Starting phenix.real_space_refine on Thu Aug 6 15:28:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wuu_37860/08_2026/8wuu_37860.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wuu_37860/08_2026/8wuu_37860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wuu_37860/08_2026/8wuu_37860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wuu_37860/08_2026/8wuu_37860.map" model { file = "/net/cci-nas-00/data/ceres_data/8wuu_37860/08_2026/8wuu_37860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wuu_37860/08_2026/8wuu_37860.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= -0.006 sd= 0.169 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1607 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 181 5.49 5 S 21 5.16 5 C 8596 2.51 5 N 2569 2.21 5 O 3196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14563 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 10751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1313, 10751 Classifications: {'peptide': 1313} Link IDs: {'PTRANS': 35, 'TRANS': 1277} Chain breaks: 4 Chain: "C" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 777 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "D" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 313 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "B" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 2373 Classifications: {'RNA': 111} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 54, 'rna3p_pyr': 44} Link IDs: {'rna2p': 13, 'rna3p': 97} Chain breaks: 1 Chain: "F" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 349 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain breaks: 1 Time building chain proxies: 2.99, per 1000 atoms: 0.21 Number of scatterers: 14563 At special positions: 0 Unit cell: (90.783, 136.174, 145.253, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 181 15.00 O 3196 8.00 N 2569 7.00 C 8596 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 649.4 milliseconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2502 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 9 sheets defined 55.0% alpha, 9.4% beta 71 base pairs and 109 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 5.242A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.609A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 180 through 196 removed outlier: 3.844A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.707A pdb=" N PHE A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 282 Processing helix chain 'A' and resid 286 through 304 removed outlier: 4.049A pdb=" N ASP A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 382 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.634A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.154A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 512 through 526 removed outlier: 3.685A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 594 through 602 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.576A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 637 through 640 Processing helix chain 'A' and resid 644 through 654 Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 703 through 714 removed outlier: 3.619A pdb=" N SER A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 727 Processing helix chain 'A' and resid 730 through 751 Processing helix chain 'A' and resid 776 through 792 Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 802 through 807 Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 872 through 889 removed outlier: 5.126A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 901 through 906 removed outlier: 3.753A pdb=" N ARG A 905 " --> pdb=" O THR A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 920 Processing helix chain 'A' and resid 925 through 940 Processing helix chain 'A' and resid 959 through 970 removed outlier: 4.226A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1001 Processing helix chain 'A' and resid 1004 through 1009 Processing helix chain 'A' and resid 1032 through 1041 removed outlier: 3.519A pdb=" N ASN A1041 " --> pdb=" O PHE A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1177 through 1186 removed outlier: 3.607A pdb=" N GLY A1186 " --> pdb=" O LEU A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 removed outlier: 3.648A pdb=" N GLN A1254 " --> pdb=" O GLU A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1280 removed outlier: 3.722A pdb=" N GLU A1268 " --> pdb=" O HIS A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 4.031A pdb=" N HIS A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A1312 " --> pdb=" O ASN A1308 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.607A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 10.180A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA4, first strand: chain 'A' and resid 1049 through 1050 Processing sheet with id=AA5, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 3.568A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA7, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.520A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.520A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1324 through 1326 529 hydrogen bonds defined for protein. 