7150 (tp-100) REVERT: P 937 SER cc_start: 0.7491 (t) cc_final: 0.7128 (m) REVERT: P 959 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7764 (mttp) REVERT: P 966 PHE cc_start: 0.7469 (t80) cc_final: 0.7262 (t80) REVERT: P 981 TYR cc_start: 0.7246 (m-10) cc_final: 0.6720 (m-10) REVERT: P 1021 MET cc_start: 0.4573 (mmt) cc_final: 0.4242 (mmt) REVERT: P 1064 GLU cc_start: 0.7409 (tp30) cc_final: 0.7081 (tp30) REVERT: P 1305 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7219 (mm-40) outliers start: 25 outliers final: 14 residues processed: 176 average time/residue: 0.2595 time to fit residues: 61.4123 Evaluate side-chains 159 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 217 SER Chi-restraints excluded: chain P residue 882 TYR 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 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 1169 MET Chi-restraints excluded: chain P residue 1179 ILE Chi-restraints excluded: chain P residue 1259 VAL Chi-restraints excluded: chain P residue 1305 GLN 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 88 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 228 GLN P 758 ASN P1044 ASN P1221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.145027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.121823 restraints weight = 27629.067| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 3.62 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 9648 Z= 0.266 Angle : 0.728 12.580 13199 Z= 0.382 Chirality : 0.045 0.170 1506 Planarity : 0.005 0.043 1517 Dihedral : 15.353 100.842 1822 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.91 % Allowed : 15.31 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.25), residues: 1025 helix: 0.29 (0.22), residues: 530 sheet: -0.50 (0.48), residues: 104 loop : -0.91 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P1074 HIS 0.008 0.002 HIS P1262 PHE 0.038 0.003 PHE P 916 TYR 0.022 0.002 TYR P 973 ARG 0.008 0.001 ARG P 967 Details of bonding type rmsd hydrogen bonds : bond 0.05215 ( 448) hydrogen bonds : angle 5.17224 ( 1260) covalent geometry : bond 0.00553 ( 9648) covalent geometry : angle 0.72754 (13199) *********************** 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 193 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 63 ARG cc_start: 0.7043 (mtp180) cc_final: 0.6417 (mtm180) REVERT: P 75 ARG cc_start: 0.8718 (mtt180) cc_final: 0.7846 (mmm-85) REVERT: P 77 ASN cc_start: 0.8201 (t0) cc_final: 0.7866 (t0) REVERT: P 163 LYS cc_start: 0.7755 (tttt) cc_final: 0.7398 (ttmt) REVERT: P 170 ILE cc_start: 0.7399 (mm) cc_final: 0.7194 (pt) REVERT: P 257 ASP cc_start: 0.7487 (t70) cc_final: 0.7133 (t0) REVERT: P 286 TYR cc_start: 0.7932 (m-80) cc_final: 0.7631 (m-10) REVERT: P 354 GLN cc_start: 0.7577 (mt0) cc_final: 0.7063 (tm-30) REVERT: P 394 ASN cc_start: 0.7805 (t0) cc_final: 0.7377 (p0) REVERT: P 418 GLU cc_start: 0.8239 (mp0) cc_final: 0.7979 (mm-30) REVERT: P 740 THR cc_start: 0.8202 (m) cc_final: 0.7810 (p) REVERT: P 742 LYS cc_start: 0.7551 (mtmt) cc_final: 0.7102 (mmtt) REVERT: P 745 ASP cc_start: 0.7856 (m-30) cc_final: 0.7448 (t0) REVERT: P 749 LYS cc_start: 0.8060 (tttt) cc_final: 0.7751 (tttm) REVERT: P 891 LEU cc_start: 0.7611 (mt) cc_final: 0.7351 (mt) REVERT: P 908 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7382 (mt) REVERT: P 926 GLN cc_start: 0.7862 (tp-100) cc_final: 0.7271 (tp-100) REVERT: P 927 ILE cc_start: 0.8766 (tp) cc_final: 0.8305 (pt) REVERT: P 937 SER cc_start: 0.7211 (t) cc_final: 0.6963 (m) REVERT: P 961 LYS cc_start: 0.7283 (mttt) cc_final: 0.7077 (mtpp) REVERT: P 967 ARG cc_start: 0.6782 (mtt180) cc_final: 0.6573 (mtt180) REVERT: P 981 TYR cc_start: 0.7481 (m-10) cc_final: 0.7037 (m-10) REVERT: P 1064 GLU cc_start: 0.7049 (tp30) cc_final: 0.6683 (tp30) REVERT: P 1089 MET cc_start: 0.5376 (mtp) cc_final: 0.5107 (mtp) outliers start: 36 outliers final: 25 residues processed: 181 average time/residue: 0.3337 time to fit residues: 80.4074 Evaluate side-chains 172 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 3.137 ------------------------------------------------------------------------------- 