Starting phenix.real_space_refine on Fri Jul 3 20:02:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wuu_37860/07_2026/8wuu_37860.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wuu_37860/07_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_37860/07_2026/8wuu_37860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wuu_37860/07_2026/8wuu_37860.map" model { file = "/net/cci-nas-00/data/ceres_data/8wuu_37860/07_2026/8wuu_37860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wuu_37860/07_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-dev-6108/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: 2.96, per 1000 atoms: 0.20 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: 0.88 Conformation dependent library (CDL) restraints added in 466.1 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: 1.63 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: 3.07 Time building geometry restraints manager: 1.22 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: 19719 1.11 - 2.22: 1291 2.22 - 3.33: 264 3.33 - 4.44: 28 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: 1548 0.036 - 0.071: 616 0.071 - 0.107: 207 0.107 - 0.142: 73 0.142 - 0.178: 10 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=" CA PRO A 117 " pdb=" N PRO A 117 " pdb=" C PRO A 117 " pdb=" CB PRO A 117 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.93e-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: 0.150 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.930 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.470 ------------------------------------------------------------------------------- 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 : 0.006 0.045 15208 Z= 0.433 Angle : 0.626 5.554 21310 Z= 0.467 Chirality : 0.045 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 0.00645 / 0.43 (15208) covalent geometry : angle 0.62596 / 0.47 (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 : 0.385 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: 0.1709 time to fit residues: 13.7564 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 : 0.426 ------------------------------------------------------------------------------- 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: 20.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 40.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.058898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.037201 restraints weight = 84836.685| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.51 r_work: 0.2780 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15208 Z= 0.198 Angle : 0.544 8.108 21310 Z= 0.309 Chirality : 0.039 0.195 2454 Planarity : 0.004 0.049 2062 Dihedral : 19.779 136.736 3920 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.44 % Allowed : 19.41 % Favored : 79.15 % 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: 1.37 (0.24), residues: 1303 helix: 1.98 (0.21), residues: 683 sheet: 0.36 (0.53), residues: 97 loop : -0.39 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 557 TYR 0.019 0.001 TYR A 815 PHE 0.015 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 0.00410 / 0.20 (15208) covalent geometry : angle 0.54421 / 0.31 (21310) hydrogen bonds : bond 0.04737 / 3.14 ( 697) hydrogen bonds : angle 4.34579 / 3.29 ( 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 : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8846 (m-40) cc_final: 0.8259 (t0) REVERT: A 383 MET cc_start: 0.8187 (mtp) cc_final: 0.7877 (ttm) REVERT: A 534 MET cc_start: 0.5981 (mtp) cc_final: 0.4367 (ptm) REVERT: A 1069 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.9026 (p) REVERT: A 1242 TYR cc_start: 0.7691 (OUTLIER) cc_final: 0.6701 (m-80) outliers start: 17 outliers final: 7 residues processed: 47 average time/residue: 0.1181 time to fit residues: 8.5284 Evaluate side-chains 36 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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: 40.0000 chunk 107 optimal weight: 10.0000 chunk 27 optimal weight: 40.0000 chunk 4 optimal weight: 6.9990 chunk 79 optimal weight: 40.0000 chunk 58 optimal weight: 30.0000 chunk 55 optimal weight: 40.0000 chunk 143 optimal weight: 30.0000 chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 24 optimal weight: 40.0000 overall best weight: 10.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 HIS ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.057640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.036135 restraints weight = 86296.606| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.46 r_work: 0.2737 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 15208 Z= 0.278 Angle : 0.588 10.251 21310 Z= 0.325 Chirality : 0.041 0.302 2454 Planarity : 0.004 0.050 2062 Dihedral : 19.850 129.348 3920 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.71 % Allowed : 19.41 % 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: 1.09 (0.23), residues: 1303 helix: 1.75 (0.20), residues: 684 sheet: -0.17 (0.50), residues: 101 loop : -0.44 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 75 TYR 0.013 0.002 TYR A 815 PHE 0.023 0.002 PHE A1235 TRP 0.011 0.002 TRP A 18 HIS 0.006 0.002 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.28 (15208) covalent geometry : angle 0.58794 / 0.33 (21310) hydrogen bonds : bond 0.05163 / 3.49 ( 697) hydrogen bonds : angle 4.38796 / 3.30 ( 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 60 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 28 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8943 (m-40) cc_final: 0.8276 (t0) REVERT: A 534 MET cc_start: 0.6293 (mtp) cc_final: 0.4650 (ptm) REVERT: A 631 MET cc_start: 0.8820 (tpp) cc_final: 0.8585 (mmm) REVERT: A 762 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7917 (pp20) REVERT: A 1069 THR cc_start: 0.9311 (OUTLIER) cc_final: 0.9056 (p) REVERT: A 1242 TYR cc_start: 0.7852 (OUTLIER) cc_final: 0.6794 (m-80) REVERT: A 1364 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8263 (mp10) outliers start: 32 outliers final: 13 residues processed: 58 average time/residue: 0.1260 time to fit residues: 11.2237 Evaluate side-chains 43 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 26 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 29 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 138 optimal weight: 50.0000 chunk 126 optimal weight: 9.9990 chunk 69 optimal weight: 50.