1536 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 179 hydrogen bonds 354 hydrogen bond angles 0 basepair planarities 71 basepair parallelities 109 stacking parallelities Total time for adding SS restraints: 4.02 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2614 1.33 - 1.45: 4470 1.45 - 1.57: 7727 1.57 - 1.68: 356 1.68 - 1.80: 41 Bond restraints: 15208 Sorted by residual: bond pdb=" C1' DC C 20 " pdb=" N1 DC C 20 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.02e+01 bond pdb=" C3' DT D 8 " pdb=" C2' DT D 8 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.46e+00 bond pdb=" C3' DC C 2 " pdb=" C2' DC C 2 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.53e+00 bond pdb=" C3' DA C 0 " pdb=" O3' DA C 0 " ideal model delta sigma weight residual 1.435 1.397 0.038 1.30e-02 5.92e+03 8.47e+00 bond pdb=" C3' DT D 0 " pdb=" O3' DT D 0 " ideal model delta sigma weight residual 1.435 1.397 0.038 1.30e-02 5.92e+03 8.39e+00 ... (remaining 15203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 19408 1.11 - 2.22: 1396 2.22 - 3.33: 466 3.33 - 4.44: 32 4.44 - 5.55: 8 Bond angle restraints: 21310 Sorted by residual: angle pdb=" N3 DT C -9 " pdb=" C4 DT C -9 " pdb=" O4 DT C -9 " ideal model delta sigma weight residual 119.90 122.69 -2.79 6.00e-01 2.78e+00 2.17e+01 angle pdb=" O4' DG C 4 " pdb=" C4' DG C 4 " pdb=" C3' DG C 4 " ideal model delta sigma weight residual 106.00 103.29 2.71 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT C -4 " pdb=" C4 DT C -4 " pdb=" O4 DT C -4 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT D 8 " pdb=" C4 DT D 8 " pdb=" O4 DT D 8 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" O4' DT C 23 " pdb=" C4' DT C 23 " pdb=" C3' DT C 23 " ideal model delta sigma weight residual 106.00 103.39 2.61 6.00e-01 2.78e+00 1.89e+01 ... (remaining 21305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.60: 8174 27.60 - 55.19: 835 55.19 - 82.79: 209 82.79 - 110.39: 6 110.39 - 137.98: 1 Dihedral angle restraints: 9225 sinusoidal: 5362 harmonic: 3863 Sorted by residual: dihedral pdb=" CA PHE A 86 " pdb=" C PHE A 86 " pdb=" N SER A 87 " pdb=" CA SER A 87 " ideal model delta harmonic sigma weight residual -180.00 -161.27 -18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ASP A 605 " pdb=" CB ASP A 605 " pdb=" CG ASP A 605 " pdb=" OD1 ASP A 605 " ideal model delta sinusoidal sigma weight residual -30.00 -89.05 59.05 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASN A1066 " pdb=" CB ASN A1066 " pdb=" CG ASN A1066 " pdb=" OD1 ASN A1066 " ideal model delta sinusoidal sigma weight residual 120.00 -168.62 -71.38 2 2.00e+01 2.50e-03 1.08e+01 ... (remaining 9222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1427 0.036 - 0.071: 624 0.071 - 0.107: 218 0.107 - 0.142: 168 0.142 - 0.178: 17 Chirality restraints: 2454 Sorted by residual: chirality pdb=" C3' DC C -1 " pdb=" C4' DC C -1 " pdb=" O3' DC C -1 " pdb=" C2' DC C -1 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" CA ILE A 48 " pdb=" N ILE A 48 " pdb=" C ILE A 48 " pdb=" CB ILE A 48 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" C1' U B 22 " pdb=" O4' U B 22 " pdb=" C2' U B 22 " pdb=" N1 U B 22 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.19e-01 ... (remaining 2451 not shown) Planarity restraints: 2062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 46 " -0.022 2.00e-02 2.50e+03 1.33e-02 4.90e+00 pdb=" N9 A B 46 " 0.036 2.00e-02 2.50e+03 pdb=" C8 A B 46 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A B 46 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A B 46 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A B 46 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A B 46 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A B 46 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A B 46 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A B 46 " 0.001 2.00e-02 2.50e+03 pdb=" C4 A B 46 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 870 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 871 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 