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 301 LEU Chi-restraints excluded: chain P residue 783 ARG Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 842 VAL Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 882 TYR Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 908 LEU Chi-restraints excluded: chain P residue 922 VAL Chi-restraints excluded: chain P residue 1051 THR Chi-restraints excluded: chain P residue 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 1270 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 52 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.147166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.125296 restraints weight = 27461.826| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 3.50 r_work: 0.3947 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9648 Z= 0.154 Angle : 0.606 9.116 13199 Z= 0.314 Chirality : 0.040 0.146 1506 Planarity : 0.004 0.045 1517 Dihedral : 15.255 99.486 1822 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.04 % Allowed : 17.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1025 helix: 0.69 (0.22), residues: 529 sheet: -0.26 (0.47), residues: 110 loop : -0.76 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P1074 HIS 0.005 0.001 HIS P1297 PHE 0.043 0.002 PHE P 916 TYR 0.013 0.001 TYR P 823 ARG 0.010 0.001 ARG P 400 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 448) hydrogen bonds : angle 4.77592 ( 1260) covalent geometry : bond 0.00328 ( 9648) covalent geometry : angle 0.60605 (13199) *********************** 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: 28 poor density : 150 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 39 ASP cc_start: 0.8627 (p0) cc_final: 0.8422 (p0) REVERT: P 63 ARG cc_start: 0.7118 (mtp180) cc_final: 0.6500 (mtm180) REVERT: P 77 ASN cc_start: 0.8073 (t0) cc_final: 0.7812 (t0) REVERT: P 163 LYS cc_start: 0.7832 (tttt) cc_final: 0.7460 (ttpt) REVERT: P 170 ILE cc_start: 0.7387 (mm) cc_final: 0.7170 (pt) REVERT: P 286 TYR cc_start: 0.8184 (m-80) cc_final: 0.7874 (m-10) REVERT: P 354 GLN cc_start: 0.7638 (mt0) cc_final: 0.7258 (tm-30) REVERT: P 394 ASN cc_start: 0.7684 (t0) cc_final: 0.7253 (p0) REVERT: P 418 GLU cc_start: 0.8408 (mp0) cc_final: 0.8185 (mm-30) REVERT: P 740 THR cc_start: 0.8255 (m) cc_final: 0.7961 (p) REVERT: P 742 LYS cc_start: 0.7693 (mtmt) cc_final: 0.7240 (mmtt) REVERT: P 745 ASP cc_start: 0.7942 (m-30) cc_final: 0.7591 (t0) REVERT: P 781 MET cc_start: 0.6529 (mmm) cc_final: 0.6262 (mtp) REVERT: P 891 LEU cc_start: 0.7579 (mt) cc_final: 0.7265 (mt) REVERT: P 892 ILE cc_start: 0.4483 (OUTLIER) cc_final: 0.3900 (pt) REVERT: P 908 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7578 (mt) REVERT: P 926 GLN cc_start: 0.7962 (tp-100) cc_final: 0.7349 (tp-100) REVERT: P 927 ILE cc_start: 0.8801 (tp) cc_final: 0.8358 (pt) REVERT: P 937 SER cc_start: 0.7571 (t) cc_final: 0.7308 (m) REVERT: P 981 TYR cc_start: 0.7487 (m-10) cc_final: 0.7000 (m-10) REVERT: P 1064 GLU cc_start: 0.7520 (tp30) cc_final: 0.7120 (tp30) outliers start: 28 outliers final: 18 residues processed: 171 average time/residue: 0.2725 time to fit residues: 62.1032 Evaluate side-chains 160 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 268 LYS Chi-restraints excluded: chain P residue 427 GLU 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 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 1179 ILE Chi-restraints excluded: chain P residue 1270 ILE 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 105 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.145209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.122840 restraints weight = 27435.318| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 3.51 r_work: 0.3911 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9648 Z= 0.215 Angle : 0.656 12.108 13199 Z= 0.341 Chirality : 0.041 0.149 1506 Planarity : 0.005 0.066 1517 Dihedral : 15.325 101.314 1822 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.69 % Allowed : 17.81 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.26), residues: 1025 helix: 0.57 (0.22), residues: 524 sheet: -0.25 (0.46), residues: 111 loop : -0.83 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P1074 HIS 0.006 0.002 HIS P 799 PHE 0.044 0.003 PHE P 916 TYR 0.017 0.002 TYR P 823 ARG 0.007 0.001 ARG P 967 Details of bonding type rmsd hydrogen bonds : bond 0.04637 ( 448) hydrogen bonds : angle 4.94904 ( 1260) covalent geometry : bond 0.00446 ( 9648) covalent geometry : angle 0.65640 (13199) *********************** 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 188 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 77 ASN cc_start: 0.8193 (t0) cc_final: 0.7909 (t0) REVERT: P 163 LYS cc_start: 0.7855 (tttt) cc_final: 0.7606 (ttpt) REVERT: P 170 ILE cc_start: 0.7373 (mm) cc_final: 0.7103 (pt) REVERT: P 354 GLN cc_start: 0.7715 (mt0) cc_final: 0.7431 (tm-30) REVERT: P 394 ASN cc_start: 0.7793 (t0) cc_final: 0.7459 (p0) REVERT: P 418 GLU cc_start: 0.8455 (mp0) cc_final: 0.8182 (mm-30) REVERT: P 740 THR cc_start: 0.8272 (m) cc_final: 0.7928 (p) REVERT: P 742 LYS cc_start: 0.7685 (mtmt) cc_final: 0.7229 (mmtt) REVERT: P 745 ASP cc_start: 0.8015 (m-30) cc_final: 0.7673 (t0) REVERT: P 892 ILE cc_start: 0.4796 (OUTLIER) cc_final: 0.4166 (pt) REVERT: P 908 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7709 (mt) REVERT: P 926 GLN cc_start: 0.7950 (tp-100) cc_final: 0.7377 (tp-100) REVERT: P 927 ILE cc_start: 0.8831 (tp) cc_final: 0.8420 (pt) REVERT: P 937 SER cc_start: 0.7505 (t) cc_final: 0.7275 (m) REVERT: P 947 ASP cc_start: 0.7416 (t0) cc_final: 0.7168 (t0) REVERT: P 981 TYR cc_start: 0.7619 (m-10) cc_final: 0.7129 (m-10) REVERT: P 1089 MET cc_start: 0.5845 (mtp) cc_final: 0.5505 (mtp) REVERT: P 1189 GLU cc_start: 0.7113 (tp30) cc_final: 0.6874 (tp30) outliers start: 34 outliers final: 24 residues processed: 178 average time/residue: 0.2451 time to fit residues: 58.6088 Evaluate side-chains 170 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 427 GLU 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 922 VAL Chi-restraints excluded: chain P residue 944 ASP 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 1179 ILE Chi-restraints excluded: chain P residue 1259 VAL Chi-restraints excluded: chain P residue 1270 ILE 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 95 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 74 optimal weight: 0.0570 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P1261 GLN P1305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.146769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.124622 restraints weight = 27259.817| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 3.51 r_work: 0.3935 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9648 Z= 0.152 Angle : 0.612 9.751 13199 Z= 0.314 Chirality : 0.040 0.154 1506 Planarity : 0.004 0.047 1517 Dihedral : 15.234 100.131 1822 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.58 % Allowed : 18.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 1025 helix: 0.72 (0.23), residues: 528 sheet: -0.18 (0.45), residues: 111 loop : -0.78 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP P1074 HIS 0.005 0.001 HIS P1297 PHE 0.047 0.002 PHE P 916 TYR 0.020 0.001 TYR P 362 ARG 0.005 0.000 ARG P 400 Details of bonding type rmsd hydrogen bonds : bond 0.04035 ( 448) hydrogen bonds : angle 4.77561 ( 1260) covalent geometry : bond 0.00328 ( 9648) covalent geometry : angle 0.61179 (13199) *********************** 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 180 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 1.045 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 77 ASN cc_start: 0.8127 (t0) cc_final: 0.7845 (t0) REVERT: P 163 LYS cc_start: 0.7761 (tttt) cc_final: 0.7522 (ttpt) REVERT: P 286 TYR cc_start: 0.8225 (m-80) cc_final: 0.7940 (m-10) REVERT: P 354 GLN cc_start: 0.7802 (mt0) cc_final: 0.7485 (tm-30) REVERT: P 383 MET cc_start: 0.6560 (ptp) cc_final: 0.6287 (ptp) REVERT: P 394 ASN cc_start: 0.7822 (t0) cc_final: 0.7535 (p0) REVERT: P 418 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8134 (mm-30) REVERT: P 740 THR cc_start: 0.8259 (m) cc_final: 0.7934 (p) REVERT: P 742 LYS cc_start: 