Starting phenix.real_space_refine on Fri Oct 23 05:15:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wdx_65909/10_2026/9wdx_65909.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wdx_65909/10_2026/9wdx_65909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wdx_65909/10_2026/9wdx_65909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wdx_65909/10_2026/9wdx_65909.map" model { file = "/net/cci-nas-00/data/ceres_data/9wdx_65909/10_2026/9wdx_65909.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wdx_65909/10_2026/9wdx_65909.cif" } resolution = 3.72 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= 0.002 sd= 0.036 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: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 5322 2.51 5 N 1462 2.21 5 O 1571 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-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8373 Number of models: 1 Model: "" Number of chains: 1 Chain: "P" Number of atoms: 8373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8373 Classifications: {'peptide': 1030} Link IDs: {'PTRANS': 26, 'TRANS': 1003} Chain breaks: 3 Time building chain proxies: 1.75, per 1000 atoms: 0.21 Number of scatterers: 8373 At special positions: 0 Unit cell: (86.7464, 115.106, 111.769, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 1571 8.00 N 1462 7.00 C 5322 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS P1210 " - pdb=" SG CYS P1280 " distance=2.03 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: 0.83 Conformation dependent library (CDL) restraints added in 286.1 milliseconds 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 9 sheets defined 54.1% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'P' and resid 58 through 63 Processing helix chain 'P' and resid 67 through 91 removed outlier: 3.635A pdb=" N ARG P 71 " --> pdb=" O THR P 67 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN P 88 " --> pdb=" O GLU P 84 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLU P 89 " --> pdb=" O ILE P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 132 Processing helix chain 'P' and resid 134 through 144 Processing helix chain 'P' and resid 150 through 164 removed outlier: 3.558A pdb=" N PHE P 164 " --> pdb=" O HIS P 160 " (cutoff:3.500A) Processing helix chain 'P' and resid 175 through 179 Processing helix chain 'P' and resid 180 through 197 Processing helix chain 'P' and resid 207 through 213 removed outlier: 3.752A pdb=" N SER P 213 " --> pdb=" O LYS P 209 " (cutoff:3.500A) Processing helix chain 'P' and resid 217 through 229 removed outlier: 3.820A pdb=" N LEU P 229 " --> pdb=" O LEU P 225 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 247 Processing helix chain 'P' and resid 270 through 283 Processing helix chain 'P' and resid 286 through 307 Processing helix chain 'P' and resid 315 through 342 Processing helix chain 'P' and resid 359 through 364 Processing helix chain 'P' and resid 368 through 383 Proline residue: P 378 - end of helix Processing helix chain 'P' and resid 389 through 394 Processing helix chain 'P' and resid 411 through 428 removed outlier: 3.818A pdb=" N HIS P 415 " --> pdb=" O PRO P 411 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASP P 428 " --> pdb=" O ARG P 424 " (cutoff:3.500A) Processing helix chain 'P' and resid 430 through 436 Processing helix chain 'P' and resid 436 through 446 removed outlier: 3.689A pdb=" N ILE P 440 " --> pdb=" O ASN P 436 " (cutoff:3.500A) Processing helix chain 'P' and resid 719 through 727 removed outlier: 4.570A pdb=" N HIS P 723 " --> pdb=" O SER P 719 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU P 727 " --> pdb=" O HIS P 723 " (cutoff:3.500A) Processing helix chain 'P' and resid 730 through 751 removed outlier: 3.502A pdb=" N MET P 751 " --> pdb=" O LEU P 747 " (cutoff:3.500A) Processing helix chain 'P' and resid 771 through 792 removed outlier: 4.183A pdb=" N LYS P 775 " --> pdb=" O GLN P 771 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER P 777 " --> pdb=" O GLY P 773 " (cutoff:3.500A) Processing helix chain 'P' and resid 802 through 806 removed outlier: 3.839A pdb=" N LEU P 806 " --> pdb=" O ASN P 803 " (cutoff:3.500A) Processing helix chain 'P' and resid 808 through 817 Processing helix chain 'P' and resid 829 through 833 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: 3.631A pdb=" N ASN P 863 " --> pdb=" O SER P 860 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG P 864 " --> pdb=" O ASP P 861 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY P 865 " --> pdb=" O LYS P 862 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 860 through 865' Processing helix chain 'P' and resid 872 through 889 removed outlier: 6.240A pdb=" N ASN P 881 " --> pdb=" O LYS P 877 " (cutoff:3.500A) removed outlier: 5.939A 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 909 through 922 Processing helix chain 'P' and resid 925 through 940 Processing helix chain 'P' and resid 959 through 970 removed outlier: 3.678A pdb=" N VAL P 963 " --> pdb=" O LYS P 959 " (cutoff:3.500A) Processing helix chain 'P' and resid 980 through 1001 removed outlier: 4.240A pdb=" N ALA P 984 " --> pdb=" O ASN P 980 " (cutoff:3.500A) Processing helix chain 'P' and resid 1004 through 1009 removed outlier: 4.317A pdb=" N PHE P1008 " --> pdb=" O LEU P1004 " (cutoff:3.500A) Processing helix chain 'P' and resid 1017 through 1021 removed outlier: 3.651A pdb=" N LYS P1020 " --> pdb=" O ASP P1017 " (cutoff:3.500A) Processing helix chain 'P' and resid 1043 through 1047 removed outlier: 3.563A pdb=" N PHE P1046 " --> pdb=" O MET P1043 " (cutoff:3.500A) Processing helix chain 'P' and resid 1077 through 1088 Processing helix chain 'P' and resid 1167 through 1177 removed outlier: 3.961A pdb=" N SER P1172 " --> pdb=" O ILE P1168 " (cutoff:3.500A) removed outlier: 3.915A 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: 3.934A pdb=" N LEU P1194 " --> pdb=" O LYS P1191 " (cutoff:3.500A) Processing helix chain 'P' and resid 1229 through 1241 Processing helix chain 'P' and resid 1248 through 1262 Processing helix chain 'P' and resid 1262 through 1281 removed outlier: 4.168A pdb=" N LEU P1266 " --> pdb=" O HIS P1262 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP P1267 " --> pdb=" O LYS P1263 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG P1279 " --> pdb=" O GLU P1275 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS P1280 " --> pdb=" O PHE P1276 " (cutoff:3.500A) Processing helix chain 'P' and resid 1283 through 1297 removed outlier: 3.597A pdb=" N LEU P1287 " --> pdb=" O ALA P1283 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS P1297 " --> pdb=" O ALA P1293 " (cutoff:3.500A) 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 sheet with id=AA1, first strand: chain 'P' and resid 954 through 957 removed outlier: 6.824A pdb=" N ILE P 759 " --> pdb=" O ILE P 956 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N TYR P 5 " --> pdb=" O ASN P 758 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N VAL P 760 " --> pdb=" O TYR P 5 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE P 7 " --> pdb=" O VAL P 760 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 29 through 33 removed outlier: 3.532A pdb=" N LYS P 30 " --> pdb=" O LYS P 45 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS P 45 " --> pdb=" O LYS P 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 35 through 36 removed outlier: 6.335A pdb=" N LEU P 35 " --> pdb=" O ARG P1359 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ASP P1361 " --> pdb=" O LEU P 35 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU P1203 " --> pdb=" O ILE P1348 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU P1219 " --> pdb=" O ALA P1215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 837 through 840 Processing sheet with id=AA5, first strand: chain 'P' and resid 1050 through 1051 Processing sheet with id=AA6, first strand: chain 'P' and resid 1063 through 1065 removed outlier: 7.014A pdb=" N GLU P1064 " --> pdb=" O VAL P1073 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 1163 through 1164 Processing sheet with id=AA8, first strand: chain 'P' and resid 1147 through 1151 removed outlier: 3.702A pdb=" N LYS P1151 " --> pdb=" O LYS P1156 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS P1156 " --> pdb=" O LYS P1151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 1324 through 1326 387 hydrogen bonds defined for protein. 1107 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2763 1.34 - 1.46: 1413 1.46 - 1.57: 4301 1.57 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 8510 Sorted by residual: bond pdb=" CB PRO P 871 " pdb=" CG PRO P 871 " ideal model delta sigma weight residual 1.492 1.536 -0.044 5.00e-02 4.00e+02 7.85e-01 bond pdb=" CA GLN P 794 " pdb=" C GLN P 794 " ideal model delta sigma weight residual 1.531 1.522 0.009 1.12e-02 7.97e+03 5.98e-01 bond pdb=" C ASN P 199 " pdb=" O ASN P 199 " ideal model delta sigma weight residual 1.235 1.232 0.003 4.70e-03 4.53e+04 5.06e-01 bond pdb=" C GLU P1341 " pdb=" N VAL P1342 " ideal model delta sigma weight residual 1.338 1.331 0.007 1.01e-02 9.80e+03 4.42e-01 bond pdb=" CA VAL P 27 " pdb=" C VAL P 27 " ideal model delta sigma weight residual 1.526 1.532 -0.005 7.90e-03 1.60e+04 4.37e-01 ... (remaining 8505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 11274 1.41 - 2.82: 126 2.82 - 4.23: 27 4.23 - 5.64: 5 5.64 - 7.04: 3 Bond angle restraints: 11435 Sorted by residual: angle pdb=" N VAL P1342 " pdb=" CA VAL P1342 " pdb=" C VAL P1342 " ideal model delta sigma weight residual 112.98 110.40 2.58 1.25e+00 6.40e-01 4.27e+00 angle pdb=" CA LEU P1291 " pdb=" CB LEU P1291 " pdb=" CG LEU P1291 " ideal model delta sigma weight residual 116.30 123.34 -7.04 3.50e+00 8.16e-02 4.05e+00 angle pdb=" N VAL P 838 " pdb=" CA VAL P 838 " pdb=" C VAL P 838 " ideal model delta sigma weight residual 110.05 107.89 2.16 1.09e+00 8.42e-01 3.94e+00 angle pdb=" CA LYS P 377 " pdb=" C LYS P 377 " pdb=" N PRO P 378 " ideal model delta sigma weight residual 118.44 121.52 -3.08 1.59e+00 3.96e-01 3.75e+00 angle pdb=" C GLU P 84 " pdb=" N ILE P 85 " pdb=" CA ILE P 85 " ideal model delta sigma weight residual 121.09 118.05 3.04 1.65e+00 3.67e-01 3.39e+00 ... (remaining 11430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 4878 17.18 - 34.37: 306 34.37 - 51.55: 67 51.55 - 68.73: 6 68.73 - 85.91: 5 Dihedral angle restraints: 5262 sinusoidal: 2232 harmonic: 3030 Sorted by residual: dihedral pdb=" CA LYS P1047 " pdb=" C LYS P1047 " pdb=" N THR P1048 " pdb=" CA THR P1048 " ideal model delta harmonic sigma weight residual 180.00 164.37 15.63 0 5.00e+00 4.00e-02 9.78e+00 dihedral pdb=" N LEU P1004 " pdb=" CA LEU P1004 " pdb=" CB LEU P1004 " pdb=" CG LEU P1004 " ideal model delta sinusoidal sigma weight residual -60.00 -119.34 59.34 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ASN