871 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 871 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 693 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C PHE A 693 " 0.032 2.00e-02 2.50e+03 pdb=" O PHE A 693 " -0.012 2.00e-02 2.50e+03 pdb=" N MET A 694 " -0.011 2.00e-02 2.50e+03 ... (remaining 2059 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 558 2.70 - 3.25: 13515 3.25 - 3.80: 25377 3.80 - 4.35: 32906 4.35 - 4.90: 50111 Nonbonded interactions: 122467 Sorted by model distance: nonbonded pdb=" OG SER A 512 " pdb=" OE1 GLU A 617 " model vdw 2.145 3.040 nonbonded pdb=" OE1 GLU A 977 " pdb=" OH TYR A1242 " model vdw 2.219 3.040 nonbonded pdb=" O2' C B 3 " pdb=" O5' C B 4 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR A 5 " pdb=" O HIS A 754 " model vdw 2.236 3.040 nonbonded pdb=" OE2 GLU A1162 " pdb=" OH TYR A1187 " model vdw 2.242 3.040 ... (remaining 122462 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.110 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6106 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 : 0.007 0.045 15208 Z= 0.443 Angle : 0.692 5.554 21310 Z= 0.514 Chirality : 0.053 0.178 2454 Planarity : 0.004 0.049 2062 Dihedral : 20.532 137.981 6723 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 20.42 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.24), residues: 1303 helix: 1.87 (0.21), residues: 689 sheet: -0.26 (0.51), residues: 114 loop : -0.42 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 165 TYR 0.018 0.002 TYR A 136 PHE 0.027 0.002 PHE A1235 TRP 0.015 0.002 TRP A 18 HIS 0.006 0.002 HIS A1311 Details of bonding type rmsd/Z covalent geometry : bond 0.00651 / 0.44 (15208) covalent geometry : angle 0.69213 / 0.51 (21310) hydrogen bonds : bond 0.11500 / 7.35 ( 697) hydrogen bonds : angle 4.97462 / 3.70 ( 1890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.557 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: A 235 ASN cc_start: 0.8409 (m-40) cc_final: 0.8048 (t0) REVERT: A 534 MET cc_start: 0.3165 (mtp) cc_final: 0.0839 (ptm) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2285 time to fit residues: 18.5298 Evaluate side-chains 31 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 40.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 40.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 GLN A1066 ASN A1221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.059139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.037463 restraints weight = 84730.122| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.49 r_work: 0.2787 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15208 Z= 0.168 Angle : 0.531 7.971 21310 Z= 0.301 Chirality : 0.039 0.225 2454 Planarity : 0.004 0.048 2062 Dihedral : 19.745 132.398 3920 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.44 % Allowed : 19.66 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.23), residues: 1303 helix: 2.00 (0.21), residues: 683 sheet: 0.24 (0.56), residues: 85 loop : -0.36 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 778 TYR 0.019 0.001 TYR A 815 PHE 0.013 0.001 PHE A1235 TRP 0.015 0.001 TRP A 18 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 (15208) covalent geometry : angle 0.53139 / 0.30 (21310) hydrogen bonds : bond 0.04581 / 3.04 ( 697) hydrogen bonds : angle 4.29726 / 3.26 ( 1890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 32 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8844 (m-40) cc_final: 0.8256 (t0) REVERT: A 383 MET cc_start: 0.8068 (mtp) cc_final: 0.7762 (ttm) REVERT: A 534 MET cc_start: 0.5963 (mtp) cc_final: 0.4312 (ptm) REVERT: A 1069 THR cc_start: 0.9286 (OUTLIER) cc_final: 0.9040 (p) REVERT: A 1242 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.6693 (m-80) outliers start: 17 outliers final: 7 residues processed: 47 average time/residue: 0.1297 time to fit residues: 9.2277 Evaluate side-chains 35 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 86 optimal weight: 30.0000 chunk 107 optimal weight: 9.9990 chunk 27 optimal weight: 40.0000 chunk 4 optimal weight: 8.9990 chunk 79 optimal weight: 40.0000 chunk 58 optimal weight: 30.0000 chunk 55 optimal weight: 40.0000 chunk 143 optimal weight: 50.0000 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 24 optimal weight: 40.0000 overall best weight: 12.