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.058012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.037020 restraints weight = 85376.670| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.39 r_work: 0.2745 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15208 Z= 0.182 Angle : 0.497 8.033 21310 Z= 0.282 Chirality : 0.038 0.181 2454 Planarity : 0.003 0.049 2062 Dihedral : 19.786 124.358 3920 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.69 % Allowed : 20.08 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.24), residues: 1303 helix: 1.91 (0.21), residues: 692 sheet: -0.20 (0.50), residues: 101 loop : -0.38 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 215 TYR 0.011 0.001 TYR A 155 PHE 0.012 0.001 PHE A1235 TRP 0.009 0.001 TRP A 18 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 (15208) covalent geometry : angle 0.49724 / 0.28 (21310) hydrogen bonds : bond 0.04323 / 2.91 ( 697) hydrogen bonds : angle 4.21195 / 3.18 ( 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 47 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 27 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8951 (m-40) cc_final: 0.8242 (t0) REVERT: A 461 ARG cc_start: 0.9297 (OUTLIER) cc_final: 0.8723 (ptm160) REVERT: A 534 MET cc_start: 0.6034 (mtp) cc_final: 0.4213 (ptm) REVERT: A 631 MET cc_start: 0.8896 (tpp) cc_final: 0.8595 (mmm) REVERT: A 762 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7870 (pp20) REVERT: A 1069 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.9041 (p) REVERT: A 1242 TYR cc_start: 0.7801 (OUTLIER) cc_final: 0.6736 (m-80) REVERT: A 1364 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8264 (mp10) outliers start: 20 outliers final: 9 residues processed: 47 average time/residue: 0.1375 time to fit residues: 9.7107 Evaluate side-chains 40 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 26 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 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 Chi-restraints excluded: chain A residue 1364 GLN 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: 20.0000 chunk 107 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 109 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 overall best weight: 6.3388 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.057694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.036006 restraints weight = 88021.569| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.58 r_work: 0.2725 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15208 Z= 0.176 Angle : 0.481 8.412 21310 Z= 0.274 Chirality : 0.037 0.161 2454 Planarity : 0.003 0.051 2062 Dihedral : 19.697 115.723 3920 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.78 % Allowed : 20.34 % 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: 1.35 (0.24), residues: 1303 helix: 1.99 (0.21), residues: 690 sheet: -0.05 (0.52), residues: 97 loop : -0.39 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 215 TYR 0.010 0.001 TYR A 521 PHE 0.015 0.001 PHE A 375 TRP 0.009 0.001 TRP A 18 HIS 0.005 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (15208) covalent geometry : angle 0.48116 / 0.27 (21310) hydrogen bonds : bond 0.04183 / 2.81 ( 697) hydrogen bonds : angle 4.09782 / 3.08 ( 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 50 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 29 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8964 (m-40) cc_final: 0.8234 (t0) REVERT: A 461 ARG cc_start: 0.9281 (OUTLIER) cc_final: 0.8703 (ptm160) REVERT: A 534 MET cc_start: 0.6306 (mtp) cc_final: 0.4667 (ptm) REVERT: A 631 MET cc_start: 0.8983 (tpp) cc_final: 0.8692 (mmm) REVERT: A 762 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7926 (pp20) REVERT: A 879 MET cc_start: 0.0310 (mpp) cc_final: -0.0171 (mpp) REVERT: A 1069 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.9041 (p) REVERT: A 1242 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.6857 (m-80) outliers start: 21 outliers final: 11 residues processed: 49 average time/residue: 0.1354 time to fit residues: 10.0999 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 : 0.459 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 86 optimal weight: 50.0000 chunk 73 optimal weight: 4.9990 chunk 64 optimal weight: 20.0000 chunk 21 optimal weight: 30.0000 chunk 89 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 142 optimal weight: 40.