P1208 " pdb=" C ASN P1208 " pdb=" N GLY P1209 " pdb=" CA GLY P1209 " ideal model delta harmonic sigma weight residual 180.00 164.63 15.37 0 5.00e+00 4.00e-02 9.45e+00 ... (remaining 5259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 738 0.027 - 0.053: 325 0.053 - 0.080: 133 0.080 - 0.107: 54 0.107 - 0.133: 23 Chirality restraints: 1273 Sorted by residual: chirality pdb=" CA ILE P1360 " pdb=" N ILE P1360 " pdb=" C ILE P1360 " pdb=" CB ILE P1360 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA VAL P 870 " pdb=" N VAL P 870 " pdb=" C VAL P 870 " pdb=" CB VAL P 870 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA VAL P 842 " pdb=" N VAL P 842 " pdb=" C VAL P 842 " pdb=" CB VAL P 842 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 1270 not shown) Planarity restraints: 1465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL P 870 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO P 871 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO P 871 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO P 871 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE P 410 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO P 411 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO P 411 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO P 411 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL P 741 " 0.005 2.00e-02 2.50e+03 1.03e-02 1.05e+00 pdb=" C VAL P 741 " -0.018 2.00e-02 2.50e+03 pdb=" O VAL P 741 " 0.007 2.00e-02 2.50e+03 pdb=" N LYS P 742 " 0.006 2.00e-02 2.50e+03 ... (remaining 1462 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2457 2.83 - 3.35: 8670 3.35 - 3.86: 13804 3.86 - 4.38: 15720 4.38 - 4.90: 25591 Nonbonded interactions: 66242 Sorted by model distance: nonbonded pdb=" O ASP P1361 " pdb=" OD1 ASP P1361 " model vdw 2.312 3.040 nonbonded pdb=" O THR P 770 " pdb=" CG2 THR P 770 " model vdw 2.549 3.460 nonbonded pdb=" NH2 ARG P 967 " pdb=" OD1 ASP P 986 " model vdw 2.605 3.120 nonbonded pdb=" N THR P 58 " pdb=" O THR P 58 " model vdw 2.612 2.496 nonbonded pdb=" C THR P 134 " pdb=" OG1 THR P 134 " model vdw 2.614 2.616 ... (remaining 66237 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.160 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.000 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8511 Z= 0.107 Angle : 0.457 7.044 11437 Z= 0.245 Chirality : 0.039 0.133 1273 Planarity : 0.003 0.052 1465 Dihedral : 11.826 85.915 3299 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.31 % Allowed : 7.73 % Favored : 90.97 % 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: -0.33 (0.27), residues: 1022 helix: 0.87 (0.24), residues: 502 sheet: -1.55 (0.47), residues: 108 loop : -1.15 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 967 TYR 0.006 0.001 TYR P1141 PHE 0.010 0.001 PHE P1008 TRP 0.005 0.001 TRP P1074 HIS 0.003 0.001 HIS P 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.11 ( 8510) covalent geometry : angle 0.45683 / 0.24 (11435) SS BOND : bond 0.00264 / 0.14 ( 1) SS BOND : angle 0.80299 / 0.47 ( 2) hydrogen bonds : bond 0.14952 / 10.23 ( 387) hydrogen bonds : angle 5.93273 / 4.18 ( 1107) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 236 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 54 ASP cc_start: 0.7233 (t0) cc_final: 0.6870 (t0) REVERT: P 63 ARG cc_start: 0.7603 (ttm170) cc_final: 0.7087 (ttm-80) REVERT: P 66 ARG cc_start: 0.6937 (ptp90) cc_final: 0.6509 (ptp90) REVERT: P 69 ARG cc_start: 0.7243 (ttp80) cc_final: 0.6942 (tmm160) REVERT: P 77 ASN cc_start: 0.7969 (t0) cc_final: 0.6708 (t0) REVERT: P 81 TYR cc_start: 0.6462 (m-80) cc_final: 0.6019 (m-80) REVERT: P 140 LYS cc_start: 0.8354 (tttt) cc_final: 0.7901 (tmmt) REVERT: P 141 LYS cc_start: 0.7812 (tttt) cc_final: 0.7464 (tttt) REVERT: P 161 MET cc_start: 0.7632 (mtm) cc_final: 0.7241 (mtp) REVERT: P 163 LYS cc_start: 0.8437 (tppt) cc_final: 0.7877 (tppt) REVERT: P 199 ASN cc_start: 0.8650 (m-40) cc_final: 0.8441 (m-40) REVERT: P 237 LEU cc_start: 0.7158 (tp) cc_final: 0.6787 (tt) REVERT: P 246 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7180 (mp) REVERT: P 261 ASP cc_start: 0.7608 (t0) cc_final: 0.7230 (t0) REVERT: P 263 LYS cc_start: 0.7801 (mmtp) cc_final: 0.6787 (mmtm) REVERT: P 281 GLN cc_start: 0.6964 (tm-30) cc_final: 0.6704 (tm-30) REVERT: P 288 ASP cc_start: 0.7118 (m-30) cc_final: 0.6529 (m-30) REVERT: P 322 ILE cc_start: 0.8398 (tt) cc_final: 0.8064 (pt) REVERT: P 323 LYS cc_start: 0.8520 (mmtt) cc_final: 0.8082 (mmmm) REVERT: P 326 ASP cc_start: 0.8124 (m-30) cc_final: 0.7825 (m-30) REVERT: P 396 GLU cc_start: 0.6719 (mp0) cc_final: 0.6327 (mp0) REVERT: P 401 LYS cc_start: 0.8237 (mttt) cc_final: 0.7384 (mttp) REVERT: P 416 LEU cc_start: 0.8216 (tp) cc_final: 0.7960 (tp) REVERT: P 423 LEU cc_start: 0.8470 (mt) cc_final: 0.8002 (pp) REVERT: P 424 ARG cc_start: 0.8213 (tpm170) cc_final: 0.7823 (tpm170) REVERT: P 430 TYR cc_start: 0.7894 (m-10) cc_final: 0.7412 (m-10) REVERT: P 722 GLU cc_start: 0.7592 (pp20) cc_final: 0.6346 (pp20) REVERT: P 727 LEU cc_start: 0.7735 (mm) cc_final: 0.7441 (mp) REVERT: P 754 HIS cc_start: 0.6378 (m-70) cc_final: 0.6017 (m170) REVERT: P 781 MET cc_start: 0.7859 (tpp) cc_final: 0.7568 (tpt) REVERT: P 785 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7662 (mt-10) REVERT: P 803 ASN cc_start: 0.7451 (p0) cc_final: 0.7086 (p0) REVERT: P 810 LYS cc_start: 0.8775 (mtpp) cc_final: 0.8232 (mttt) REVERT: P 836 TYR cc_start: 0.7351 (m-10) cc_final: 0.7035 (m-10) REVERT: P 842 VAL cc_start: 0.8499 (t) cc_final: 0.8114 (m) REVERT: P 849 ASP cc_start: 0.7990 (t0) cc_final: 0.7550 (t0) REVERT: P 853 ASP cc_start: 0.6987 (t0) cc_final: 0.6431 (t0) REVERT: P 859 ARG cc_start: 0.6852 (ptp-110) cc_final: 0.6467 (ptp-110) REVERT: P 862 LYS cc_start: 0.8251 (mmmt) cc_final: 0.7922 (mmmt) REVERT: P 874 GLU cc_start: 0.8415 (mp0) cc_final: 0.8120 (mp0) REVERT: P 878 LYS cc_start: 0.8389 (tppt) cc_final: 0.7947 (mmmm) REVERT: P 890 LYS cc_start: 0.8560 (mttm) cc_final: 0.8305 (mmtt) REVERT: P 902 LYS cc_start: 0.7669 (ttmt) cc_final: 0.7160 (ttpp) REVERT: P 926 GLN cc_start: 0.7514 (tm-30) cc_final: 0.7152 (tm-30) REVERT: P 969 ASP cc_start: 0.6050 (t0) cc_final: 0.5715 (t0) REVERT: P 971 GLN cc_start: 0.6826 (tm-30) cc_final: 0.6502 (tm-30) REVERT: P 999 LYS cc_start: 0.8422 (ttmt) cc_final: 0.8075 (ttmm) REVERT: P 1003 LYS cc_start: 0.8125 (mttt) cc_final: 0.7485 (mtpp) REVERT: P 1004 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.5762 (mp) REVERT: P 1005 GLU cc_start: 0.7063 (pp20) cc_final: 0.6712 (pp20) REVERT: P 1016 TYR cc_start: 0.6783 (m-10) cc_final: 0.6405 (m-10) REVERT: P 1018 VAL cc_start: 0.8804 (m) cc_final: 0.8593 (t) REVERT: P 1021 MET cc_start: 0.7103 (mmm) cc_final: 0.6421 (mmm) REVERT: P 1037 PHE cc_start: 0.8185 (p90) cc_final: 0.7701 (p90) REVERT: P 1043 MET cc_start: 0.7447 (tpp) cc_final: 0.7200 (tpp) REVERT: P 1049 GLU cc_start: 0.6954 (tm-30) cc_final: 0.6673 (tm-30) REVERT: P 1052 LEU cc_start: 0.8300 (mt) cc_final: 0.8080 (mt) REVERT: P 1059 LYS cc_start: 0.7991 (tmtt) cc_final: 0.7484 (tmtt) REVERT: P 1060 ARG cc_start: 0.7560 (mtp85) cc_final: 0.7282 (ttt180) REVERT: P 1080 PHE cc_start: 0.5319 (OUTLIER) cc_final: 0.4866 (m-10) REVERT: P 1085 LYS cc_start: 0.7912 (mmmm) cc_final: 0.7678 (mmmm) REVERT: P 1097 LYS cc_start: 0.7287 (pttm) cc_final: 0.6881 (pttp) REVERT: P 1171 ARG cc_start: 0.7562 (ttp80) cc_final: 0.7333 (ptm-80) REVERT: P 1188 LYS cc_start: 0.7805 (ttmt) cc_final: 0.7582 (ttpt) REVERT: P 1202 SER cc_start: 0.8220 (m) cc_final: 0.7599 (p) REVERT: P 1258 PHE cc_start: 0.7727 (t80) cc_final: 0.7511 (t80) REVERT: P 1267 ASP cc_start: 0.7607 (t70) cc_final: 0.7332 (t0) REVERT: P 1272 GLN cc_start: 0.8914 (tp40) cc_final: 0.8128 (tp-100) REVERT: P 1275 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7094 (mm-30) REVERT: P 1276 PHE cc_start: 0.7516 (t80) cc_final: 0.7006 (t80) REVERT: P 1289 LYS cc_start: 0.8399 (mttt) cc_final: 0.7928 (mttt) REVERT: P 1308 ASN cc_start: 0.7701 (t0) cc_final: 0.7330 (t0) REVERT: P 1333 ARG cc_start: 0.7575 (mtt90) cc_final: 0.7154 (mtt90) REVERT: P 1334 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7659 (mmtm) outliers start: 12 outliers final: 3 residues processed: 246 average time/residue: 0.1114 time to fit residues: 35.1979 Evaluate side-chains 226 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 220 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 134 THR Chi-restraints excluded: chain P residue 246 LEU Chi-restraints excluded: chain P residue 1004 LEU Chi-restraints excluded: chain P residue 1008 PHE Chi-restraints excluded: chain P residue 1080 PHE Chi-restraints excluded: chain P residue 1280 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 100, 38, 61] chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 228 GLN P 285 GLN ** P 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 840 HIS P 869 ASN P 885 GLN ** P 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 980 ASN P 982 HIS P 983 HIS ** P1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1066 ASN ** P1286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1297 HIS ** P1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1349 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.164565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.140623 restraints weight = 14808.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.145912 restraints weight = 8361.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.149537 restraints weight = 5386.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.151979 restraints weight = 3758.