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 HIS ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.057778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.036443 restraints weight = 86142.904| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.48 r_work: 0.2741 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 15208 Z= 0.310 Angle : 0.615 7.373 21310 Z= 0.334 Chirality : 0.042 0.230 2454 Planarity : 0.004 0.050 2062 Dihedral : 19.755 126.660 3920 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.54 % Allowed : 19.07 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.23), residues: 1303 helix: 1.82 (0.20), residues: 684 sheet: -0.06 (0.49), residues: 103 loop : -0.43 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 557 TYR 0.011 0.002 TYR A 815 PHE 0.021 0.002 PHE A1235 TRP 0.011 0.002 TRP A 18 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.31 (15208) covalent geometry : angle 0.61502 / 0.33 (21310) hydrogen bonds : bond 0.05107 / 3.44 ( 697) hydrogen bonds : angle 4.40013 / 3.31 ( 1890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 27 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8904 (m-40) cc_final: 0.8258 (t0) REVERT: A 534 MET cc_start: 0.6256 (mtp) cc_final: 0.4705 (ptm) REVERT: A 631 MET cc_start: 0.8804 (tpp) cc_final: 0.8568 (mmm) REVERT: A 762 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7894 (pp20) REVERT: A 1069 THR cc_start: 0.9290 (OUTLIER) cc_final: 0.9041 (p) REVERT: A 1242 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.6816 (m-80) REVERT: A 1364 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8249 (mp10) outliers start: 30 outliers final: 11 residues processed: 56 average time/residue: 0.1195 time to fit residues: 10.6332 Evaluate side-chains 41 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 26 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1274 SER Chi-restraints excluded: chain A residue 1364 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 121 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 138 optimal weight: 50.0000 chunk 126 optimal weight: 0.5980 chunk 69 optimal weight: 30.0000 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.058371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.036936 restraints weight = 85133.674| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.46 r_work: 0.2774 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15208 Z= 0.144 Angle : 0.471 7.905 21310 Z= 0.270 Chirality : 0.037 0.202 2454 Planarity : 0.003 0.049 2062 Dihedral : 19.687 119.963 3920 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.53 % Allowed : 19.75 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.24), residues: 1303 helix: 2.02 (0.21), residues: 689 sheet: -0.08 (0.50), residues: 103 loop : -0.32 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 780 TYR 0.009 0.001 TYR A 815 PHE 0.012 0.001 PHE A 518 TRP 0.007 0.001 TRP A 18 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (15208) covalent geometry : angle 0.47148 / 0.27 (21310) hydrogen bonds : bond 0.04054 / 2.70 ( 697) hydrogen bonds : angle 4.09602 / 3.10 ( 1890) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 26 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8834 (m-40) cc_final: 0.8176 (t0) REVERT: A 534 MET cc_start: 0.6079 (mtp) cc_final: 0.4332 (ptm) REVERT: A 631 MET cc_start: 0.8760 (tpp) cc_final: 0.8502 (mmm) REVERT: A 762 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7850 (pp20) REVERT: A 1069 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.9059 (p) REVERT: A 1242 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.6768 (m-80) outliers start: 18 outliers final: 11 residues processed: 44 average time/residue: 0.1312 time to fit residues: 8.9881 Evaluate side-chains 39 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 25 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1330 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 37 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 109 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 62 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.058159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.036703 restraints weight = 88546.173| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.51 r_work: 0.2740 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15208 Z= 0.142 Angle : 0.465 8.404 21310 Z= 0.264 Chirality : 0.037 0.201 2454 Planarity : 0.003 0.051 2062 Dihedral : 19.603 114.212 3920 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.53 % Allowed : 20.51 % Favored : 77.97 % 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: 1.46 (0.24), residues: 1303 helix: 2.06 (0.21), residues: 690 sheet: -0.06 (0.51), residues: 101 loop : -0.29 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG A 215 TYR 0.010 0.001 TYR A 155 PHE 0.011 0.001 PHE A 518 TRP 0.008 0.001 TRP A 18 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (15208) covalent geometry : angle 0.46491 / 0.26 (21310) hydrogen bonds : bond 0.03969 / 2.66 ( 697) hydrogen bonds : angle 4.02686 / 3.04 ( 1890) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 26 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8915 (m-40) cc_final: 0.8209 (t0) REVERT: A 461 ARG cc_start: 0.9275 (OUTLIER) cc_final: 0.8675 (ptm160) REVERT: A 534 MET cc_start: 0.6248 (mtp) cc_final: 0.4606 (ptm) REVERT: A 631 MET cc_start: 0.8851 (tpp) cc_final: 0.8566 (mmm) REVERT: A 762 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7894 (pp20) REVERT: A 879 MET cc_start: 0.0336 (mpp) cc_final: -0.0293 (mpp) REVERT: A 1069 THR cc_start: 0.9297 (OUTLIER) cc_final: 0.9051 (p) REVERT: A 1242 TYR cc_start: 0.7774 (OUTLIER) cc_final: 0.6734 (m-80) REVERT: A 1364 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8159 (mp10) outliers start: 18 outliers final: 9 residues processed: 43 average time/residue: 0.1287 time to fit residues: 8.6851 Evaluate side-chains 39 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 25 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1364 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 86 optimal weight: 40.0000 chunk 73 optimal weight: 3.9990 chunk 64 optimal weight: 30.0000 chunk 21 optimal weight: 30.0000 chunk 89 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 chunk 142 optimal weight: 50.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 522 ASN ** A 817 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 = 0.3606 r_free = 0.3606 target = 0.058048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.036285 restraints weight = 87959.338| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.65 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15208 Z= 0.146 Angle : 0.459 8.221 21310 Z= 0.261 Chirality : 0.036 0.193 2454 Planarity : 0.003 0.050 2062 Dihedral : 19.571 107.456 3920 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.86 % Allowed : 20.34 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.24), residues: 1303 helix: 2.07 (0.21), residues: 690 sheet: 0.03 (0.57), residues: 85 loop : -0.29 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 884 TYR 0.009 0.001 TYR A 155 PHE 0.010 0.001 PHE A 518 TRP 0.008 0.001 TRP A 883 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (15208) covalent geometry : angle 0.45871 / 0.26 (21310) hydrogen bonds : bond 0.03855 / 2.59 ( 697) hydrogen bonds : angle 3.97602 / 3.00 ( 1890) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 26 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8955 (m-40) cc_final: 0.8242 (t0) REVERT: A 383 MET cc_start: 0.8221 (mtp) cc_final: 0.8010 (ttt) REVERT: A 461 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8489 (ptm160) REVERT: A 465 MET cc_start: 0.8830 (tmm) cc_final: 0.8612 (tmm) REVERT: A 534 MET cc_start: 0.6160 (mtp) cc_final: 0.4627 (ptm) REVERT: A 631 MET cc_start: 0.8854 (tpp) cc_final: 0.8571 (mmm) REVERT: A 762 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7610 (pp20) REVERT: A 879 MET cc_start: -0.0012 (mpp) cc_final: -0.0340 (mpp) REVERT: A 1069 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.9041 (p) REVERT: A 1242 TYR cc_start: 0.7807 (OUTLIER) cc_final: 0.6983 (m-80) REVERT: A 1364 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8092 (mt0) outliers start: 22 outliers final: 11 residues processed: 47 average time/residue: 0.1242 time to fit residues: 9.1335 Evaluate side-chains 40 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 24 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1364 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 78 optimal weight: 5.9990 chunk 142 optimal weight: 50.0000 chunk 68 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 104 optimal weight: 20.0000 chunk 116 optimal weight: 5.9990 chunk 98 optimal weight: 40.0000 chunk 101 optimal weight: 20.0000 chunk 114 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.057933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.036214 restraints weight = 87884.783| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.62 r_work: 0.2735 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15208 Z= 0.150 Angle : 0.463 7.915 21310 Z= 0.261 Chirality : 0.036 0.191 2454 Planarity : 0.003 0.051 2062 Dihedral : 19.543 101.643 3920 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.53 % Allowed : 20.42 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.24), residues: 1303 helix: 2.11 (0.21), residues: 690 sheet: -0.06 (0.57), residues: 85 loop : -0.29 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 215 TYR 0.010 0.001 TYR A 155 PHE 0.012 0.001 PHE A 375 TRP 0.027 0.002 TRP A 883 