0.7639 (mtmt) cc_final: 0.7214 (mmtt) REVERT: P 745 ASP cc_start: 0.8051 (m-30) cc_final: 0.7787 (t0) REVERT: P 892 ILE cc_start: 0.4350 (OUTLIER) cc_final: 0.3770 (pt) REVERT: P 908 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7696 (mt) REVERT: P 926 GLN cc_start: 0.7930 (tp-100) cc_final: 0.7331 (tp-100) REVERT: P 927 ILE cc_start: 0.8794 (tp) cc_final: 0.8375 (pt) REVERT: P 937 SER cc_start: 0.7570 (t) cc_final: 0.7353 (m) REVERT: P 981 TYR cc_start: 0.7455 (m-10) cc_final: 0.6793 (m-10) REVERT: P 1089 MET cc_start: 0.5933 (mtp) cc_final: 0.5562 (mtp) REVERT: P 1305 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7025 (mm-40) outliers start: 33 outliers final: 18 residues processed: 171 average time/residue: 0.2573 time to fit residues: 58.7484 Evaluate side-chains 160 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 418 GLU 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 944 ASP 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 1270 ILE Chi-restraints excluded: chain P residue 1305 GLN 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 87 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 0.0470 chunk 15 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.147004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.125352 restraints weight = 27843.945| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 3.72 r_work: 0.3935 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.5891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 9648 Z= 0.152 Angle : 0.628 9.718 13199 Z= 0.319 Chirality : 0.040 0.175 1506 Planarity : 0.004 0.047 1517 Dihedral : 15.195 100.170 1822 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.15 % Allowed : 18.46 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1025 helix: 0.68 (0.22), residues: 528 sheet: -0.04 (0.46), residues: 111 loop : -0.71 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP P1074 HIS 0.006 0.001 HIS P 167 PHE 0.045 0.002 PHE P 916 TYR 0.020 0.001 TYR P 362 ARG 0.007 0.001 ARG P 139 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 448) hydrogen bonds : angle 4.74397 ( 1260) covalent geometry : bond 0.00337 ( 9648) covalent geometry : angle 0.62819 (13199) *********************** 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 171 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 60 GLU cc_start: 0.7535 (pt0) cc_final: 0.7222 (pm20) REVERT: P 77 ASN cc_start: 0.8171 (t0) cc_final: 0.7881 (t0) REVERT: P 163 LYS cc_start: 0.7635 (tttt) cc_final: 0.7421 (ttpt) REVERT: P 286 TYR cc_start: 0.8195 (m-80) cc_final: 0.7892 (m-10) REVERT: P 354 GLN cc_start: 0.7786 (mt0) cc_final: 0.7424 (tm-30) REVERT: P 383 MET cc_start: 0.6258 (ptp) cc_final: 0.6006 (ptp) REVERT: P 394 ASN cc_start: 0.7980 (t0) cc_final: 0.7578 (p0) REVERT: P 418 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8113 (mm-30) REVERT: P 740 THR cc_start: 0.8270 (m) cc_final: 0.7945 (p) REVERT: P 742 LYS cc_start: 0.7623 (mtmt) cc_final: 0.7144 (mmtt) REVERT: P 745 ASP cc_start: 0.8063 (m-30) cc_final: 0.7802 (t0) REVERT: P 892 ILE cc_start: 0.4363 (OUTLIER) cc_final: 0.4006 (pt) REVERT: P 908 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7715 (mt) REVERT: P 926 GLN cc_start: 0.7942 (tp-100) cc_final: 0.7352 (tp-100) REVERT: P 927 ILE cc_start: 0.8795 (tp) cc_final: 0.8376 (pt) REVERT: P 981 TYR cc_start: 0.7316 (m-10) cc_final: 0.6698 (m-10) REVERT: P 1089 MET cc_start: 0.5850 (mtp) cc_final: 0.5454 (mtp) outliers start: 29 outliers final: 24 residues processed: 163 average time/residue: 0.2481 time to fit residues: 54.7034 Evaluate side-chains 162 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 58 THR 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 281 GLN Chi-restraints excluded: chain P residue 418 GLU Chi-restraints excluded: chain P residue 813 LEU Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 842 VAL Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 882 TYR Chi-restraints excluded: chain P residue 892 ILE Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 908 LEU Chi-restraints excluded: chain P residue 922 VAL Chi-restraints