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.153756 restraints weight = 2835.269| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8511 Z= 0.255 Angle : 0.651 11.370 11437 Z= 0.344 Chirality : 0.045 0.176 1273 Planarity : 0.004 0.055 1465 Dihedral : 5.351 55.789 1136 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.50 % Allowed : 13.06 % Favored : 84.44 % 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: -0.60 (0.26), residues: 1022 helix: 0.70 (0.24), residues: 496 sheet: -1.85 (0.48), residues: 98 loop : -1.30 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 220 TYR 0.027 0.002 TYR P 373 PHE 0.011 0.002 PHE P1008 TRP 0.007 0.002 TRP P1074 HIS 0.010 0.001 HIS P 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.25 ( 8510) covalent geometry : angle 0.65051 / 0.34 (11435) SS BOND : bond 0.00617 / 0.32 ( 1) SS BOND : angle 1.05562 / 0.62 ( 2) hydrogen bonds : bond 0.05079 / 3.37 ( 387) hydrogen bonds : angle 5.32605 / 3.71 ( 1107) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 0.311 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 14 ASN cc_start: 0.8038 (p0) cc_final: 0.7796 (p0) REVERT: P 54 ASP cc_start: 0.7251 (t0) cc_final: 0.6910 (t0) REVERT: P 63 ARG cc_start: 0.7621 (ttm170) cc_final: 0.7209 (ttm-80) REVERT: P 77 ASN cc_start: 0.8057 (t0) cc_final: 0.6754 (t0) REVERT: P 81 TYR cc_start: 0.6340 (m-80) cc_final: 0.5950 (m-80) REVERT: P 136 TYR cc_start: 0.6337 (m-80) cc_final: 0.6025 (m-80) REVERT: P 140 LYS cc_start: 0.8444 (tttt) cc_final: 0.8024 (tmmt) REVERT: P 141 LYS cc_start: 0.7943 (tttt) cc_final: 0.7610 (tttt) REVERT: P 161 MET cc_start: 0.7666 (mtm) cc_final: 0.7117 (mtt) REVERT: P 163 LYS cc_start: 0.8504 (tppt) cc_final: 0.7780 (tppt) REVERT: P 180 ASP cc_start: 0.7103 (t0) cc_final: 0.6116 (t0) REVERT: P 207 ASP cc_start: 0.7605 (t0) cc_final: 0.6728 (p0) REVERT: P 237 LEU cc_start: 0.7224 (tp) cc_final: 0.6870 (tt) REVERT: P 246 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7249 (mt) REVERT: P 263 LYS cc_start: 0.7755 (mmtp) cc_final: 0.6896 (mmtm) REVERT: P 281 GLN cc_start: 0.6959 (tm-30) cc_final: 0.6693 (tm-30) REVERT: P 288 ASP cc_start: 0.7459 (m-30) cc_final: 0.6916 (m-30) REVERT: P 321 MET cc_start: 0.7143 (ttm) cc_final: 0.6745 (mtp) REVERT: P 322 ILE cc_start: 0.8128 (tt) cc_final: 0.7842 (pt) REVERT: P 323 LYS cc_start: 0.8453 (mmtt) cc_final: 0.8115 (mmmm) REVERT: P 326 ASP cc_start: 0.8125 (m-30) cc_final: 0.7815 (m-30) REVERT: P 401 LYS cc_start: 0.8041 (mttt) cc_final: 0.7623 (mttp) REVERT: P 416 LEU cc_start: 0.8122 (tp) cc_final: 0.7494 (tp) REVERT: P 420 HIS cc_start: 0.7899 (m-70) cc_final: 0.7687 (m-70) REVERT: P 430 TYR cc_start: 0.7798 (m-10) cc_final: 0.7506 (m-10) REVERT: P 434 LYS cc_start: 0.8487 (mttt) cc_final: 0.7975 (mttm) REVERT: P 722 GLU cc_start: 0.7663 (pp20) cc_final: 0.6280 (pp20) REVERT: P 754 HIS cc_start: 0.6271 (m-70) cc_final: 0.5873 (m170) REVERT: P 781 MET cc_start: 0.7814 (tpp) cc_final: 0.7566 (tpt) REVERT: P 785 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7702 (mt-10) REVERT: P 803 ASN cc_start: 0.7367 (p0) cc_final: 0.7059 (p0) REVERT: P 810 LYS cc_start: 0.8483 (mtpp) cc_final: 0.8131 (mttt) REVERT: P 820 ARG cc_start: 0.7662 (mmm160) cc_final: 0.7296 (mmm160) REVERT: P 836 TYR cc_start: 0.7387 (m-10) cc_final: 0.6945 (m-10) REVERT: P 842 VAL cc_start: 0.8498 (t) cc_final: 0.8102 (m) REVERT: P 853 ASP cc_start: 0.7050 (t0) cc_final: 0.6560 (t0) REVERT: P 859 ARG cc_start: 0.6814 (ptp-110) cc_final: 0.6411 (ptp-110) REVERT: P 874 GLU cc_start: 0.8317 (mp0) cc_final: 0.8105 (mp0) REVERT: P 879 MET cc_start: 0.7123 (mmm) cc_final: 0.6886 (mmm) REVERT: P 885 GLN cc_start: 0.7685 (mt0) cc_final: 0.7345 (mp10) REVERT: P 890 LYS cc_start: 0.8629 (mttm) cc_final: 0.8341 (mmtt) REVERT: P 902 LYS cc_start: 0.7836 (ttmt) cc_final: 0.7240 (ttpp) REVERT: P 913 LYS cc_start: 0.8485 (ptpp) cc_final: 0.8218 (pttm) REVERT: P 926 GLN cc_start: 0.7886 (tm-30) cc_final: 0.7680 (tm-30) REVERT: P 939 MET cc_start: 0.6545 (ptp) cc_final: 0.6151 (ptp) REVERT: P 965 ASP cc_start: 0.6260 (m-30) cc_final: 0.5848 (m-30) REVERT: P 971 GLN cc_start: 0.6947 (tm-30) cc_final: 0.6536 (tm-30) REVERT: P 973 TYR cc_start: 0.6725 (m-80) cc_final: 0.5208 (m-80) REVERT: P 999 LYS cc_start: 0.8456 (ttmt) cc_final: 0.8094 (ttmm) REVERT: P 1003 LYS cc_start: 0.8266 (mttt) cc_final: 0.7688 (mtpp) REVERT: P 1004 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.6063 (mp) REVERT: P 1005 GLU cc_start: 0.6985 (pp20) cc_final: 0.6719 (pp20) REVERT: P 1016 TYR cc_start: 0.6879 (m-10) cc_final: 0.6460 (m-10) REVERT: P 1018 VAL cc_start: 0.8896 (m) cc_final: 0.8659 (t) REVERT: P 1021 MET cc_start: 0.6940 (mmm) cc_final: 0.6318 (mmm) REVERT: P 1037 PHE cc_start: 0.8245 (p90) cc_final: 0.7976 (p90) REVERT: P 1043 MET cc_start: 0.7556 (tpp) cc_final: 0.7192 (tpp) REVERT: P 1049 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6749 (tm-30) REVERT: P 1052 LEU cc_start: 0.8086 (mt) cc_final: 0.7835 (mt) REVERT: P 1059 LYS cc_start: 0.7938 (tmtt) cc_final: 0.7518 (tmtt) REVERT: P 1080 PHE cc_start: 0.5396 (OUTLIER) cc_final: 0.4539 (m-10) REVERT: P 1085 LYS cc_start: 0.8006 (mmmm) cc_final: 0.7784 (mmmm) REVERT: P 1097 LYS cc_start: 0.7300 (pttm) cc_final: 0.6987 (pttp) REVERT: P 1169 MET cc_start: 0.7349 (tmm) cc_final: 0.7140 (tmm) REVERT: P 1181 PHE cc_start: 0.6468 (t80) cc_final: 0.6172 (t80) REVERT: P 1188 LYS cc_start: 0.8176 (ttmt) cc_final: 0.7823 (ttpt) REVERT: P 1202 SER cc_start: 0.8189 (m) cc_final: 0.7556 (p) REVERT: P 1237 TYR cc_start: 0.7155 (t80) cc_final: 0.6763 (t80) REVERT: P 1258 PHE cc_start: 0.7510 (t80) cc_final: 0.7116 (t80) REVERT: P 1263 LYS cc_start: 0.8031 (tppt) cc_final: 0.7341 (tppp) REVERT: P 1267 ASP cc_start: 0.7429 (t70) cc_final: 0.7165 (t0) REVERT: P 1272 GLN cc_start: 0.8873 (tp40) cc_final: 0.8307 (tp-100) REVERT: P 1275 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7363 (mm-30) REVERT: P 1278 LYS cc_start: 0.7996 (mmmt) cc_final: 0.7499 (mmmt) REVERT: P 1289 LYS cc_start: 0.8460 (mttt) cc_final: 0.7978 (mttt) outliers start: 23 outliers final: 14 residues processed: 239 average time/residue: 0.1048 time to fit residues: 32.7952 Evaluate side-chains 236 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 219 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 246 LEU Chi-restraints excluded: chain P residue 301 LEU Chi-restraints excluded: chain P residue 329 HIS Chi-restraints excluded: chain P residue 397 ASP Chi-restraints excluded: chain P residue 833 LEU Chi-restraints excluded: chain P residue 869 ASN Chi-restraints excluded: chain P residue 922 VAL Chi-restraints excluded: chain P residue 927 ILE Chi-restraints excluded: chain P residue 1004 LEU Chi-restraints excluded: chain P residue 1008 PHE Chi-restraints excluded: chain P residue 1080 PHE Chi-restraints excluded: chain P residue 1189 GLU Chi-restraints excluded: chain P residue 1233 VAL Chi-restraints excluded: chain P residue 1279 ARG Chi-restraints excluded: chain P residue 1280 CYS Chi-restraints excluded: chain P residue 1311 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: [95, 61, 16, 3, 30, 23, 25, 76, 4, 43, 44] chunk 95 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 817 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.166531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.141831 restraints weight = 14693.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.147141 restraints weight = 8424.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.150890 restraints weight = 5508.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.153370 restraints weight = 3892.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.155233 restraints weight = 2962.078| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8511 Z= 0.134 Angle : 0.585 11.232 11437 Z= 0.301 Chirality : 0.042 0.188 1273 Planarity : 0.004 0.044 1465 Dihedral : 5.232 57.520 1135 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.94 % Allowed : 14.91 % Favored : 82.15 % 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: -0.56 (0.26), residues: 1022 helix: 0.75 (0.24), residues: 509 sheet: -1.99 (0.46), residues: 98 loop : -1.33 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 220 TYR 0.023 0.001 TYR P 814 PHE 0.017 0.001 PHE P1235 TRP 0.007 0.001 TRP P1074 HIS 0.008 0.001 HIS P 799 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 8510) covalent geometry : angle 0.58537 / 0.30 (11435) SS BOND : bond 0.00067 / 0.04 ( 1) SS BOND : angle 0.28217 / 0.16 ( 2) hydrogen bonds : bond 0.04188 / 2.78 ( 387) hydrogen bonds : angle 4.98513 / 3.51 ( 1107) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 228 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 14 ASN cc_start: 0.8018 (p0) cc_final: 0.7793 (p0) REVERT: P 30 LYS cc_start: 0.6948 (ttmt) cc_final: 0.6004 (ttmt) REVERT: P 54 ASP cc_start: 0.7180 (t0) cc_final: 0.6814 (t0) REVERT: P 63 ARG cc_start: 0.7628 (ttm170) cc_final: 0.7219 (ttm-80) REVERT: P 69 ARG cc_start: 0.7279 (ttp80) cc_final: 0.6990 (tmm160) REVERT: P 77 ASN cc_start: 0.8030 (t0) cc_final: 0.6702 (t0) REVERT: P 81 TYR cc_start: 0.6314 (m-80) cc_final: 0.5924 (m-80) REVERT: P 136 TYR cc_start: 0.6153 (m-80) cc_final: 0.5873 (m-80) REVERT: P 140 LYS cc_start: 0.8360 (tttt) cc_final: 0.7955 (tmmt) REVERT: P 141 LYS cc_start: 0.7825 (tttt) cc_final: 0.7612 (tttt) REVERT: P 161 MET cc_start: 0.7597 (mtm) cc_final: 0.7184 (mtt) REVERT: P 163 LYS cc_start: 0.8393 (tppt) cc_final: 0.7319 (tppt) REVERT: P 180 ASP cc_start: 0.7335 (t0) cc_final: 0.6883 (t70) REVERT: P 207 ASP cc_start: 0.7506 (t0) cc_final: 0.6861 (p0) REVERT: P 220 ARG cc_start: 0.7827 (mmm160) cc_final: 0.7251 (mmm160) REVERT: P 237 LEU cc_start: 0.7118 (tp) cc_final: 0.6810 (tt) REVERT: P 246 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7129 (mt) REVERT: P 263 LYS cc_start: 0.7602 (mmtp) cc_final: 0.6744 (mmtm) REVERT: P 281 GLN cc_start: 0.6860 (tm-30) cc_final: 0.6538 (tm-30) REVERT: P 288 ASP cc_start: 0.7190 (m-30) cc_final: 0.6567 (m-30) REVERT: P 321 MET cc_start: 0.6803 (ttm) cc_final: 0.6565 (mtp) REVERT: P 322 ILE cc_start: 0.8227 (tt) cc_final: 0.7831 (pt) REVERT: P 323 LYS cc_start: 0.8442 (mmtt) cc_final: 0.7741 (mmmm) REVERT: P 326 ASP cc_start: 0.8014 (m-30) cc_final: 0.7676 (m-30) REVERT: P 396 GLU cc_start: 0.6874 (mp0) cc_final: 0.6535 (pm20) REVERT: P 401 LYS cc_start: 0.7981 (mttt) cc_final: 0.7555 (mttp) REVERT: P 416 LEU cc_start: 0.8144 (tp) cc_final: 0.7439 (tp) REVERT: P 420 HIS cc_start: 0.7887 (m-70) cc_final: 0.7635 (m-70) REVERT: P 430 TYR cc_start: 0.7828 (m-10) cc_final: 0.7516 (m-10) REVERT: P 434 LYS cc_start: 0.8483 (mttt) cc_final: 0.8229 (mttt) REVERT: P 722 GLU cc_start: 0.7421 (pp20) cc_final: 0.6631 (pp20) REVERT: P 727 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7407 (mp) REVERT: P 754 HIS cc_start: 0.6198 (m-70) cc_final: 0.5780 (m170) REVERT: P 781 MET cc_start: 0.7729 (tpp) cc_final: 0.7438 (tpt) REVERT: P 785 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7644 (mt-10) REVERT: P 803 ASN cc_start: 0.7395 (p0) cc_final: 0.7058 (p0) REVERT: P 817 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7357 (mp10) REVERT: P 820 ARG cc_start: 0.7679 (mmm160) cc_final: 0.7303 (mmm160) REVERT: P 824 VAL cc_start: 0.7823 (OUTLIER) cc_final: 0.7452 (p) REVERT: P 836 TYR cc_start: 0.7336 (m-10) cc_final: 0.7075 (m-10) REVERT: P 842 VAL cc_start: 0.8486 (t) cc_final: 0.8096 (m) REVERT: P 853 ASP cc_start: 0.7157 (t0) cc_final: 0.6583 (t0) REVERT: P 856 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8031 (t) REVERT: P 866 LYS cc_start: 0.8423 (mmmm) cc_final: 0.8154 (mmmm) REVERT: P 874 GLU cc_start: 0.8367 (mp0) cc_final: 0.8147 (mp0) REVERT: P 890 LYS cc_start: 0.8579 (mttm) cc_final: 0.8325 (mmtt) REVERT: P 902 LYS cc_start: 0.7819 (ttmt) cc_final: 0.7317 (tmmt) REVERT: P 913 LYS cc_start: 0.8433 (ptpp) cc_final: 0.8151 (pttm) REVERT: P 939 MET cc_start: 0.6624 (ptp) cc_final: 0.6198 (ptp) REVERT: P 952 GLU cc_start: 0.6548 (pm20) cc_final: 0.6333 (pm20) REVERT: P 971 GLN cc_start: 0.6854 (tm-30) cc_final: 0.6361 (tm-30) REVERT: P 999 LYS cc_start: 0.8362 (ttmt) cc_final: 0.8035 (ttmm) REVERT: P 1003 LYS cc_start: 0.8289 (mttt) cc_final: 0.7748 (mttm) REVERT: P 1004 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.5800 (mp) REVERT: P 1005 GLU cc_start: 0.6986 (pp20) cc_final: 0.6681 (pp20) REVERT: P 1018 VAL cc_start: 0.8919 (m) cc_final: 0.8655 (t) REVERT: P 1021 MET cc_start: 0.6940 (mmm) cc_final: 0.6302 (mmm) REVERT: P 1037 PHE cc_start: 0.8182 (p90) cc_final: 0.7761 (p90) REVERT: P 1043 MET cc_start: 0.7459 (tpp) cc_final: 0.7147 (tpp) REVERT: P 1049 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6837 (tm-30) REVERT: P 1052 LEU cc_start: 0.8115 (mt) cc_final: 0.7884 (mt) REVERT: P 1059 LYS cc_start: 0.7928 (tmtt) cc_final: 0.7484 (tmtt) REVERT: P 1085 LYS cc_start: 0.8013 (mmmm) cc_final: 0.7782 (mmmm) REVERT: P 1097 LYS cc_start: 0.7298 (pttm) cc_final: 0.7058 (pttp) REVERT: P 1169 MET cc_start: 0.6676 (tmm) cc_final: 0.6429 (tmm) REVERT: P 1202 SER cc_start: 0.8010 (m) cc_final: 0.7530 (p) REVERT: P 1258 PHE cc_start: 0.7354 (t80) cc_final: 0.7040 (t80) REVERT: P 1263 LYS cc_start: 0.7974 (tppt) cc_final: 0.7436 (tptm) REVERT: P 1267 ASP cc_start: 0.7445 (t70) cc_final: 0.7121 (t0) REVERT: P 1272 GLN cc_start: 0.8850 (tp40) cc_final: 0.8337 (tp-100) REVERT: P 1275 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7335 (mm-30) REVERT: P 1289 LYS cc_start: 0.8528 (mttt) cc_final: 0.8040 (mttt) REVERT: P 1308 ASN cc_start: 0.7541 (t0) cc_final: 0.7140 (t0) REVERT: P 1313 PHE cc_start: 0.8430 (m-80) cc_final: 0.7702 (m-80) REVERT: P 1333 ARG cc_start: 0.7689 (mtt90) cc_final: 0.7411 (mtt90) outliers start: 27 outliers final: 16 residues processed: 243 average time/residue: 0.1046 time to fit residues: 33.0979 Evaluate side-chains 240 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 217 SER Chi-restraints excluded: chain P residue 246 LEU Chi-restraints excluded: chain P residue 329 HIS Chi-restraints excluded: chain P residue 397 ASP Chi-restraints excluded: chain P residue 727 LEU Chi-restraints excluded: chain P residue 817 GLN Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 838 VAL Chi-restraints excluded: chain P residue 856 VAL Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 921 LEU Chi-restraints excluded: chain P residue 927 ILE Chi-restraints excluded: chain P residue 1004 LEU Chi-restraints excluded: chain P residue 1008 PHE Chi-restraints excluded: chain P residue 1080 PHE Chi-restraints excluded: chain P residue 1206 LEU Chi-restraints excluded: chain P residue 1279 ARG Chi-restraints excluded: chain P residue 1280 CYS Chi-restraints excluded: chain P residue 1311 HIS Chi-restraints excluded: chain P residue 1318 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: [38, 24, 44, 64, 12, 79, 5, 43, 77, 11, 2] chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 869 ASN P 885 GLN ** P1308 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 = 0.4239 r_free = 0.4239 target = 0.166020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.142234 restraints weight = 14782.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.147424 restraints weight = 8554.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.151014 restraints weight = 5597.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.153559 restraints weight = 3955.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.154924 restraints weight = 2985.615| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8511 Z= 0.133 Angle : 0.580 12.561 11437 Z= 0.296 Chirality : 0.042 0.172 1273 Planarity : 0.003 0.039 1465 Dihedral : 5.212 57.162 1135 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.83 % Allowed : 17.52 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.26), residues: 1022 helix: 0.85 (0.24), residues: 509 sheet: -2.30 (0.46), residues: 88 loop : -1.26 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P1333 TYR 0.016 0.001 TYR P 814 PHE 0.017 0.001 PHE P1235 TRP 0.006 0.001 TRP P1074 HIS 0.007 0.001 HIS P 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 8510) covalent geometry : angle 0.58011 / 0.30 (11435) SS BOND : bond 0.00122 / 0.06 ( 1) SS BOND : angle 0.36111 / 0.21 ( 2) hydrogen bonds : bond 0.03930 / 2.59 ( 387) hydrogen bonds : angle 4.84606 / 3.40 ( 1107) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 30 LYS cc_start: 0.6837 (ttmt) cc_final: 0.6137 (ttmt) REVERT: P 54 ASP cc_start: 0.7146 (t0) cc_final: 0.6713 (t0) REVERT: P 63 ARG cc_start: 0.7591 (ttm170) cc_final: 0.7240 (ttm-80) REVERT: P 69 ARG cc_start: 0.7296 (ttp80) cc_final: 0.7085 (tmm160) REVERT: P 140 LYS cc_start: 0.8432 (tttt) cc_final: 0.7858 (ttpp) REVERT: P 163 LYS cc_start: 0.8423 (tppt) cc_final: 0.7386 (tppt) REVERT: P 179 SER cc_start: 0.8185 (t) cc_final: 0.7933 (p) REVERT: P 180 ASP cc_start: 0.7284 (t0) cc_final: 0.6632 (t70) REVERT: P 207 ASP cc_start: 0.7559 (t0) cc_final: 0.6873 (p0) REVERT: P 220 ARG cc_start: 0.7795 (mmm160) cc_final: 0.7410 (mmm160) REVERT: P 246 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7172 (mt) REVERT: P 263 LYS cc_start: 0.7861 (mmtp) cc_final: 0.7063 (mmtm) REVERT: P 276 ASP cc_start: 0.6925 (m-30) cc_final: 0.6506 (m-30) REVERT: P 288 ASP cc_start: 0.7152 (m-30) cc_final: 0.6586 (m-30) REVERT: P 296 LEU cc_start: 0.8016 (tp) cc_final: 0.7814 (tp) REVERT: P 322 ILE cc_start: 0.8057 (tt) cc_final: 0.7696 (pt) REVERT: P 323 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8001 (mmmm) REVERT: P 326 ASP cc_start: 0.7916 (m-30) cc_final: 0.7623 (m-30) REVERT: P 401 LYS cc_start: 0.7924 (mttt) cc_final: 0.7511 (mttp) REVERT: P 416 LEU cc_start: 0.8122 (tp) cc_final: 0.7416 (tp) REVERT: P 420 HIS cc_start: 0.7836 (m-70) cc_final: 0.7597 (m-70) REVERT: P 430 TYR cc_start: 0.7812 (m-10) cc_final: 0.7514 (m-10) REVERT: P 434 LYS cc_start: 0.8476 (mttt) cc_final: 0.8229 (mttt) REVERT: P 722 GLU cc_start: 0.7287 (pp20) cc_final: 0.6492 (pp20) REVERT: P 727 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7415 (mp) REVERT: P 754 HIS cc_start: 0.5978 (m-70) cc_final: 0.5546 (m170) REVERT: P 781 MET cc_start: 0.7629 (tpp) cc_final: 0.7410 (tpt) REVERT: P 803 ASN cc_start: 0.7825 (p0) cc_final: 0.7420 (p0) REVERT: P 820 ARG cc_start: 0.7608 (mmm160) cc_final: 0.7301 (mmm160) REVERT: P 824 VAL cc_start: 0.7786 (OUTLIER) cc_final: 0.7330 (p) REVERT: P 836 TYR cc_start: 0.7320 (m-10) cc_final: 0.7032 (m-10) REVERT: P 842 VAL cc_start: 0.8475 (t) cc_final: 0.8075 (m) REVERT: P 853 ASP cc_start: 0.7091 (t0) cc_final: 0.6482 (t0) REVERT: P 866 LYS cc_start: 0.8322 (mmmm) cc_final: 0.7674 (mmmm) REVERT: P 874 GLU cc_start: 0.8200 (mp0) cc_final: 0.7960 (mp0) REVERT: P 885 GLN cc_start: 0.7587 (mt0) cc_final: 0.7255 (mp10) REVERT: P 890 LYS cc_start: 0.8548 (mttm) cc_final: 0.8333 (mmtt) REVERT: P 901 THR cc_start: 0.8321 (p) cc_final: 0.7898 (t) REVERT: P 902 LYS cc_start: 0.7847 (ttmt) cc_final: 0.7464 (ttpp) REVERT: P 913 LYS cc_start: 0.8433 (ptpp) cc_final: 0.8125 (pttm) REVERT: P 952 GLU cc_start: 0.6622 (pm20) cc_final: 0.6301 (pm20) REVERT: P 965 ASP cc_start: 0.6422 (m-30) cc_final: 0.5944 (m-30) REVERT: P 999 LYS cc_start: 0.8508 (ttmt) cc_final: 0.8120 (ttmm) REVERT: P 1003 LYS cc_start: 0.8208 (mttt) cc_final: 0.7660 (mttm) REVERT: P 1004 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.5865 (mp) REVERT: P 1005 GLU cc_start: 0.6979 (pp20) cc_final: 0.6739 (pp20) REVERT: P 1018 VAL cc_start: 0.8935 (m) cc_final: 0.8642 (t) REVERT: P 1021 MET cc_start: 0.6820 (mmm) cc_final: 0.6247 (mmm) REVERT: P 1037 PHE cc_start: 0.8114 (p90) cc_final: 0.7694 (p90) REVERT: P 1043 MET cc_start: 0.7425 (tpp) cc_final: 0.7129 (tpp) REVERT: P 1049 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6788 (tm-30) REVERT: P 1059 LYS cc_start: 0.7891 (tmtt) cc_final: 0.7446 (tmtt) REVERT: P 1085 LYS cc_start: 0.8002 (mmmm) cc_final: 0.7760 (mmmm) REVERT: P 1169 MET cc_start: 0.6428 (tmm) cc_final: 0.6198 (tmm) REVERT: P 1202 SER cc_start: 0.7995 (m) cc_final: 0.7530 (p) REVERT: P 1258 PHE cc_start: 0.7319 (t80) cc_final: 0.7046 (t80) REVERT: P 1263 LYS cc_start: 0.8079 (tppt) cc_final: 0.7337 (tptm) REVERT: P 1267 ASP cc_start: 0.7418 (t70) cc_final: 0.7045 (t0) REVERT: P 1271 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7741 (pp20) REVERT: P 1272 GLN cc_start: 0.8797 (tp40) cc_final: 0.8447 (tp-100) REVERT: P 1275 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7412 (mm-30) REVERT: P 1289 LYS cc_start: 0.8493 (mttt) cc_final: 0.8010 (mttt) REVERT: P 1333 ARG cc_start: 0.7598 (mtt90) cc_final: 0.7386 (mtt90) outliers start: 26 outliers final: 15 residues processed: 236 average time/residue: 0.1028 time to fit residues: 31.8466 Evaluate side-chains 233 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 214 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 41 HIS Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 217 SER Chi-restraints excluded: chain P residue 246 LEU Chi-restraints excluded: chain P residue 329 HIS Chi-restraints excluded: chain P residue 397 ASP Chi-restraints excluded: chain P residue 727 LEU Chi-restraints excluded: chain P residue 824 VAL Chi-restraints excluded: chain P residue 838 VAL Chi-restraints excluded: chain P residue 869 ASN Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 921 LEU Chi-restraints excluded: chain P residue 1004 LEU Chi-restraints excluded: chain P residue 1008 PHE Chi-restraints excluded: chain P residue 1080 PHE Chi-restraints excluded: chain P residue 1206 LEU Chi-restraints excluded: chain P residue 1280 CYS Chi-restraints excluded: chain P residue 1311 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: [44, 58, 3, 84, 9, 23, 81, 97, 5, 21, 17] chunk 44 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1349 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.165125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.141008 restraints weight = 14723.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.146342 restraints weight = 8348.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.150037 restraints weight = 5373.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.152647 restraints weight = 3769.