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (15208) covalent geometry : angle 0.46314 / 0.26 (21310) hydrogen bonds : bond 0.03853 / 2.59 ( 697) hydrogen bonds : angle 3.93976 / 2.97 ( 1890) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 26 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8922 (m-40) cc_final: 0.8202 (t0) REVERT: A 461 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8660 (ptm160) REVERT: A 465 MET cc_start: 0.9125 (tmm) cc_final: 0.8883 (tmm) REVERT: A 534 MET cc_start: 0.6267 (mtp) cc_final: 0.4534 (ptm) REVERT: A 631 MET cc_start: 0.8977 (tpp) cc_final: 0.8687 (mmm) REVERT: A 762 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7875 (pp20) REVERT: A 879 MET cc_start: 0.0055 (mpp) cc_final: -0.0432 (mpp) REVERT: A 1069 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8879 (p) REVERT: A 1242 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.6906 (m-80) REVERT: A 1260 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8714 (tm-30) outliers start: 18 outliers final: 11 residues processed: 43 average time/residue: 0.1276 time to fit residues: 8.5679 Evaluate side-chains 41 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 25 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1274 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 49 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 74 optimal weight: 30.0000 chunk 45 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 31 optimal weight: 0.0070 chunk 108 optimal weight: 20.0000 chunk 101 optimal weight: 0.0020 overall best weight: 3.0012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.058267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.036899 restraints weight = 87391.741| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.52 r_work: 0.2760 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15208 Z= 0.107 Angle : 0.424 8.023 21310 Z= 0.243 Chirality : 0.035 0.177 2454 Planarity : 0.003 0.051 2062 Dihedral : 19.473 100.225 3920 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.53 % Allowed : 20.34 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.24), residues: 1303 helix: 2.21 (0.21), residues: 685 sheet: -0.41 (0.49), residues: 114 loop : -0.18 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 215 TYR 0.009 0.001 TYR A1237 PHE 0.009 0.001 PHE A 518 TRP 0.011 0.001 TRP A 883 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.11 (15208) covalent geometry : angle 0.42357 / 0.24 (21310) hydrogen bonds : bond 0.03447 / 2.29 ( 697) hydrogen bonds : angle 3.81703 / 2.89 ( 1890) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 25 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8922 (m-40) cc_final: 0.8179 (t0) REVERT: A 461 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8618 (ptm160) REVERT: A 465 MET cc_start: 0.9125 (tmm) cc_final: 0.8899 (tmm) REVERT: A 534 MET cc_start: 0.5891 (mtp) cc_final: 0.3930 (ptm) REVERT: A 762 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7861 (pp20) REVERT: A 879 MET cc_start: 0.0426 (mpp) cc_final: -0.0063 (mpp) REVERT: A 1069 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8884 (p) REVERT: A 1242 TYR cc_start: 0.7762 (OUTLIER) cc_final: 0.6920 (m-80) REVERT: A 1260 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8714 (tm-30) outliers start: 18 outliers final: 12 residues processed: 41 average time/residue: 0.1068 time to fit residues: 6.8333 Evaluate side-chains 42 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 25 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1274 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 93 optimal weight: 5.9990 chunk 62 optimal weight: 30.0000 chunk 68 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 116 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 ASN ** A 817 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 = 0.3592 r_free = 0.3592 target = 0.057515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.036020 restraints weight = 89152.901| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.56 r_work: 0.2720 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15208 Z= 0.199 Angle : 0.499 7.313 21310 Z= 0.275 Chirality : 0.037 0.192 2454 Planarity : 0.003 0.051 2062 Dihedral : 19.538 97.993 3920 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.53 % Allowed : 20.59 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.24), residues: 1303 helix: 2.12 (0.21), residues: 685 sheet: -0.57 (0.46), residues: 126 loop : -0.21 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 340 TYR 0.011 0.001 TYR A 155 PHE 0.018 0.001 PHE A1235 TRP 0.012 0.001 TRP A 883 