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.057724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.036334 restraints weight = 87689.256| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.50 r_work: 0.2729 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15208 Z= 0.149 Angle : 0.456 7.655 21310 Z= 0.262 Chirality : 0.036 0.148 2454 Planarity : 0.003 0.051 2062 Dihedral : 19.647 110.328 3920 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.61 % Allowed : 20.93 % Favored : 77.46 % 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: 1.43 (0.24), residues: 1303 helix: 2.09 (0.21), residues: 684 sheet: -0.14 (0.56), residues: 85 loop : -0.34 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 884 TYR 0.011 0.001 TYR A 823 PHE 0.009 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 0.00298 / 0.15 (15208) covalent geometry : angle 0.45618 / 0.26 (21310) hydrogen bonds : bond 0.03902 / 2.63 ( 697) hydrogen bonds : angle 4.01179 / 3.02 ( 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 46 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 27 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8964 (m-40) cc_final: 0.8232 (t0) REVERT: A 461 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.8695 (ptm160) REVERT: A 534 MET cc_start: 0.6454 (mtp) cc_final: 0.4821 (ptm) REVERT: A 762 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7880 (pp20) REVERT: A 879 MET cc_start: 0.0342 (mpp) cc_final: -0.0153 (mpp) REVERT: A 1069 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.9044 (p) REVERT: A 1242 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.6847 (m-80) REVERT: A 1260 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8774 (tm-30) outliers start: 19 outliers final: 11 residues processed: 45 average time/residue: 0.1368 time to fit residues: 9.6189 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 : 0.492 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 78 optimal weight: 8.9990 chunk 142 optimal weight: 40.0000 chunk 68 optimal weight: 30.0000 chunk 50 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 98 optimal weight: 40.0000 chunk 101 optimal weight: 0.0000 chunk 114 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 overall best weight: 2.9790 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.058140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.036311 restraints weight = 88262.069| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.64 r_work: 0.2746 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15208 Z= 0.112 Angle : 0.436 8.181 21310 Z= 0.250 Chirality : 0.035 0.145 2454 Planarity : 0.003 0.051 2062 Dihedral : 19.537 103.697 3920 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.61 % Allowed : 21.02 % 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: 1.48 (0.24), residues: 1303 helix: 2.13 (0.21), residues: 685 sheet: -0.48 (0.46), residues: 126 loop : -0.21 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 467 TYR 0.009 0.001 TYR A 155 PHE 0.009 0.001 PHE A 518 TRP 0.025 0.002 TRP A 883 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 (15208) covalent geometry : angle 0.43581 / 0.25 (21310) hydrogen bonds : bond 0.03540 / 2.37 ( 697) hydrogen bonds : angle 3.88816 / 2.93 ( 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 45 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 26 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8948 (m-40) cc_final: 0.8200 (t0) REVERT: A 461 ARG cc_start: 0.9263 (OUTLIER) cc_final: 0.8675 (ptm160) REVERT: A 534 MET cc_start: 0.6276 (mtp) cc_final: 0.4535 (ptm) REVERT: A 762 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7888 (pp20) REVERT: A 1069 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.8983 (p) REVERT: A 1242 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.6978 (m-80) REVERT: A 1260 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8732 (tm-30) REVERT: A 1364 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8268 (mt0) outliers start: 19 outliers final: 11 residues processed: 44 average time/residue: 0.1443 time to fit residues: 9.6951 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 : 0.469 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 1364 GLN 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: 3.9990 chunk 74 optimal weight: 30.0000 chunk 45 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 overall best weight: 6.3588 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.057620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.035843 restraints weight = 88314.422| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.61 r_work: 0.2723 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15208 Z= 0.173 Angle : 0.475 7.821 21310 Z= 0.267 Chirality : 0.036 0.144 2454 Planarity : 0.003 0.051 2062 Dihedral : 19.559 99.554 3920 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.53 % Allowed : 21.27 % Favored : 77.20 % 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: 2.13 (0.21), residues: 685 sheet: -0.44 (0.49), residues: 112 loop : -0.29 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 557 TYR 0.010 0.001 TYR A 155 PHE 0.014 0.001 PHE A1235 TRP 0.011 0.001 TRP A 18 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (15208) covalent geometry : angle 0.47479 / 0.27 (21310) hydrogen bonds : bond 0.04011 / 2.72 ( 697) hydrogen bonds : angle 3.95906 / 2.97 ( 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 45 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 27 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8988 (m-40) cc_final: 0.8235 (t0) REVERT: A 461 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8670 (ptm160) REVERT: A 534 MET cc_start: 0.6276 (mtp) cc_final: 0.4517 (ptm) REVERT: A 762 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7924 (pp20) REVERT: A 1069 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8888 (p) REVERT: A 1242 TYR cc_start: 0.7762 (OUTLIER) cc_final: 0.6847 (m-80) REVERT: A 1260 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8727 (tm-30) REVERT: A 1364 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8257 (mt0) outliers start: 18 outliers final: 10 residues processed: 44 average time/residue: 0.1220 time to fit residues: 8.4606 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 : 0.492 ------------------------------------------------------------------------------- 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 710 LYS 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 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 1364 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 93 optimal weight: 9.9990 chunk 62 optimal weight: 30.0000 chunk 68 optimal weight: 8.9990 chunk 17 optimal weight: 0.0980 chunk 18 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 overall best weight: 6.