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.154406 restraints weight = 2823.429| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8511 Z= 0.141 Angle : 0.603 11.607 11437 Z= 0.307 Chirality : 0.043 0.182 1273 Planarity : 0.003 0.038 1465 Dihedral : 5.239 56.773 1135 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.94 % Allowed : 18.17 % Favored : 78.89 % 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: -0.44 (0.26), residues: 1022 helix: 0.89 (0.24), residues: 502 sheet: -2.26 (0.46), residues: 88 loop : -1.24 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P1019 TYR 0.013 0.001 TYR P 814 PHE 0.014 0.001 PHE P1235 TRP 0.006 0.001 TRP P1074 HIS 0.006 0.001 HIS P 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 8510) covalent geometry : angle 0.60273 / 0.31 (11435) SS BOND : bond 0.00168 / 0.09 ( 1) SS BOND : angle 0.41958 / 0.25 ( 2) hydrogen bonds : bond 0.03858 / 2.54 ( 387) hydrogen bonds : angle 4.75487 / 3.32 ( 1107) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 30 LYS cc_start: 0.6915 (ttmt) cc_final: 0.5975 (ttmt) REVERT: P 63 ARG cc_start: 0.7717 (ttm170) cc_final: 0.7323 (ttm-80) REVERT: P 69 ARG cc_start: 0.7280 (ttp80) cc_final: 0.7037 (tmm160) REVERT: P 77 ASN cc_start: 0.8159 (t0) cc_final: 0.7139 (t0) REVERT: P 81 TYR cc_start: 0.6345 (m-80) cc_final: 0.6087 (m-80) REVERT: P 130 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7685 (mt-10) REVERT: P 140 LYS cc_start: 0.8359 (tttt) cc_final: 0.7941 (tmmt) REVERT: P 156 LEU cc_start: 0.8463 (mt) cc_final: 0.8182 (mt) REVERT: P 163 LYS cc_start: 0.8353 (tppt) cc_final: 0.7239 (tppt) REVERT: P 179 SER cc_start: 0.8111 (t) cc_final: 0.7707 (p) REVERT: P 181 VAL cc_start: 0.7256 (OUTLIER) cc_final: 0.6849 (t) REVERT: P 183 LYS cc_start: 0.7595 (ptpp) cc_final: 0.6987 (ptmm) REVERT: P 207 ASP cc_start: 0.7663 (t0) cc_final: 0.7202 (t0) REVERT: P 209 LYS cc_start: 0.7962 (mmtt) cc_final: 0.7658 (mmtt) REVERT: P 220 ARG cc_start: 0.7883 (mmm160) cc_final: 0.7539 (mmm160) REVERT: P 226 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7511 (mm) REVERT: P 246 LEU cc_start: 0.7488 (mm) cc_final: 0.7220 (mp) REVERT: P 263 LYS cc_start: 0.7828 (mmtp) cc_final: 0.6921 (mmtm) REVERT: P 276 ASP cc_start: 0.7015 (m-30) cc_final: 0.6530 (m-30) REVERT: P 288 ASP cc_start: 0.7151 (m-30) cc_final: 0.6531 (m-30) REVERT: P 296 LEU cc_start: 0.7847 (tp) cc_final: 0.7635 (tp) REVERT: P 322 ILE cc_start: 0.8110 (tt) cc_final: 0.7796 (pt) REVERT: P 323 LYS cc_start: 0.8511 (mmtt) cc_final: 0.7689 (mmmm) REVERT: P 326 ASP cc_start: 0.7977 (m-30) cc_final: 0.7660 (m-30) REVERT: P 401 LYS cc_start: 0.7914 (mttt) cc_final: 0.7459 (mttp) REVERT: P 416 LEU cc_start: 0.8151 (tp) cc_final: 0.7406 (tp) REVERT: P 420 HIS cc_start: 0.7928 (m-70) cc_final: 0.7649 (m-70) REVERT: P 430 TYR cc_start: 0.7914 (m-10) cc_final: 0.7512 (m-10) REVERT: P 434 LYS cc_start: 0.8531 (mttt) cc_final: 0.8054 (mttm) REVERT: P 722 GLU cc_start: 0.7424 (pp20) cc_final: 0.6630 (pp20) REVERT: P 727 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7418 (mp) REVERT: P 754 HIS cc_start: 0.6032 (m-70) cc_final: 0.5598 (m170) REVERT: P 770 THR cc_start: 0.8297 (OUTLIER) cc_final: 0.8039 (p) REVERT: P 781 MET cc_start: 0.7783 (tpp) cc_final: 0.7574 (tpt) REVERT: P 803 ASN cc_start: 0.7925 (p0) cc_final: 0.7506 (p0) REVERT: P 820 ARG cc_start: 0.7617 (mmm160) cc_final: 0.7244 (mmm160) REVERT: P 836 TYR cc_start: 0.7326 (m-10) cc_final: 0.7063 (m-10) REVERT: P 842 VAL cc_start: 0.8468 (t) cc_final: 0.8100 (m) REVERT: P 849 ASP cc_start: 0.8286 (t0) cc_final: 0.8014 (t0) REVERT: P 853 ASP cc_start: 0.7234 (t0) cc_final: 0.6617 (t0) REVERT: P 874 GLU cc_start: 0.8362 (mp0) cc_final: 0.7982 (mp0) REVERT: P 890 LYS cc_start: 0.8565 (mttm) cc_final: 0.8328 (mmtt) REVERT: P 901 THR cc_start: 0.8255 (p) cc_final: 0.7772 (t) REVERT: P 913 LYS cc_start: 0.8428 (ptpp) cc_final: 0.8110 (pttm) REVERT: P 952 GLU cc_start: 0.6698 (pm20) cc_final: 0.6316 (pm20) REVERT: P 999 LYS cc_start: 0.8382 (ttmt) cc_final: 0.8043 (ttmm) REVERT: P 1003 LYS cc_start: 0.8337 (mttt) cc_final: 0.7785 (mttm) REVERT: P 1004 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.5757 (mp) REVERT: P 1005 GLU cc_start: 0.6981 (pp20) cc_final: 0.6644 (pp20) REVERT: P 1018 VAL cc_start: 0.8989 (m) cc_final: 0.8655 (t) REVERT: P 1021 MET cc_start: 0.6907 (mmm) cc_final: 0.6215 (mmm) REVERT: P 1037 PHE cc_start: 0.8243 (p90) cc_final: 0.7762 (p90) REVERT: P 1043 MET cc_start: 0.7474 (tpp) cc_final: 0.7192 (tpp) REVERT: P 1049 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6868 (tm-30) REVERT: P 1059 LYS cc_start: 0.7895 (tmtt) cc_final: 0.7362 (tmtt) REVERT: P 1085 LYS cc_start: 0.7858 (mmmm) cc_final: 0.7604 (mmmm) REVERT: P 1189 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7203 (pm20) REVERT: P 1202 SER cc_start: 0.7998 (m) cc_final: 0.7592 (p) REVERT: P 1258 PHE cc_start: 0.7305 (t80) cc_final: 0.7059 (t80) REVERT: P 1263 LYS cc_start: 0.8008 (tppt) cc_final: 0.7366 (tptm) REVERT: P 1267 ASP cc_start: 0.7481 (t70) cc_final: 0.7123 (t0) REVERT: P 1271 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7720 (pp20) REVERT: P 1272 GLN cc_start: 0.8848 (tp40) cc_final: 0.8370 (tp-100) REVERT: P 1275 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7443 (mm-30) REVERT: P 1289 LYS cc_start: 0.8523 (mttt) cc_final: 0.8029 (mttt) REVERT: P 1332 ASP cc_start: 0.7074 (t0) cc_final: 0.6813 (t0) outliers start: 27 outliers final: 16 residues processed: 236 average time/residue: 0.1036 time to fit residues: 32.3295 Evaluate side-chains 232 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 41 HIS Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 217 SER Chi-restraints excluded: chain P residue 226 ILE Chi-restraints excluded: chain P residue 329 HIS Chi-restraints excluded: chain P residue 397 ASP Chi-restraints excluded: chain P residue 727 LEU Chi-restraints excluded: chain P residue 770 THR Chi-restraints excluded: chain P residue 838 VAL Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 921 LEU Chi-restraints excluded: chain P residue 1004 LEU Chi-restraints excluded: chain P residue 1008 PHE Chi-restraints excluded: chain P residue 1080 PHE Chi-restraints excluded: chain P residue 1189 GLU Chi-restraints excluded: chain P residue 1206 LEU Chi-restraints excluded: chain P residue 1278 LYS Chi-restraints excluded: chain P residue 1280 CYS Chi-restraints excluded: chain P residue 1311 HIS Chi-restraints excluded: chain P residue 1349 HIS Chi-restraints excluded: chain P residue 1359 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: [85, 56, 68, 66, 92, 65, 1, 81, 25, 67, 10] chunk 85 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN ** P 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1041 ASN ** 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 = 0.4233 r_free = 0.4233 target = 0.165383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.141897 restraints weight = 14653.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.147170 restraints weight = 8431.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.150632 restraints weight = 5471.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.153109 restraints weight = 3877.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.154838 restraints weight = 2940.363| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8511 Z= 0.150 Angle : 0.622 12.607 11437 Z= 0.317 Chirality : 0.043 0.190 1273 Planarity : 0.003 0.038 1465 Dihedral : 5.170 57.239 1133 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.83 % Allowed : 18.82 % Favored : 78.35 % 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: -0.45 (0.26), residues: 1022 helix: 0.85 (0.24), residues: 502 sheet: -2.20 (0.47), residues: 88 loop : -1.21 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P1171 TYR 0.010 0.001 TYR P 814 PHE 0.016 0.001 PHE P1235 TRP 0.006 0.001 TRP P1074 HIS 0.014 0.001 HIS P1349 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 8510) covalent geometry : angle 0.62185 / 0.32 (11435) SS BOND : bond 0.00190 / 0.10 ( 1) SS BOND : angle 0.42311 / 0.25 ( 2) hydrogen bonds : bond 0.03932 / 2.56 ( 387) hydrogen bonds : angle 4.75741 / 3.32 ( 1107) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 30 LYS cc_start: 0.6920 (ttmt) cc_final: 0.6161 (ttmt) REVERT: P 54 ASP cc_start: 0.7349 (t0) cc_final: 0.6886 (t0) REVERT: P 63 ARG cc_start: 0.7704 (ttm170) cc_final: 0.7322 (ttm-80) REVERT: P 69 ARG cc_start: 0.7258 (ttp80) cc_final: 0.7048 (tmm160) REVERT: P 140 LYS cc_start: 0.8399 (tttt) cc_final: 0.7974 (tmmt) REVERT: P 156 LEU cc_start: 0.8486 (mt) cc_final: 0.8211 (mt) REVERT: P 163 LYS cc_start: 0.8354 (tppt) cc_final: 0.7249 (tppt) REVERT: P 179 SER cc_start: 0.8092 (t) cc_final: 0.7733 (p) REVERT: P 183 LYS cc_start: 0.7602 (ptpp) cc_final: 0.7014 (ptmm) REVERT: P 207 ASP cc_start: 0.7644 (t0) cc_final: 0.6979 (p0) REVERT: P 220 ARG cc_start: 0.7834 (mmm160) cc_final: 0.7478 (mmm160) REVERT: P 226 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7552 (mm) REVERT: P 246 LEU cc_start: 0.7526 (mm) cc_final: 0.7232 (mp) REVERT: P 263 LYS cc_start: 0.7819 (mmtp) cc_final: 0.6941 (mmtm) REVERT: P 276 ASP cc_start: 0.6954 (m-30) cc_final: 0.6172 (m-30) REVERT: P 288 ASP cc_start: 0.7076 (m-30) cc_final: 0.6461 (m-30) REVERT: P 323 LYS cc_start: 0.8515 (mmtt) cc_final: 0.8080 (mmmm) REVERT: P 401 LYS cc_start: 0.7899 (mttt) cc_final: 0.7552 (mttp) REVERT: P 416 LEU cc_start: 0.8141 (tp) cc_final: 0.7388 (tp) REVERT: P 420 HIS cc_start: 0.7919 (m-70) cc_final: 0.7651 (m-70) REVERT: P 430 TYR cc_start: 0.7894 (m-10) cc_final: 0.7520 (m-10) REVERT: P 434 LYS cc_start: 0.8534 (mttt) cc_final: 0.8066 (mttm) REVERT: P 722 GLU cc_start: 0.7393 (pp20) cc_final: 0.6591 (pp20) REVERT: P 754 HIS cc_start: 0.6022 (m-70) cc_final: 0.5551 (m-70) REVERT: P 803 ASN cc_start: 0.7918 (p0) cc_final: 0.7397 (p0) REVERT: P 813 LEU cc_start: 0.8207 (mm) cc_final: 0.7866 (mm) REVERT: P 820 ARG cc_start: 0.7518 (mmm160) cc_final: 0.7201 (mmm160) REVERT: P 836 TYR cc_start: 0.7346 (m-10) cc_final: 0.7068 (m-10) REVERT: P 842 VAL cc_start: 0.8464 (t) cc_final: 0.8115 (m) REVERT: P 849 ASP cc_start: 0.8099 (t0) cc_final: 0.7795 (t0) REVERT: P 853 ASP cc_start: 0.7224 (t0) cc_final: 0.6672 (t0) REVERT: P 874 GLU cc_start: 0.8372 (mp0) cc_final: 0.7960 (mp0) REVERT: P 890 LYS cc_start: 0.8562 (mttm) cc_final: 0.8336 (mmtt) REVERT: P 901 THR cc_start: 0.8291 (p) cc_final: 0.7808 (t) REVERT: P 913 LYS cc_start: 0.8519 (ptpp) cc_final: 0.8217 (pttm) REVERT: P 952 GLU cc_start: 0.6727 (pm20) cc_final: 0.6384 (pm20) REVERT: P 961 LYS cc_start: 0.6221 (tmmt) cc_final: 0.5693 (tmtt) REVERT: P 965 ASP cc_start: 0.6071 (m-30) cc_final: 0.5809 (m-30) REVERT: P 999 LYS cc_start: 0.8357 (ttmt) cc_final: 0.8001 (ttmm) REVERT: P 1003 LYS cc_start: 0.8263 (mttt) cc_final: 0.7712 (mttp) REVERT: P 1004 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.5922 (mp) REVERT: P 1005 GLU cc_start: 0.6959 (pp20) cc_final: 0.6700 (pp20) REVERT: P 1018 VAL cc_start: 0.8967 (m) cc_final: 0.8613 (t) REVERT: P 1021 MET cc_start: 0.6846 (mmm) cc_final: 0.6208 (mmm) REVERT: P 1037 PHE cc_start: 0.8219 (p90) cc_final: 0.7764 (p90) REVERT: P 1043 MET cc_start: 0.7478 (tpp) cc_final: 0.7164 (tpp) REVERT: P 1049 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6844 (tm-30) REVERT: P 1059 LYS cc_start: 0.7871 (tmtt) cc_final: 0.7354 (tmtt) REVERT: P 1085 LYS cc_start: 0.7861 (mmmm) cc_final: 0.7616 (mmmm) REVERT: P 1189 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7341 (pm20) REVERT: P 1202 SER cc_start: 0.8001 (m) cc_final: 0.7584 (p) REVERT: P 1258 PHE cc_start: 0.7289 (t80) cc_final: 0.7071 (t80) REVERT: P 1267 ASP cc_start: 0.7511 (t70) cc_final: 0.7138 (t0) REVERT: P 1271 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7707 (pp20) REVERT: P 1272 GLN cc_start: 0.8796 (tp40) cc_final: 0.8322 (tp-100) REVERT: P 1275 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7436 (mm-30) REVERT: P 1288 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7742 (m-30) REVERT: P 1289 LYS cc_start: 0.8512 (mttt) cc_final: 0.8013 (mttt) REVERT: P 1332 ASP cc_start: 0.7098 (t0) cc_final: 0.6868 (t0) REVERT: P 1333 ARG cc_start: 0.7626 (mtt90) cc_final: 0.7345 (mtt90) REVERT: P 1346 THR cc_start: 0.6434 (OUTLIER) cc_final: 0.6031 (t) outliers start: 26 outliers final: 17 residues processed: 231 average time/residue: 0.1094 time to fit residues: 33.2211 Evaluate side-chains 229 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 41 HIS Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 217 SER Chi-restraints excluded: chain P residue 226 ILE Chi-restraints excluded: chain P residue 301 LEU Chi-restraints excluded: chain P residue 329 HIS Chi-restraints excluded: chain P residue 397 ASP Chi-restraints excluded: chain P residue 838 VAL Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 921 LEU Chi-restraints excluded: chain P residue 1004 LEU Chi-restraints excluded: chain P residue 1008 PHE Chi-restraints excluded: chain P residue 1080 PHE Chi-restraints excluded: chain P residue 1189 GLU Chi-restraints excluded: chain P residue 1206 LEU Chi-restraints excluded: chain P residue 1278 LYS Chi-restraints excluded: chain P residue 1280 CYS Chi-restraints excluded: chain P residue 1288 ASP Chi-restraints excluded: chain P residue 1311 HIS Chi-restraints excluded: chain P residue 1346 THR Chi-restraints excluded: chain P residue 1359 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: [16, 24, 70, 100, 59, 34, 36, 39, 85, 18, 50] chunk 16 optimal weight: 0.0070 chunk 24 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 50 optimal weight: 0.0270 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.166751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.143014 restraints weight = 14932.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.148216 restraints weight = 8430.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.151940 restraints weight = 5463.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.154594 restraints weight = 3806.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.156324 restraints weight = 2841.607| |-----------------------------------------------------------------------------| r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8511 Z= 0.118 Angle : 0.624 12.814 11437 Z= 0.316 Chirality : 0.043 0.215 1273 Planarity : 0.003 0.040 1465 Dihedral : 5.068 58.215 1133 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.39 % Allowed : 20.24 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.26), residues: 1022 helix: 0.93 (0.24), residues: 498 sheet: -1.82 (0.52), residues: 78 loop : -1.11 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P1019 TYR 0.009 0.001 TYR P 814 PHE 0.019 0.001 PHE P1235 TRP 0.006 0.001 TRP P1074 HIS 0.004 0.001 HIS P 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 8510) covalent geometry : angle 0.62427 / 0.32 (11435) SS BOND : bond 0.00009 / 0.00 ( 1) SS BOND : angle 0.16372 / 0.10 ( 2) hydrogen bonds : bond 0.03699 / 2.41 ( 387) hydrogen bonds : angle 4.69534 / 3.29 ( 1107) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 30 LYS cc_start: 0.6924 (ttmt) cc_final: 0.5884 (ttmt) REVERT: P 54 ASP cc_start: 0.7305 (t0) cc_final: 0.7000 (t0) REVERT: P 63 ARG cc_start: 0.7739 (ttm170) cc_final: 0.7334 (ttm-80) REVERT: P 69 ARG cc_start: 0.7206 (ttp80) cc_final: 0.6968 (tmm160) REVERT: P 77 ASN cc_start: 0.8052 (t0) cc_final: 0.7306 (t0) REVERT: P 140 LYS cc_start: 0.8159 (tttt) cc_final: 0.7698 (tmmt) REVERT: P 156 LEU cc_start: 0.8496 (mt) cc_final: 0.8158 (mt) REVERT: P 163 LYS cc_start: 0.8233 (tppt) cc_final: 0.7582 (tppt) REVERT: P 179 SER cc_start: 0.8000 (t) cc_final: 0.7648 (p) REVERT: P 183 LYS cc_start: 0.7619 (ptpp) cc_final: 0.7145 (ptmm) REVERT: P 207 ASP cc_start: 0.7677 (t0) cc_final: 0.6975 (p0) REVERT: P 220 ARG cc_start: 0.7752 (mmm160) cc_final: 0.7426 (mmm160) REVERT: P 226 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7510 (mm) REVERT: P 246 LEU cc_start: 0.7481 (mm) cc_final: 0.7156 (mp) REVERT: P 263 LYS cc_start: 0.7753 (mmtp) cc_final: 0.6864 (mmtm) REVERT: P 276 ASP cc_start: 0.6905 (m-30) cc_final: 0.6206 (m-30) REVERT: P 288 ASP cc_start: 0.7041 (m-30) cc_final: 0.6752 (m-30) REVERT: P 291 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7745 (mp) REVERT: P 323 LYS cc_start: 0.8534 (mmtt) cc_final: 0.7760 (mmmm) REVERT: P 326 ASP cc_start: 0.8139 (m-30) cc_final: 0.7897 (m-30) REVERT: P 398 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7603 (tp) REVERT: P 401 LYS cc_start: 0.7861 (mttt) cc_final: 0.7456 (mttp) REVERT: P 416 LEU cc_start: 0.8197 (tp) cc_final: 0.7473 (tp) REVERT: P 420 HIS cc_start: 0.7882 (m-70) cc_final: 0.7588 (m-70) REVERT: P 430 TYR cc_start: 0.7937 (m-10) cc_final: 0.7504 (m-10) REVERT: P 434 LYS cc_start: 0.8528 (mttt) cc_final: 0.8255 (mttt) REVERT: P 722 GLU cc_start: 0.7324 (pp20) cc_final: 0.6513 (pp20) REVERT: P 754 HIS cc_start: 0.5967 (m-70) cc_final: 0.5576 (m170) REVERT: P 781 MET cc_start: 0.8151 (tpt) cc_final: 0.7707 (tpt) REVERT: P 813 LEU cc_start: 0.8041 (mm) cc_final: 0.7740 (mm) REVERT: P 820 ARG cc_start: 0.7448 (mmm160) cc_final: 0.7204 (mmm160) REVERT: P 836 TYR cc_start: 0.7283 (m-10) cc_final: 0.7055 (m-10) REVERT: P 842 VAL cc_start: 0.8483 (t) cc_final: 0.8108 (m) REVERT: P 849 ASP cc_start: 0.8273 (t0) cc_final: 0.7955 (t0) REVERT: P 853 ASP cc_start: 0.7148 (t0) cc_final: 0.6570 (t0) REVERT: P 873 GLU cc_start: 0.8678 (mp0) cc_final: 0.8335 (mm-30) REVERT: P 874 GLU cc_start: 0.8357 (mp0) cc_final: 0.8009 (mp0) REVERT: P 890 LYS cc_start: 0.8536 (mttm) cc_final: 0.8318 (mmtt) REVERT: P 901 THR cc_start: 0.8136 (p) cc_final: 0.7682 (t) REVERT: P 913 LYS cc_start: 0.8397 (ptpp) cc_final: 0.8082 (pttm) REVERT: P 952 GLU cc_start: 0.6728 (pm20) cc_final: 0.6395 (pm20) REVERT: P 961 LYS cc_start: 0.6090 (tmmt) cc_final: 0.5746 (tmmt) REVERT: P 965 ASP cc_start: 0.6036 (m-30) cc_final: 0.5657 (m-30) REVERT: P 999 LYS cc_start: 0.8384 (ttmt) cc_final: 0.8015 (ttmm) REVERT: P 1003 LYS cc_start: 0.8241 (mttt) cc_final: 0.7688 (mttm) REVERT: P 1004 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6149 (mm) REVERT: P 1005 GLU cc_start: 0.6960 (pp20) cc_final: 0.6662 (pp20) REVERT: P 1018 VAL cc_start: 0.9004 (m) cc_final: 0.8634 (t) REVERT: P 1021 MET cc_start: 0.6860 (mmm) cc_final: 0.6164 (mmm) REVERT: P 1037 PHE cc_start: 0.8203 (p90) cc_final: 0.7982 (p90) REVERT: P 1043 MET cc_start: 0.7413 (tpp) cc_final: 0.7163 (tpp) REVERT: P 1049 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6801 (tm-30) REVERT: P 1059 LYS cc_start: 0.7871 (tmtt) cc_final: 0.7314 (tmtt) REVERT: P 1085 LYS cc_start: 0.7575 (mmmm) cc_final: 0.7330 (mmmm) REVERT: P 1097 LYS cc_start: 0.7509 (pttt) cc_final: 0.7198 (pttm) REVERT: P 1189 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7165 (pm20) REVERT: P 1202 SER cc_start: 0.7986 (m) cc_final: 0.7565 (p) REVERT: P 1258 PHE cc_start: 0.7418 (t80) cc_final: 0.7206 (t80) REVERT: P 1267 ASP cc_start: 0.7513 (t70) cc_final: 0.7155 (t0) REVERT: P 1271 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7659 (pp20) REVERT: P 1272 GLN cc_start: 0.8699 (tp40) cc_final: 0.8200 (tp-100) REVERT: P 1275 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7394 (mm-30) REVERT: P 1289 LYS cc_start: 0.8356 (mttt) cc_final: 0.7815 (mttt) REVERT: P 1332 ASP cc_start: 0.7065 (t0) cc_final: 0.6790 (t0) REVERT: P 1333 ARG cc_start: 0.7633 (mtt90) cc_final: 0.7332 (mtt90) REVERT: P 1346 THR cc_start: 0.6395 (OUTLIER) cc_final: 0.5985 (t) outliers start: 22 outliers final: 15 residues processed: 229 average time/residue: 0.0990 time to fit residues: 30.3194 Evaluate side-chains 229 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 41 HIS Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 217 SER Chi-restraints excluded: chain P residue 226 ILE Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 329 HIS Chi-restraints excluded: chain P residue 397 ASP Chi-restraints excluded: chain P residue 398 LEU Chi-restraints excluded: chain P residue 838 VAL Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 921 LEU Chi-restraints excluded: chain P residue 1004 LEU Chi-restraints excluded: chain P residue 1008 PHE Chi-restraints excluded: chain P residue 1080 PHE Chi-restraints excluded: chain P residue 1189 GLU Chi-restraints excluded: chain P residue 1206 LEU Chi-restraints excluded: chain P residue 1278 LYS Chi-restraints excluded: chain P residue 1280 CYS Chi-restraints excluded: chain P residue 1311 HIS Chi-restraints excluded: chain P residue 1346 THR Chi-restraints excluded: chain P residue 1359 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: [14, 84, 89, 86, 28, 74, 56, 73, 19, 60, 51] chunk 14 optimal weight: 0.4980 chunk 84 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 60 optimal weight: 0.0770 chunk 51 optimal weight: 1.9990 overall best weight: 1.1144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1041 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 = 0.4233 r_free = 0.4233 target = 0.165586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.142184 restraints weight = 14716.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.147235 restraints weight = 8423.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.150849 restraints weight = 5493.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.153224 restraints weight = 3881.