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.20 (15208) covalent geometry : angle 0.49874 / 0.28 (21310) hydrogen bonds : bond 0.04150 / 2.81 ( 697) hydrogen bonds : angle 3.97241 / 2.98 ( 1890) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 25 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8981 (m-40) cc_final: 0.8242 (t0) REVERT: A 461 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8658 (ptm160) REVERT: A 534 MET cc_start: 0.6362 (mtp) cc_final: 0.4648 (ptm) REVERT: A 762 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7932 (pp20) REVERT: A 879 MET cc_start: 0.0552 (mpp) cc_final: 0.0021 (mpp) REVERT: A 1069 THR cc_start: 0.9205 (OUTLIER) cc_final: 0.8893 (p) REVERT: A 1242 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.6887 (m-80) REVERT: A 1260 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8733 (tm-30) outliers start: 18 outliers final: 11 residues processed: 42 average time/residue: 0.1270 time to fit residues: 8.2788 Evaluate side-chains 41 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 25 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1274 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 120 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 26 optimal weight: 50.0000 chunk 7 optimal weight: 10.0000 chunk 140 optimal weight: 40.0000 chunk 93 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 69 optimal weight: 40.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.057146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.036114 restraints weight = 89723.738| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.57 r_work: 0.2696 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15208 Z= 0.213 Angle : 0.524 8.204 21310 Z= 0.288 Chirality : 0.038 0.195 2454 Planarity : 0.003 0.050 2062 Dihedral : 19.650 97.694 3920 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.44 % Allowed : 20.59 % Favored : 77.97 % 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: 1.33 (0.24), residues: 1303 helix: 2.00 (0.21), residues: 690 sheet: -0.66 (0.47), residues: 122 loop : -0.27 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 557 TYR 0.013 0.001 TYR A 521 PHE 0.016 0.001 PHE A1235 TRP 0.009 0.001 TRP A 883 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.21 (15208) covalent geometry : angle 0.52376 / 0.29 (21310) hydrogen bonds : bond 0.04335 / 2.95 ( 697) hydrogen bonds : angle 4.07815 / 3.05 ( 1890) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 25 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 461 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.8684 (ptm160) REVERT: A 534 MET cc_start: 0.6036 (mtp) cc_final: 0.4462 (ptm) REVERT: A 762 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7844 (pp20) REVERT: A 879 MET cc_start: 0.0866 (mpp) cc_final: 0.0262 (mpp) REVERT: A 1069 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.9051 (p) REVERT: A 1242 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.6810 (m-80) REVERT: A 1260 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8785 (tm-30) outliers start: 17 outliers final: 11 residues processed: 41 average time/residue: 0.1480 time to fit residues: 9.3617 Evaluate side-chains 39 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 23 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1260 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 33 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 64 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 29 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.057549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.036099 restraints weight = 88054.759| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.48 r_work: 0.2725 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15208 Z= 0.150 Angle : 0.478 8.169 21310 Z= 0.266 Chirality : 0.036 0.191 2454 Planarity : 0.003 0.051 2062 Dihedral : 19.601 98.555 3920 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.44 % Allowed : 20.76 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.24), residues: 1303 helix: 2.12 (0.21), residues: 684 sheet: -0.60 (0.47), residues: 122 loop : -0.24 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 557 TYR 0.010 0.001 TYR A 521 PHE 0.009 0.001 PHE A 569 TRP 0.009 0.001 TRP A 883 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (15208) covalent geometry : angle 0.47762 / 0.27 (21310) hydrogen bonds : bond 0.03938 / 2.65 ( 697) hydrogen bonds : angle 3.97596 / 2.99 ( 1890) =============================================================================== Job complete usr+sys time: 3834.70 seconds wall clock time: 66 minutes 21.72 seconds (3981.72 seconds total)