excluded: chain P residue 944 ASP 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 1179 ILE Chi-restraints excluded: chain P residue 1270 ILE 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 68 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 805 GLN ** P 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.147232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.125163 restraints weight = 27122.799| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 3.42 r_work: 0.3943 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9648 Z= 0.148 Angle : 0.627 9.720 13199 Z= 0.318 Chirality : 0.040 0.158 1506 Planarity : 0.004 0.047 1517 Dihedral : 15.156 100.118 1822 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.15 % Allowed : 18.13 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1025 helix: 0.71 (0.23), residues: 524 sheet: -0.04 (0.46), residues: 111 loop : -0.66 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P1074 HIS 0.006 0.001 HIS P 982 PHE 0.049 0.002 PHE P 916 TYR 0.025 0.001 TYR P1001 ARG 0.007 0.001 ARG P 780 Details of bonding type rmsd hydrogen bonds : bond 0.03929 ( 448) hydrogen bonds : angle 4.75440 ( 1260) covalent geometry : bond 0.00324 ( 9648) covalent geometry : angle 0.62702 (13199) *********************** 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 170 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 60 GLU cc_start: 0.7584 (pt0) cc_final: 0.7238 (pm20) REVERT: P 77 ASN cc_start: 0.8092 (t0) cc_final: 0.7780 (t0) REVERT: P 163 LYS cc_start: 0.7818 (tttt) cc_final: 0.7569 (ttpt) REVERT: P 286 TYR cc_start: 0.8044 (m-80) cc_final: 0.7750 (m-10) REVERT: P 354 GLN cc_start: 0.7734 (mt0) cc_final: 0.7412 (tm-30) REVERT: P 383 MET cc_start: 0.6563 (ptp) cc_final: 0.6199 (ptp) REVERT: P 394 ASN cc_start: 0.7961 (t0) cc_final: 0.7479 (p0) REVERT: P 418 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8143 (mm-30) REVERT: P 740 THR cc_start: 0.8184 (m) cc_final: 0.7860 (p) REVERT: P 742 LYS cc_start: 0.7520 (mtmt) cc_final: 0.7061 (mmtt) REVERT: P 745 ASP cc_start: 0.8057 (m-30) cc_final: 0.7718 (t0) REVERT: P 892 ILE cc_start: 0.4613 (OUTLIER) cc_final: 0.4006 (pt) REVERT: P 908 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7841 (mt) REVERT: P 926 GLN cc_start: 0.7925 (tp-100) cc_final: 0.7326 (tp-100) REVERT: P 927 ILE cc_start: 0.8777 (tp) cc_final: 0.8359 (pt) REVERT: P 981 TYR cc_start: 0.7199 (m-10) cc_final: 0.6475 (m-10) REVERT: P 1089 MET cc_start: 0.5867 (mtp) cc_final: 0.5439 (mtp) REVERT: P 1305 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.6995 (mm-40) outliers start: 29 outliers final: 23 residues processed: 159 average time/residue: 0.3507 time to fit residues: 76.5271 Evaluate side-chains 159 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 217 SER Chi-restraints excluded: chain P residue 224 ASN Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 281 GLN Chi-restraints excluded: chain P residue 418 GLU Chi-restraints excluded: chain P residue 776 ASN Chi-restraints excluded: chain P residue 782 LYS Chi-restraints excluded: chain P residue 813 LEU Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 842 VAL Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 882 TYR Chi-restraints excluded: chain P residue 892 ILE Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 908 LEU Chi-restraints excluded: chain P residue 944 ASP 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 1179 ILE Chi-restraints excluded: chain P residue 1259 VAL Chi-restraints excluded: chain P residue 1270 ILE Chi-restraints excluded: chain P residue 1305 GLN 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 74 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 55 optimal weight: 0.0870 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 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 = 0.4367 r_free = 0.4367 target = 0.147841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.125284 restraints weight = 27449.129| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 3.53 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9648 Z= 0.139 Angle : 0.653 