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.057596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.035833 restraints weight = 89302.692| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.60 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15208 Z= 0.166 Angle : 0.464 7.842 21310 Z= 0.264 Chirality : 0.036 0.137 2454 Planarity : 0.003 0.051 2062 Dihedral : 19.570 99.395 3920 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.44 % Allowed : 21.53 % Favored : 77.03 % 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: 2.11 (0.21), residues: 684 sheet: -0.47 (0.49), residues: 110 loop : -0.28 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 307 TYR 0.018 0.001 TYR A 815 PHE 0.010 0.001 PHE A 569 TRP 0.009 0.001 TRP A 883 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 (15208) covalent geometry : angle 0.46357 / 0.26 (21310) hydrogen bonds : bond 0.03830 / 2.59 ( 697) hydrogen bonds : angle 3.93846 / 2.96 ( 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: 17 poor density : 26 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ASN cc_start: 0.9031 (m-40) cc_final: 0.8281 (t0) REVERT: A 461 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8472 (ptm160) REVERT: A 534 MET cc_start: 0.6025 (mtp) cc_final: 0.4503 (ptm) REVERT: A 762 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7623 (pp20) REVERT: A 1069 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8892 (p) REVERT: A 1242 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7078 (m-80) REVERT: A 1364 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8097 (mt0) outliers start: 17 outliers final: 11 residues processed: 41 average time/residue: 0.1183 time to fit residues: 7.5759 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 : 0.423 ------------------------------------------------------------------------------- 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 688 PHE 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 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 1364 GLN 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: 9.9990 chunk 140 optimal weight: 30.0000 chunk 93 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 overall best weight: 9.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 854 ASN A1262 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.057015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.035083 restraints weight = 89079.683| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.63 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15208 Z= 0.244 Angle : 0.544 8.360 21310 Z= 0.301 Chirality : 0.038 0.136 2454 Planarity : 0.003 0.051 2062 Dihedral : 19.661 98.037 3920 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.53 % Allowed : 21.78 % Favored : 76.69 % 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: 1.25 (0.24), residues: 1303 helix: 1.94 (0.20), residues: 690 sheet: -0.68 (0.46), residues: 122 loop : -0.31 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 557 TYR 0.013 0.002 TYR A 521 PHE 0.021 0.002 PHE A1235 TRP 0.011 0.001 TRP A 18 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.24 (15208) covalent geometry : angle 0.54401 / 0.30 (21310) hydrogen bonds : bond 0.04603 / 3.13 ( 697) hydrogen bonds : angle 4.11548 / 3.08 ( 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: 18 poor density : 24 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8506 (ptm160) REVERT: A 534 MET cc_start: 0.5783 (mtp) cc_final: 0.4238 (ptm) REVERT: A 762 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7608 (pp20) REVERT: A 1069 THR cc_start: 0.9326 (OUTLIER) cc_final: 0.9081 (p) REVERT: A 1242 TYR cc_start: 0.7914 (OUTLIER) cc_final: 0.7077 (m-80) REVERT: A 1364 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8111 (mt0) outliers start: 18 outliers final: 11 residues processed: 40 average time/residue: 0.1377 time to fit residues: 8.2320 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 : 0.414 ------------------------------------------------------------------------------- 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 688 PHE 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 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 1364 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 33 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 64 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.057789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.036217 restraints weight = 87218.696| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 3.55 r_work: 0.2736 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15208 Z= 0.110 Angle : 0.450 8.811 21310 Z= 0.257 Chirality : 0.035 0.140 2454 Planarity : 0.003 0.051 2062 Dihedral : 19.583 99.795 3920 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.19 % Allowed : 21.95 % Favored : 76.86 % 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: 1.47 (0.24), residues: 1303 helix: 2.15 (0.21), residues: 684 sheet: -0.49 (0.49), residues: 110 loop : -0.27 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 557 TYR 0.013 0.001 TYR A 815 PHE 0.009 0.001 PHE A1045 TRP 0.007 0.001 TRP A 883 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.11 (15208) covalent geometry : angle 0.44968 / 0.26 (21310) hydrogen bonds : bond 0.03689 / 2.48 ( 697) hydrogen bonds : angle 3.90217 / 2.94 ( 1890) =============================================================================== Job complete usr+sys time: 3805.95 seconds wall clock time: 65 minutes 59.64 seconds (3959.64 seconds total)