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.155080 restraints weight = 2952.601| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8511 Z= 0.146 Angle : 0.647 13.173 11437 Z= 0.327 Chirality : 0.044 0.200 1273 Planarity : 0.003 0.040 1465 Dihedral : 5.118 58.244 1133 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.94 % Allowed : 20.13 % Favored : 76.93 % 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: -0.38 (0.26), residues: 1022 helix: 0.81 (0.24), residues: 501 sheet: -1.85 (0.51), residues: 78 loop : -1.15 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P1019 TYR 0.010 0.001 TYR P 988 PHE 0.016 0.001 PHE P1235 TRP 0.005 0.001 TRP P1074 HIS 0.005 0.001 HIS P 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 ( 8510) covalent geometry : angle 0.64706 / 0.33 (11435) SS BOND : bond 0.00155 / 0.08 ( 1) SS BOND : angle 0.29723 / 0.17 ( 2) hydrogen bonds : bond 0.03842 / 2.51 ( 387) hydrogen bonds : angle 4.76434 / 3.32 ( 1107) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 30 LYS cc_start: 0.6914 (ttmt) cc_final: 0.6298 (ttmt) REVERT: P 54 ASP cc_start: 0.7303 (t0) cc_final: 0.6951 (t0) REVERT: P 63 ARG cc_start: 0.7712 (ttm170) cc_final: 0.7312 (ttm-80) REVERT: P 69 ARG cc_start: 0.7273 (ttp80) cc_final: 0.7009 (tmm160) REVERT: P 77 ASN cc_start: 0.7868 (t0) cc_final: 0.6533 (t0) REVERT: P 81 TYR cc_start: 0.6509 (m-80) cc_final: 0.6227 (m-80) REVERT: P 137 HIS cc_start: 0.6811 (m-70) cc_final: 0.6319 (m-70) REVERT: P 140 LYS cc_start: 0.8340 (tttt) cc_final: 0.7827 (tmmt) REVERT: P 156 LEU cc_start: 0.8479 (mt) cc_final: 0.8157 (mt) REVERT: P 163 LYS cc_start: 0.8273 (tppt) cc_final: 0.7606 (tppt) REVERT: P 180 ASP cc_start: 0.6945 (t0) cc_final: 0.6506 (t70) REVERT: P 183 LYS cc_start: 0.7606 (ptpp) cc_final: 0.7256 (ptmm) REVERT: P 207 ASP cc_start: 0.7632 (t0) cc_final: 0.6982 (p0) REVERT: P 220 ARG cc_start: 0.7788 (mmm160) cc_final: 0.7442 (mmm160) REVERT: P 226 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7513 (mm) REVERT: P 237 LEU cc_start: 0.7089 (tp) cc_final: 0.6718 (tp) REVERT: P 246 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7204 (mp) REVERT: P 263 LYS cc_start: 0.7786 (mmtp) cc_final: 0.6905 (mmtm) REVERT: P 276 ASP cc_start: 0.6827 (m-30) cc_final: 0.6031 (m-30) REVERT: P 288 ASP cc_start: 0.7080 (m-30) cc_final: 0.6465 (m-30) REVERT: P 291 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7748 (mp) REVERT: P 323 LYS cc_start: 0.8588 (mmtt) cc_final: 0.7555 (mmmm) REVERT: P 326 ASP cc_start: 0.8079 (m-30) cc_final: 0.7755 (m-30) REVERT: P 401 LYS cc_start: 0.7856 (mttt) cc_final: 0.7477 (mttp) REVERT: P 416 LEU cc_start: 0.8360 (tp) cc_final: 0.7697 (tp) REVERT: P 420 HIS cc_start: 0.7838 (m-70) cc_final: 0.7588 (m-70) REVERT: P 430 TYR cc_start: 0.7926 (m-10) cc_final: 0.7523 (m-10) REVERT: P 434 LYS cc_start: 0.8547 (mttt) cc_final: 0.8085 (mttm) REVERT: P 722 GLU cc_start: 0.7389 (pp20) cc_final: 0.6159 (pp20) REVERT: P 754 HIS cc_start: 0.6038 (m-70) cc_final: 0.5540 (m-70) REVERT: P 781 MET cc_start: 0.8040 (tpt) cc_final: 0.7657 (tpt) REVERT: P 813 LEU cc_start: 0.8184 (mm) cc_final: 0.7879 (mm) REVERT: P 820 ARG cc_start: 0.7439 (mmm160) cc_final: 0.7223 (mmm160) REVERT: P 836 TYR cc_start: 0.7305 (m-10) cc_final: 0.7056 (m-10) REVERT: P 842 VAL cc_start: 0.8472 (t) cc_final: 0.8116 (m) REVERT: P 849 ASP cc_start: 0.7779 (t0) cc_final: 0.7359 (t0) REVERT: P 853 ASP cc_start: 0.7176 (t0) cc_final: 0.6630 (t0) REVERT: P 874 GLU cc_start: 0.8327 (mp0) cc_final: 0.7958 (mp0) REVERT: P 885 GLN cc_start: 0.7567 (mt0) cc_final: 0.7257 (mp10) REVERT: P 901 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.7788 (t) REVERT: P 913 LYS cc_start: 0.8448 (ptpp) cc_final: 0.8216 (pttm) REVERT: P 952 GLU cc_start: 0.6762 (pm20) cc_final: 0.6539 (pm20) REVERT: P 961 LYS cc_start: 0.6160 (tmmt) cc_final: 0.5700 (tmmt) REVERT: P 965 ASP cc_start: 0.6057 (m-30) cc_final: 0.5681 (m-30) REVERT: P 999 LYS cc_start: 0.8409 (ttmt) cc_final: 0.8040 (ttmm) REVERT: P 1003 LYS cc_start: 0.8239 (mttt) cc_final: 0.7705 (mttp) REVERT: P 1004 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.5970 (mp) REVERT: P 1005 GLU cc_start: 0.6981 (pp20) cc_final: 0.6656 (pp20) REVERT: P 1018 VAL cc_start: 0.8976 (m) cc_final: 0.8601 (t) REVERT: P 1021 MET cc_start: 0.6798 (mmm) cc_final: 0.6168 (mmm) REVERT: P 1043 MET cc_start: 0.7484 (tpp) cc_final: 0.7200 (tpp) REVERT: P 1049 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6811 (tm-30) REVERT: P 1059 LYS cc_start: 0.7846 (tmtt) cc_final: 0.7314 (tmtt) REVERT: P 1085 LYS cc_start: 0.7595 (mmmm) cc_final: 0.7361 (mmmm) REVERT: P 1097 LYS cc_start: 0.7530 (pttt) cc_final: 0.7148 (pttm) REVERT: P 1202 SER cc_start: 0.7989 (m) cc_final: 0.7616 (p) REVERT: P 1258 PHE cc_start: 0.7481 (t80) cc_final: 0.7250 (t80) REVERT: P 1271 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7715 (pp20) REVERT: P 1272 GLN cc_start: 0.8666 (tp40) cc_final: 0.8126 (tp-100) REVERT: P 1275 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7186 (mm-30) REVERT: P 1288 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7812 (t70) REVERT: P 1289 LYS cc_start: 0.8489 (mttt) cc_final: 0.7891 (mttt) REVERT: P 1313 PHE cc_start: 0.8271 (m-80) cc_final: 0.7265 (m-80) REVERT: P 1332 ASP cc_start: 0.7041 (t0) cc_final: 0.6763 (t0) REVERT: P 1333 ARG cc_start: 0.7617 (mtt90) cc_final: 0.7308 (mtt90) REVERT: P 1346 THR cc_start: 0.6465 (OUTLIER) cc_final: 0.6056 (t) outliers start: 27 outliers final: 16 residues processed: 233 average time/residue: 0.1041 time to fit residues: 32.1325 Evaluate side-chains 234 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 211 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 41 HIS Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 217 SER Chi-restraints excluded: chain P residue 226 ILE Chi-restraints excluded: chain P residue 246 LEU Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 329 HIS Chi-restraints excluded: chain P residue 397 ASP Chi-restraints excluded: chain P residue 759 ILE Chi-restraints excluded: chain P residue 838 VAL Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 901 THR Chi-restraints excluded: chain P residue 921 LEU Chi-restraints excluded: chain P residue 1004 LEU Chi-restraints excluded: chain P residue 1008 PHE Chi-restraints excluded: chain P residue 1080 PHE Chi-restraints excluded: chain P residue 1225 GLU Chi-restraints excluded: chain P residue 1278 LYS Chi-restraints excluded: chain P residue 1280 CYS Chi-restraints excluded: chain P residue 1288 ASP Chi-restraints excluded: chain P residue 1311 HIS Chi-restraints excluded: chain P residue 1346 THR Chi-restraints excluded: chain P residue 1359 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: [22, 59, 21, 85, 30, 18, 80, 51, 54, 45, 23] chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1041 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 = 0.4211 r_free = 0.4211 target = 0.163633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.140327 restraints weight = 14777.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.145403 restraints weight = 8508.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.148931 restraints weight = 5529.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.151236 restraints weight = 3917.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.153012 restraints weight = 2990.566| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8511 Z= 0.198 Angle : 0.703 13.410 11437 Z= 0.359 Chirality : 0.045 0.206 1273 Planarity : 0.004 0.040 1465 Dihedral : 5.311 59.780 1133 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.83 % Allowed : 20.78 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.26), residues: 1022 helix: 0.71 (0.24), residues: 498 sheet: -1.95 (0.51), residues: 78 loop : -1.21 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P1019 TYR 0.022 0.001 TYR P 981 PHE 0.015 0.001 PHE P1235 TRP 0.010 0.002 TRP P 18 HIS 0.005 0.001 HIS P 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.20 ( 8510) covalent geometry : angle 0.70284 / 0.36 (11435) SS BOND : bond 0.00279 / 0.15 ( 1) SS BOND : angle 0.46314 / 0.27 ( 2) hydrogen bonds : bond 0.04140 / 2.73 ( 387) hydrogen bonds : angle 4.90398 / 3.40 ( 1107) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 30 LYS cc_start: 0.6967 (ttmt) cc_final: 0.6050 (ttmt) REVERT: P 54 ASP cc_start: 0.7334 (t0) cc_final: 0.6815 (t0) REVERT: P 63 ARG cc_start: 0.7641 (ttm170) cc_final: 0.7298 (ttm-80) REVERT: P 66 ARG cc_start: 0.7009 (ptp-110) cc_final: 0.6591 (ptp-170) REVERT: P 69 ARG cc_start: 0.7251 (ttp80) cc_final: 0.6907 (tmm160) REVERT: P 77 ASN cc_start: 0.7833 (t0) cc_final: 0.6391 (t0) REVERT: P 81 TYR cc_start: 0.6548 (m-80) cc_final: 0.6153 (m-80) REVERT: P 137 HIS cc_start: 0.6925 (m-70) cc_final: 0.6603 (m-70) REVERT: P 140 LYS cc_start: 0.8545 (tttt) cc_final: 0.8019 (ttpp) REVERT: P 156 LEU cc_start: 0.8550 (mt) cc_final: 0.8217 (mt) REVERT: P 163 LYS cc_start: 0.8317 (tppt) cc_final: 0.7694 (tppt) REVERT: P 179 SER cc_start: 0.8094 (t) cc_final: 0.7764 (p) REVERT: P 180 ASP cc_start: 0.7122 (t0) cc_final: 0.6467 (t70) REVERT: P 183 LYS cc_start: 0.7605 (ptpp) cc_final: 0.7272 (ptmm) REVERT: P 207 ASP cc_start: 0.7611 (t0) cc_final: 0.7017 (p0) REVERT: P 209 LYS cc_start: 0.7972 (tptt) cc_final: 0.7734 (mmtt) REVERT: P 220 ARG cc_start: 0.7815 (mmm160) cc_final: 0.7460 (mmm160) REVERT: P 226 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7561 (mm) REVERT: P 237 LEU cc_start: 0.7169 (tp) cc_final: 0.6762 (tp) REVERT: P 246 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7228 (mp) REVERT: P 263 LYS cc_start: 0.7573 (mmtp) cc_final: 0.6794 (mmtm) REVERT: P 275 LEU cc_start: 0.8094 (tp) cc_final: 0.7726 (tp) REVERT: P 288 ASP cc_start: 0.7117 (m-30) cc_final: 0.6543 (m-30) REVERT: P 291 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7773 (mp) REVERT: P 317 LEU cc_start: 0.7725 (tp) cc_final: 0.7469 (tp) REVERT: P 326 ASP cc_start: 0.8184 (m-30) cc_final: 0.7942 (m-30) REVERT: P 401 LYS cc_start: 0.7894 (mttt) cc_final: 0.7542 (mttp) REVERT: P 416 LEU cc_start: 0.8315 (tp) cc_final: 0.7684 (tp) REVERT: P 420 HIS cc_start: 0.7863 (m-70) cc_final: 0.7620 (m-70) REVERT: P 430 TYR cc_start: 0.7898 (m-10) cc_final: 0.7560 (m-10) REVERT: P 434 LYS cc_start: 0.8563 (mttt) cc_final: 0.8122 (mttm) REVERT: P 722 GLU cc_start: 0.7438 (pp20) cc_final: 0.6192 (pp20) REVERT: P 754 HIS cc_start: 0.6119 (m-70) cc_final: 0.5783 (m-70) REVERT: P 781 MET cc_start: 0.7996 (tpt) cc_final: 0.7576 (tpt) REVERT: P 813 LEU cc_start: 0.8209 (mm) cc_final: 0.7807 (mm) REVERT: P 817 GLN cc_start: 0.7969 (mp10) cc_final: 0.7574 (mp10) REVERT: P 836 TYR cc_start: 0.7340 (m-10) cc_final: 0.7081 (m-10) REVERT: P 842 VAL cc_start: 0.8452 (t) cc_final: 0.8063 (m) REVERT: P 853 ASP cc_start: 0.7194 (t0) cc_final: 0.6687 (t0) REVERT: P 873 GLU cc_start: 0.8582 (mp0) cc_final: 0.8152 (mm-30) REVERT: P 874 GLU cc_start: 0.8354 (mp0) cc_final: 0.8016 (mp0) REVERT: P 901 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.7916 (t) REVERT: P 902 LYS cc_start: 0.7840 (ttmt) cc_final: 0.7488 (ttpp) REVERT: P 913 LYS cc_start: 0.8565 (ptpp) cc_final: 0.8224 (pttm) REVERT: P 961 LYS cc_start: 0.6299 (tmmt) cc_final: 0.5919 (tmmt) REVERT: P 999 LYS cc_start: 0.8366 (ttmt) cc_final: 0.8003 (ttmm) REVERT: P 1003 LYS cc_start: 0.8305 (mttt) cc_final: 0.7713 (mttm) REVERT: P 1004 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.6532 (mm) REVERT: P 1005 GLU cc_start: 0.6969 (pp20) cc_final: 0.6718 (pp20) REVERT: P 1018 VAL cc_start: 0.8887 (m) cc_final: 0.8644 (t) REVERT: P 1021 MET cc_start: 0.6816 (mmm) cc_final: 0.6194 (mmm) REVERT: P 1043 MET cc_start: 0.7541 (tpp) cc_final: 0.7235 (tpp) REVERT: P 1049 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6838 (tm-30) REVERT: P 1059 LYS cc_start: 0.7849 (tmtt) cc_final: 0.7329 (tmtt) REVERT: P 1085 LYS cc_start: 0.7620 (mmmm) cc_final: 0.7386 (mmmm) REVERT: P 1097 LYS cc_start: 0.7542 (pttt) cc_final: 0.7211 (pttm) REVERT: P 1202 SER cc_start: 0.8094 (m) cc_final: 0.7610 (p) REVERT: P 1258 PHE cc_start: 0.7363 (t80) cc_final: 0.7143 (t80) REVERT: P 1271 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7608 (pp20) REVERT: P 1272 GLN cc_start: 0.8746 (tp40) cc_final: 0.8427 (tp-100) REVERT: P 1275 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7427 (mm-30) REVERT: P 1289 LYS cc_start: 0.8496 (mttt) cc_final: 0.7996 (mttt) REVERT: P 1313 PHE cc_start: 0.8287 (m-80) cc_final: 0.7490 (m-80) REVERT: P 1332 ASP cc_start: 0.7079 (t0) cc_final: 0.6790 (t0) REVERT: P 1333 ARG cc_start: 0.7614 (mtt90) cc_final: 0.7321 (mtt90) REVERT: P 1346 THR cc_start: 0.6431 (OUTLIER) cc_final: 0.6025 (t) outliers start: 26 outliers final: 18 residues processed: 231 average time/residue: 0.1083 time to fit residues: 32.9480 Evaluate side-chains 235 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 41 HIS Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 217 SER Chi-restraints excluded: chain P residue 226 ILE Chi-restraints excluded: chain P residue 246 LEU Chi-restraints excluded: chain P residue 260 GLU Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 329 HIS Chi-restraints excluded: chain P residue 397 ASP Chi-restraints excluded: chain P residue 759 ILE Chi-restraints excluded: chain P residue 838 VAL Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 901 THR Chi-restraints excluded: chain P residue 921 LEU Chi-restraints excluded: chain P residue 1004 LEU Chi-restraints excluded: chain P residue 1008 PHE Chi-restraints excluded: chain P residue 1080 PHE Chi-restraints excluded: chain P residue 1225 GLU Chi-restraints excluded: chain P residue 1278 LYS Chi-restraints excluded: chain P residue 1279 ARG Chi-restraints excluded: chain P residue 1280 CYS Chi-restraints excluded: chain P residue 1311 HIS Chi-restraints excluded: chain P residue 1346 THR Chi-restraints excluded: chain P residue 1359 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: [68, 28, 53, 41, 97, 38, 44, 21, 72, 81, 14] chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 0.0670 chunk 41 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 81 optimal weight: 0.0980 chunk 14 optimal weight: 0.4980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.167689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.144566 restraints weight = 14719.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.149639 restraints weight = 8434.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.153219 restraints weight = 5479.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.155715 restraints weight = 3845.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.157358 restraints weight = 2895.654| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8511 Z= 0.128 Angle : 0.688 13.623 11437 Z= 0.347 Chirality : 0.044 0.196 1273 Planarity : 0.003 0.041 1465 Dihedral : 5.204 59.715 1133 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.50 % Allowed : 21.33 % Favored : 76.17 % 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: -0.37 (0.26), residues: 1022 helix: 0.84 (0.24), residues: 496 sheet: -1.80 (0.51), residues: 78 loop : -1.15 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P1019 TYR 0.017 0.001 TYR P 882 PHE 0.012 0.001 PHE P1235 TRP 0.008 0.002 TRP P 883 HIS 0.003 0.001 HIS P1349 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 8510) covalent geometry : angle 0.68802 / 0.35 (11435) SS BOND : bond 0.00007 / 0.00 ( 1) SS BOND : angle 0.17441 / 0.10 ( 2) hydrogen bonds : bond 0.03735 / 2.46 ( 387) hydrogen bonds : angle 4.73663 / 3.30 ( 1107) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 215 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 30 LYS cc_start: 0.6991 (ttmt) cc_final: 0.6136 (ttmt) REVERT: P 54 ASP cc_start: 0.7290 (t0) cc_final: 0.6935 (t0) REVERT: P 63 ARG cc_start: 0.7694 (ttm170) cc_final: 0.7314 (ttm-80) REVERT: P 69 ARG cc_start: 0.7188 (ttp80) cc_final: 0.6857 (tmm160) REVERT: P 77 ASN cc_start: 0.8068 (t0) cc_final: 0.6813 (t0) REVERT: P 81 TYR cc_start: 0.6471 (m-80) cc_final: 0.6187 (m-80) REVERT: P 137 HIS cc_start: 0.7342 (m-70) cc_final: 0.7046 (m-70) REVERT: P 140 LYS cc_start: 0.8579 (tttt) cc_final: 0.7949 (tmmt) REVERT: P 143 VAL cc_start: 0.8060 (t) cc_final: 0.7795 (p) REVERT: P 156 LEU cc_start: 0.8469 (mt) cc_final: 0.8134 (mt) REVERT: P 163 LYS cc_start: 0.8227 (tppt) cc_final: 0.7621 (tppt) REVERT: P 180 ASP cc_start: 0.6981 (t0) cc_final: 0.6454 (t70) REVERT: P 183 LYS cc_start: 0.7576 (ptpp) cc_final: 0.7257 (ptmm) REVERT: P 207 ASP cc_start: 0.7659 (t0) cc_final: 0.7289 (t0) REVERT: P 220 ARG cc_start: 0.7632 (mmm160) cc_final: 0.7346 (mmm160) REVERT: P 226 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7516 (mm) REVERT: P 246 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7190 (mp) REVERT: P 263 LYS cc_start: 0.7743 (mmtp) cc_final: 0.6928 (mmtm) REVERT: P 275 LEU cc_start: 0.8105 (tp) cc_final: 0.7659 (tp) REVERT: P 288 ASP cc_start: 0.7026 (m-30) cc_final: 0.6742 (m-30) REVERT: P 291 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7802 (mp) REVERT: P 323 LYS cc_start: 0.8498 (mmtt) cc_final: 0.8210 (mmtt) REVERT: P 326 ASP cc_start: 0.8197 (m-30) cc_final: 0.7920 (m-30) REVERT: P 401 LYS cc_start: 0.7838 (mttt) cc_final: 0.7499 (mttp) REVERT: P 416 LEU cc_start: 0.8238 (tp) cc_final: 0.7601 (tp) REVERT: P 420 HIS cc_start: 0.7721 (m-70) cc_final: 0.7485 (m-70) REVERT: P 430 TYR cc_start: 0.7805 (m-10) cc_final: 0.7503 (m-10) REVERT: P 434 LYS cc_start: 0.8507 (mttt) cc_final: 0.8269 (mttt) REVERT: P 722 GLU cc_start: 0.7262 (pp20) cc_final: 0.6434 (pp20) REVERT: P 754 HIS cc_start: 0.5949 (m-70) cc_final: 0.5506 (m170) REVERT: P 781 MET cc_start: 0.7862 (tpt) cc_final: 0.7445 (tpt) REVERT: P 813 LEU cc_start: 0.8012 (mm) cc_final: 0.7706 (mm) REVERT: P 834 SER cc_start: 0.8234 (t) cc_final: 0.7856 (p) REVERT: P 836 TYR cc_start: 0.7282 (m-10) cc_final: 0.7072 (m-10) REVERT: P 842 VAL cc_start: 0.8452 (t) cc_final: 0.8088 (m) REVERT: P 849 ASP cc_start: 0.8334 (t0) cc_final: 0.8004 (t0) REVERT: P 853 ASP cc_start: 0.7182 (t0) cc_final: 0.6515 (t0) REVERT: P 873 GLU cc_start: 0.8659 (mp0) cc_final: 0.8380 (mm-30) REVERT: P 874 GLU cc_start: 0.8243 (mp0) cc_final: 0.7890 (mp0) REVERT: P 901 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7613 (t) REVERT: P 913 LYS cc_start: 0.8424 (ptpp) cc_final: 0.8108 (pttm) REVERT: P 939 MET cc_start: 0.6928 (ptp) cc_final: 0.6671 (ptp) REVERT: P 952 GLU cc_start: 0.6894 (pm20) cc_final: 0.6546 (pm20) REVERT: P 998 ILE cc_start: 0.8585 (tt) cc_final: 0.8373 (tt) REVERT: P 999 LYS cc_start: 0.8404 (ttmt) cc_final: 0.7993 (ttmm) REVERT: P 1003 LYS cc_start: 0.8156 (mttt) cc_final: 0.7595 (mtpp) REVERT: P 1004 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6201 (mm) REVERT: P 1005 GLU cc_start: 0.6978 (pp20) cc_final: 0.6743 (pp20) REVERT: P 1018 VAL cc_start: 0.8900 (m) cc_final: 0.8623 (t) REVERT: P 1021 MET cc_start: 0.6773 (mmm) cc_final: 0.6150 (mmm) REVERT: P 1043 MET cc_start: 0.7367 (tpp) cc_final: 0.7138 (tpp) REVERT: P 1049 GLU cc_start: 0.7032 (tm-30) cc_final: 0.6712 (tm-30) REVERT: P 1059 LYS cc_start: 0.7836 (tmtt) cc_final: 0.7307 (tmtt) REVERT: P 1097 LYS cc_start: 0.7472 (pttt) cc_final: 0.7157 (pttm) REVERT: P 1202 SER cc_start: 0.7967 (m) cc_final: 0.7560 (p) REVERT: P 1258 PHE cc_start: 0.7459 (t80) cc_final: 0.7249 (t80) REVERT: P 1267 ASP cc_start: 0.7507 (t70) cc_final: 0.7190 (t0) REVERT: P 1271 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7967 (tm-30) REVERT: P 1272 GLN cc_start: 0.8610 (tp40) cc_final: 0.8025 (tp-100) REVERT: P 1275 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7401 (mm-30) REVERT: P 1288 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7849 (t70) REVERT: P 1289 LYS cc_start: 0.8318 (mttt) cc_final: 0.7679 (mttt) REVERT: P 1313 PHE cc_start: 0.8173 (m-80) cc_final: 0.7191 (m-80) REVERT: P 1332 ASP cc_start: 0.6842 (t0) cc_final: 0.6551 (t0) REVERT: P 1333 ARG cc_start: 0.7549 (mtt90) cc_final: 0.7203 (mtt90) REVERT: P 1346 THR cc_start: 0.6350 (OUTLIER) cc_final: 0.5944 (t) outliers start: 23 outliers final: 16 residues processed: 232 average time/residue: 0.1047 time to fit residues: 31.9835 Evaluate side-chains 240 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 41 HIS Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 217 SER Chi-restraints excluded: chain P residue 226 ILE Chi-restraints excluded: chain P residue 246 LEU Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 329 HIS Chi-restraints excluded: chain P residue 397 ASP Chi-restraints excluded: chain P residue 759 ILE Chi-restraints excluded: chain P residue 838 VAL Chi-restraints excluded: chain P residue 870 VAL Chi-restraints excluded: chain P residue 901 THR Chi-restraints excluded: chain P residue 921 LEU Chi-restraints excluded: chain P residue 1004 LEU Chi-restraints excluded: chain P residue 1008 PHE Chi-restraints excluded: chain P residue 1080 PHE Chi-restraints excluded: chain P residue 1225 GLU Chi-restraints excluded: chain P residue 1278 LYS Chi-restraints excluded: chain P residue 1280 CYS Chi-restraints excluded: chain P residue 1288 ASP Chi-restraints excluded: chain P residue 1311 HIS Chi-restraints excluded: chain P residue 1346 THR Chi-restraints excluded: chain P residue 1359 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: [5, 56, 66, 47, 61, 20, 78, 25, 54, 89, 24] chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 885 GLN ** P 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1091 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 = 0.4247 r_free = 0.4247 target = 0.167250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.144339 restraints weight = 14710.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.149502 restraints weight = 8394.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.153090 restraints weight = 5434.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.155536 restraints weight = 3803.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.157237 restraints weight = 2850.609| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8511 Z= 0.146 Angle : 0.724 13.527 11437 Z= 0.366 Chirality : 0.045 0.208 1273 Planarity : 0.004 0.042 1465 Dihedral : 5.242 59.598 1133 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.94 % Allowed : 21.65 % Favored : 75.41 % 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: -0.37 (0.26), residues: 1022 helix: 0.81 (0.24), residues: 499 sheet: -1.80 (0.52), residues: 78 loop : -1.14 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P1019 TYR 0.026 0.001 TYR P 136 PHE 0.028 0.001 PHE P 897 TRP 0.007 0.002 TRP P 883 HIS 0.005 0.001 HIS P 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 8510) covalent geometry : angle 0.72421 / 0.37 (11435) SS BOND : bond 0.00104 / 0.05 ( 1) SS BOND : angle 0.25891 / 0.15 ( 2) hydrogen bonds : bond 0.03862 / 2.55 ( 387) hydrogen bonds : angle 4.76636 / 3.30 ( 1107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1495.77 seconds wall clock time: 26 minutes 36.83 seconds (1596.83 seconds total)