17.258 13199 Z= 0.325 Chirality : 0.040 0.163 1506 Planarity : 0.004 0.048 1517 Dihedral : 15.131 99.928 1822 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.50 % Allowed : 19.65 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 1025 helix: 0.79 (0.23), residues: 514 sheet: -0.19 (0.47), residues: 111 loop : -0.59 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.005 TRP P1074 HIS 0.006 0.001 HIS P 167 PHE 0.055 0.002 PHE P 916 TYR 0.023 0.001 TYR P 362 ARG 0.007 0.001 ARG P 139 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 448) hydrogen bonds : angle 4.73438 ( 1260) covalent geometry : bond 0.00310 ( 9648) covalent geometry : angle 0.65345 (13199) ********************** 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 162 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 1.016 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 60 GLU cc_start: 0.7746 (pt0) cc_final: 0.7399 (pm20) REVERT: P 77 ASN cc_start: 0.7925 (t0) cc_final: 0.7617 (t0) REVERT: P 163 LYS cc_start: 0.7924 (tttt) cc_final: 0.7666 (ttpt) REVERT: P 286 TYR cc_start: 0.7762 (m-80) cc_final: 0.7506 (m-10) REVERT: P 354 GLN cc_start: 0.7589 (mt0) cc_final: 0.7334 (tm-30) REVERT: P 383 MET cc_start: 0.6565 (ptp) cc_final: 0.6224 (ptp) REVERT: P 394 ASN cc_start: 0.8051 (t0) cc_final: 0.7542 (p0) REVERT: P 418 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7856 (mm-30) REVERT: P 740 THR cc_start: 0.8139 (m) cc_final: 0.7781 (p) REVERT: P 742 LYS cc_start: 0.7377 (mtmt) cc_final: 0.6954 (mmtt) REVERT: P 745 ASP cc_start: 0.7874 (m-30) cc_final: 0.7587 (t0) REVERT: P 892 ILE cc_start: 0.4964 (OUTLIER) cc_final: 0.4419 (pt) REVERT: P 926 GLN cc_start: 0.7794 (tp-100) cc_final: 0.7197 (tp-100) REVERT: P 927 ILE cc_start: 0.8730 (tp) cc_final: 0.8304 (pt) REVERT: P 981 TYR cc_start: 0.6990 (m-10) cc_final: 0.6291 (m-10) REVERT: P 1089 MET cc_start: 0.5657 (mtp) cc_final: 0.5196 (mtp) outliers start: 23 outliers final: 20 residues processed: 153 average time/residue: 0.3047 time to fit residues: 63.4725 Evaluate side-chains 158 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 224 ASN Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 281 GLN Chi-restraints excluded: chain P residue 418 GLU Chi-restraints excluded: chain P residue 782 LYS Chi-restraints excluded: chain P residue 813 LEU Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 842 VAL Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 882 TYR Chi-restraints excluded: chain P residue 892 ILE Chi-restraints excluded: chain P residue 893 THR Chi-restraints excluded: chain P residue 944 ASP Chi-restraints excluded: chain P residue 1145 VAL Chi-restraints excluded: chain P residue 1169 MET Chi-restraints excluded: chain P residue 1179 ILE Chi-restraints excluded: chain P residue 1270 ILE 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 5 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 407 ASN ** P 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.145641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.123165 restraints weight = 27191.489| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 3.50 r_work: 0.3914 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.6347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9648 Z= 0.204 Angle : 0.690 15.473 13199 Z= 0.349 Chirality : 0.042 0.229 1506 Planarity : 0.005 0.057 1517 Dihedral : 15.224 101.182 1822 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.93 % Allowed : 19.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.26), residues: 1025 helix: 0.53 (0.22), residues: 526 sheet: -0.03 (0.49), residues: 99 loop : -0.71 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.006 TRP P 18 HIS 0.008 0.001 HIS P 167 PHE 0.053 0.003 PHE P 916 TYR 0.021 0.002 TYR P 362 ARG 0.009 0.001 ARG P1335 Details of bonding type rmsd hydrogen bonds : bond 0.04417 ( 448) hydrogen bonds : angle 4.96272 ( 1260) covalent geometry : bond 0.00434 ( 9648) covalent geometry : angle 0.68985 (13199) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5750.61 seconds wall clock time: 102 minutes 25.51 seconds (6145.51 seconds total)